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DNA and Natural Algorithms Group  

NSDL National Science Digital Library

This research group at the California Institute of Technology is studying the capability of DNA and other biomolecules to process information and implement algorithms. A general overview of the group's purpose and motivation is provided, as well as a number of publications.



Renormalization Group Limit Cycle for Three-Stranded DNA  

NASA Astrophysics Data System (ADS)

We show that there exists an Efimov-like three strand DNA bound state at the duplex melting point and it is described by a renormalization group limit cycle. A nonperturbative renormalization group is used to obtain this result in a model involving short range pairing only. Our results suggest that Efimov physics can be tested in polymeric systems.

Pal, Tanmoy; Sadhukhan, Poulomi; Bhattacharjee, Somendra M.



Finding human promoter groups based on DNA physical properties  

NASA Astrophysics Data System (ADS)

DNA rigidity is an important physical property originating from the DNA three-dimensional structure. Although the general DNA rigidity patterns in human promoters have been investigated, their distinct roles in transcription are largely unknown. In this paper, we discover four highly distinct human promoter groups based on similarity of their rigidity profiles. First, we find that all promoter groups conserve relatively rigid DNAs at the canonical TATA box [a consensus TATA(A/T)A(A/T) sequence] position, which are important physical signals in binding transcription factors. Second, we find that the genes activated by each group of promoters share significant biological functions based on their gene ontology annotations. Finally, we find that these human promoter groups correlate with the tissue-specific gene expression.

Zeng, Jia; Cao, Xiao-Qin; Zhao, Hongya; Yan, Hong



5-Methylcytosine DNA demethylation: more than losing a methyl group.  


Demethylation of 5-methylcytosine in DNA is integral to the maintenance of an intact epigenome. The balance between the presence or absence of 5-methylcytosine determines many physiological aspects of cell metabolism, with a turnover that can be measured in minutes to years. Biochemically, addition of the methyl group is shared among all living kingdoms and has been well characterized, whereas the removal or reversion of this mark seems diverse and much less understood. Here, we present a summary of how DNA demethylation can be initiated directly, utilizing the ten-eleven translocation (TET) family of proteins, activation-induced deaminase (AID), or other DNA modifying enzymes, or indirectly, via transcription, RNA metabolism, or DNA repair; how intermediates in those pathways are substrates of the DNA repair machinery; and how demethylation pathways are linked and possibly balanced, avoiding mutations. PMID:22974304

Franchini, Don-Marc; Schmitz, Kerstin-Maike; Petersen-Mahrt, Svend K



DNA hybridization probe for the Pseudomonas fluorescens group.  

PubMed Central

Plasmid pHF360 was constructed from cloned rRNA genes (rDNA) of Pseudomonas aeruginosa and used as hybridization probe for the Pseudomonas fluorescens group. The probe was tested by dot and in situ colony hybridizations to chromosomal DNAs from a wide variety of organisms. pHF360 DNA hybridized exclusively to chromosomal DNAs from bacteria representing the P. fluorescens group and separated them clearly from all other bacteria tested in the present study. Determination of the nucleotide sequence of the cloned DNA showed that it is a fragment from a 23S rRNA gene of P. aeruginosa. It was compared with the published 23S RNA sequence from Escherichia coli. Images

Festl, H; Ludwig, W; Schleifer, K H



A Chloroplast DNA Phylogeny of Lilacs (Syringa, Oleaceae): Plastome Groups Show a Strong Correlation with Crossing Groups  

Microsoft Academic Search

Phylogenetic relationships and genomic compatibility were compared for 60 accessions of Syringa using chloroplast DNA (cpDNA) and nuclear ribosomal DNA (rDNA) markers. A total of 669 cpDNA variants, 653 of which were potentially phylogenetically informative, was detected using 22 restriction enzymes. Phylogenetic analyses reveal four strongly sup- ported plastome groups that correspond to four genetically incompatible crossing groups. Relationships of

Ki-Joong Kim; Robert K. Jansen



An Altered Apurinic DNA Endonuclease Activity in Group A and Group D Xeroderma Pigmentosum Fibroblasts  

Microsoft Academic Search

Endonuclease activity upon depurinated DNA was measured in extracts of cultured fibroblasts from xeroderma pigmentosum patients. Cell lines from complementation groups A, B, C, E, and the XP-variant had slightly reduced levels of activity, but cell lines from complementation group D had one-sixth of the normal activity. An altered pH dependence and a higher apparent Km for substrate in D-cell

Urs Kuhnlein; Edward E. Penhoet; Stuart Linn



Genetic Kinship Investigation from Blood Groups to DNA Markers  

PubMed Central

The forensic application of hereditary characteristics became possible after the discovery of human blood groups by Karl Landsteiner in 1901. The foundation for their use in kinship investigation was laid by Emil von Dungern and Ludwig Hirschfeld in 1910 by clarification of the inheritance of the ABO groups. Up to the middle of the 20th century further red cell membrane systems were discovered. From the 1920s Fritz Schiff and Georg Strassmann fought for the introduction of blood groups into forensic kinship investigation. A new era of hemogenetics was opened from 1955 as genetic polymorphisms were described in serum proteins. Starting in 1958 there followed the complex HLA system of white blood cells, which from 1963 was joined by polymophisms in erythrocyte enzymes. Therefore, from the 1980s, it was possible to clarify the majority of kinship cases with a combination of conventional markers. From 1990 to 2000 the conventional markers were gradually replaced by the more effective DNA markers. Simultaneously typing shifted from the phenotype level to the genotype level. The genomic structure of conventional genetic markers could also now be explained. As a reflection of scientific progress the legal situation also changed, particularly in the form of the official guidelines for kinship investigation.

Geserick, Gunther; Wirth, Ingo



Correction of the DNA Repair Defect in Xeroderma Pigmentosum Group E by Injection of a DNA Damage-Binding Protein  

Microsoft Academic Search

Cells from a subset of patients with the DNA-repair-defective disease xeroderma pigmentosum complementation group E (XP-E) are known to lack a DNA damage-binding (DDB) activity. Purified human DDB protein was injected into XP-E cells to test whether the DNA-repair defect in these cells is caused by a defect in DDB activity. Injected DDB protein stimulated DNA repair to normal levels

Scott Keeney; Andre P. M. Eker; Tom Brody; Wim Vermeulen; Dirk Bootsma; Jan H. J. Hoeijmakers; Stuart Linn



Ribosomal and Mitochondrial DNA Analyses of Xiphinema americanum-Group Populations.  


The 18S ribosomal DNA (rDNA) and cytochrome oxidase I region of mitochondrial DNA (mtDNA) were sequenced for 24 Xiphinema americanum-group populations sourced from a number of geographically disparate locations. Sequences were subjected to phylogenetic analysis and compared. 18S rDNA strongly suggested that only X. pachtaicum, X. simile (two populations) and a X. americanum s.l. population from Portugal were different from the other 20 populations studied, whereas mtDNA indicated some heterogeneity between populations. Phylogenetically, based on mtDNA, an apparent dichotomy existed amongst X. americanum-group populations from North America and those from Asia, South America and Oceania. Analyses of 18S rDNA and mtDNA sequences underpin the classical taxonomic issues of the X. americanum-group and cast doubt on the degree of speciation within the X. americanum-group. PMID:19259456

Lazarova, Stela S; Malloch, Gaynor; Oliveira, Claudio M G; Hübschen, Judith; Neilson, Roy



Mitochondrial DNA variation and Haldane's rule in the Papilio glaucus and P. troilus species groups  

Microsoft Academic Search

Variation in mitochondrial DNA (mtDNA) was surveyed, using restriction endonucleases, in all species of the Papilio glaucus and P. troilus groups (Lepidoptera: Papilionidae). Phylogenetic and distance relationships of mtDNA generally confirmed traditional species limits in the two species groups and compared favourably with a prior survey of their allozymes. The most notable exceptions were P. rutulus and P. eurymedon, which




Short-step chemical synthesis of DNA by use of MMTrS group for protection of 5'-hydroxyl group.  


4-methoxytrithylthio (MMTrS) group was applied for the appropriately protected four canonical nucleosides. We prepared the phosphoroamidite units by use of these nucleosides and developed the synthesis of oligodeoxynucleotides without any acidic treatment. Moreover, the new DNA synthesis protocol was applied to an automated DNA synthesizer for the synthesis of longer oligodeoxynucleotides. PMID:18029620

Shiraishi, Miyuki; Utagawa, Eri; Ohkubo, Akihiro; Sekine, Mitsuo; Seio, Kohji



Biochemical Identification and Characterization of DNA Groups within the Proteus vulgaris Complex  

PubMed Central

We placed 43 isolates belonging to the Proteus vulgaris complex into proposed DNA groups (genomovars) using five previously recommended tests (tests for esculin hydrolysis, production of acid from salicin, l-rhamnose fermentation, and elaboration of DNase and lipase). On the basis of the results of these five tests, 49% of the isolates fell into DNA groups 5 and 6, 37% fell into DNA group 2, and the remaining 14% fell into DNA groups 3 and 4. Sequencing of the 16S rRNA genes of 11 members of DNA groups 5 and 6 indicated that 10 of these isolates (91%) could be unambiguously assigned to one of these two genomospecies. Overall expression of selected enzymatic and virulence-associated characteristics did not differ significantly among DNA groups.

Janda, J. Michael; Abbott, Sharon L.; Khashe, Shideh; Probert, Will



Efficient enhancement of DNA cleavage activity by introducing guanidinium groups into diiron(III) complex.  


Inspired by the structures of natural nucleases, guanidinium groups were introduced into binuclear iron(III) systems. Compared with the corresponding analogue without guanidinium groups, the new diiron(III) system led to considerable rate enhancement on DNA cleavage. The cooperativity between metal ions and guanidine groups was evidenced by the fact that no significant cleavage was observed after incubating pBR322 plasmid DNA with non-metalated ligands or free Fe3+ ion. DNA binding experiments indicated that introduction of positively charged guanidinium groups can obtain more than one order of magnitude enhancement in the affinity of complex with DNA. PMID:18039576

Chen, Xiaoqiang; Wang, Jingyun; Sun, Shiguo; Fan, Jiangli; Wu, Song; Liu, Jianfeng; Ma, Saijian; Zhang, Lizhu; Peng, Xiaojun



Enhancement of antibody response by high mobility group box protein-1-based DNA immunization  

Microsoft Academic Search

High mobility group box protein 1 (HMGB1), a major non-histone protein, released from the cells induces dendritic cell (DC) maturation and Th1 polarization. While DNA immunization has become an attractive method for eliciting the production of antibodies (Abs) in animals injected with DNA encoding an antigen, the Ab responses induced by DNA immunization remain relatively weak. In this study, we

Ryuichiro Kimura; Ryota Shiibashi; Masanori Suzuki; Yoshihide Hayashizaki; Joe Chiba



Betaine structure and the presence of hydroxyl groups alters the effects on DNA melting temperatures.  


Betaine lowers the melting temperature of deoxyribonucleic acid (DNA) and decreases its dependence on base composition. The effects of synthetic betaine analogs on the melting of DNA samples with different GC content were measured. Since many polyhydroxy compounds also lower DNA melting temperatures, hydroxyl-substituted betaine analogs were included. Some synthetic sulfonate analogs of betaine lowered the DNA melting temperatures by twice as much at the same molar concentration. They were up to twice as effective at decreasing the base pair dependence. Some carboxylate homologs of betaine, substituted with hydroxyl groups, increased the melting temperature. This effect was greater with low GC content DNA. Sulfonate analogs of betaine with hydroxyl groups usually destabilize the DNA, while their carboxylate analogs stabilize the DNA. Distances between the charges of these synthetic zwitterionic solutes influence the effect on DNA, with the optimum separation being two or three methylene groups. A betaine with two hydroxyl groups on one N-alkyl group had a greater effect than an isomer with two hydroxyl groups on separate N-alkyl substituents. We suggest that the effect of these solutes depends on structuring the hydration water of DNA, as well as interactions with the DNA structure itself. PMID:18781629

Vasudevamurthy, Madhusudan K; Lever, Michael; George, Peter M; Morison, Ken R



Three different group I introns in the nuclear large subunit ribosomal DNA of the amoeboflagellate Naegleria.  

PubMed Central

We have amplified the large subunit ribosomal DNA (LSUrDNA) of the 12 described Naegleria spp. and of 34 other Naegleria lineages that might be distinct species. Two strains yielded a product that is longer than 3 kb, which is the length of the LSUrDNA of all described Naegleria spp. Sequencing data revealed that the insert in one of these strains is a group I intron without an open reading frame (ORF), while the other strain contains two different group I introns, of which the second intron has an ORF of 175 amino acids. In the latter ORF there is a conserved His-Cys box, as in the homing endonucleases present in group I introns in the small subunit ribosomal DNA (SSUrDNA) of Naegleria spp. Although the group I introns in the LSUrDNA differ in sequence, they are more related to each other than they are to the group I introns in the SSUrDNA of Naegleria spp. The three group I introns in the LSUrDNA in Naegleria are at different locations and are probably acquired by horizontal transfer, contrary to the SSUrDNA group I introns in this genus which are of ancestral origin and are transmitted vertically.

De Jonckheere, J F; Brown, S



Hands on group work paper model for teaching DNA structure, central dogma and recombinant DNA  

Microsoft Academic Search

Understanding life on a molecular level is greatly enhanced when students are given the opportunity to visualize the molecules. Especially understanding DNA structure and function is essential for understanding key concepts of molecular biology such as DNA, central dogma and the manipulation of DNA. Researches have shown that undergraduate students typically lack a coherent view of concepts and their relationships




Sequence of figwort mosaic virus DNA (caulimovirus group).  

PubMed Central

The nucleotide sequence of an infectious clone of figwort mosaic virus (FMV) was determined using the dideoxynucleotide chain termination method. The double-stranded DNA genome (7743 base pairs) contained eight open reading frames (ORFs), seven of which corresponded approximately in size and location to the ORFs found in the genome of cauliflower mosaic virus (CaMV) and carnation etched ring virus (CERV). ORFs I and V of FMV demonstrated the highest degrees of nucleotide and amino acid sequence homology with the equivalent coding regions of CaMV and CERV. Regions II, III and IV showed somewhat less homology with the analogous regions of CaMV and CERV, and ORF VI showed homology with the corresponding gene of CaMV and CERV in only a short segment near the middle of the putative gene product. A 16 nucleotide sequence, complementary to the 3' terminus of methionine initiator tRNA (tRNAimet) and presumed to be the primer binding site for initiation of reverse transcription to produce minus strand DNA, was found in the FMV genome near the discontinuity in the minus strand. Sequences near the three interruptions in the plus strand of FMV DNA bear strong resemblance to similarly located sequences of 3 other caulimoviruses and are inferred to be initiation sites for second strand DNA synthesis. Additional conserved sequences in the small and large intergenic regions are pointed out including a highly conserved 35 bp sequence that occurs in the latter region.

Richins, R D; Scholthof, H B; Shepherd, R J



Correction of the DNA repair defect in xeroderma pigmentosum group E by injection of a DNA damage-binding protein.  

PubMed Central

Cells from a subset of patients with the DNA-repair-defective disease xeroderma pigmentosum complementation group E (XP-E) are known to lack a DNA damage-binding (DDB) activity. Purified human DDB protein was injected into XP-E cells to test whether the DNA-repair defect in these cells is caused by a defect in DDB activity. Injected DDB protein stimulated DNA repair to normal levels in those strains that lack the DDB activity but did not stimulate repair in cells from other xeroderma pigmentosum groups or in XP-E cells that contain the activity. These results provide direct evidence that defective DDB activity causes the repair defect in a subset of XP-E patients, which in turn establishes a role for this activity in nucleotide-excision repair in vivo. Images

Keeney, S; Eker, A P; Brody, T; Vermeulen, W; Bootsma, D; Hoeijmakers, J H; Linn, S



Correction of the DNA repair defect in xeroderma pigmentosum group E by injection of a DNA damage-binding protein  

SciTech Connect

Cells from a subset of patients with the DNA-repair-defective disease xeroderma pigmentosum complementation group E (XP-E) are known to lack a DNA damage-binding (DDB) activity. Purified human DDB protein was injected into XP-E cells to test whether the DNA-repair defect in these cells is caused by a defect in DDB activity. Injected DDB protein stimulated DNA repair to normal levels in those strains that lack the DDB activity but did not stimulate repair in cells from other xeroderma pigmentosum groups or in XP-E cells that contain the activity. These results provide direct evidence that defective DDB activity causes the repair defect in a subset of XP-E patients, which in turn establishes a role for this activity in nucleotide-excision repair in vivo.

Keeney, S.; Brody, T.; Linn, S. [Univ. of California, Berkeley, CA (United States); Eker, A.P.M.; Vermeulen, W.; Bootsma, D.; Hoeijmakers, J.H.J. [Erasmus Univ., Rotterdam (Netherlands)



Y-STR analysis on DNA mixture samples—Results of a collaborative project of the ENFSI DNA Working Group  

Microsoft Academic Search

The ENFSI (European Network of Forensic Science Institutes) DNA Working Group undertook a collaborative project on Y-STR typing of DNA mixture samples that were centrally prepared and thoroughly tested prior to the shipment. Four commercial Y-STR typing kits (Y-Filer, Applied Biosystems, Foster City, CA, USA; Argus Y Nonaplex, Biotype, Dresden, Germany; Powerplex Y, Promega, Madison, WI, USA; and DYSplex-3, SERAC,

Walther Parson; Harald Niederstätter; Alexandra Lindinger; Peter Gill



Liquid-crystalline phases formed by DNA duplexes containing pyrophosphate groups  

SciTech Connect

We have studied the interaction between synthetic DNA molecules containing pyrophosphate (PP) groups in various positions, which makes it possible to control the charge distribution along the DNA chain. The PP groups were either symmetrically arranged at the ends or at the center of DNA molecules or uniformly distributed along these molecules. It is shown that, similar to nonmodified DNA, the synthetic PP-modified DNA molecules can form cholesteric liquid crystals. Minima of the pair interaction potential are found, conditions of the symmetry of this potential are formulated, and the dependence of conformation angles on the effective charge is determined. The results of calculations show that the system exhibits polymorphism (i.e., several phases of cholesteric liquid crystals can exist in DNA solutions)

Volkov, Yu. S., E-mail:; Golo, V. L. [Moscow State University (Russian Federation); Kats, E. I. [Russian Academy of Sciences Chernogolovka, Landau Institute for Theoretical Physics (Russian Federation); Kuznetsova, S. A. [Institut Laue-Langevin (France)



Sulfhydryl group content of chicken progesterone receptor: effect of oxidation on DNA binding activity  

SciTech Connect

DNA binding activity of chicken progesterone receptor B form (PRB) and A form (PRA) has been examined. This activity is strongly dependent upon the presence of thiols in the buffer. Stability studies showed that PRB was more sensitive to oxidation that was PRA. Receptor preparations were fractionated by DNA-cellulose chromatography to DNA-positive and DNA-negative subpopulations, and sulfhydryl groups were quantified on immunopurified receptor by labeling with (/sup 3/H)-N-ethylmaleimide. Labeling of DNA-negative receptors with (/sup 3/H)-N-ethylmaleimide showed 21-23 sulfhydryl groups on either PRA or PRB form when the proteins were reduced and denatured. A similar number was seen without reduction if denatured DNA-positive receptor species were tested. In contrast, the DNA-negative PRB had only 10-12 sulfhydryl groups detectable without reduction. A similar number (12-13 sulfhydryl groups) was found for PRA species that lost DNA binding activity after exposure to a nonreducing environment in vitro. The authors conclude that the naturally occurring receptor forms unable to bind to DNA, as well as receptor forms that have lost DNA binding activity due to exposure to nonreducing environment in vitro, contain 10-12 oxidized cysteine residues, likely present as disulfide bonds. Since they were unable to reduce the disulfide bonds when the native DNA-negative receptor proteins were treated with dithiothreitol (DTT), they speculate that irreversible loss of DNA binding activity of receptor in vitro is due to oxidation of cysteine residues that are not accessible to DTT in the native state.

Peleg, S.; Schrader, W.T.; O'Malley, B.W.



Xeroderma Pigmentosum Group E Cells Lack a Nuclear Factor That Binds to Damaged DNA  

Microsoft Academic Search

The disease xeroderma pigmentosum is characterized by deficient repair of damaged DNA. Fusions of cells from different patients have defined nine genetic complementation groups (A through I), implying that DNA repair in humans involves multiple gene products. In this report, an extension of the gel electrophoresis binding assay was used to identify at least one nuclear factor that (i) bound

Gilbert Chu; Elaine Chang



A group, of interacting yeast DNA rephcatlon genes  

Microsoft Academic Search

Mutations in the cell-division-cycle genes CDC46 and CDC47 were originally isolated as suppressors of mutations in two other cell-division-cycle genes (CDC45 and CDC54). We found several combinations of mutations in these genes that result in allele-specific suppression and synthetic lethality, confirming that this set of genes forms a group of genetically interacting components. Here, we show that the other genes,

Kevin M. Hennessy; Angela Lee; Ellson Chen; David Botstein



Control region sequences for East Asian individuals in the Scientific Working Group on DNA Analysis Methods forensic mtDNA data set  

Microsoft Academic Search

The Scientific Working Group on DNA Analysis Methods (SWGDAM) mitochondrial DNA (mtDNA) population data set is used to infer the relative rarity of mtDNA profiles obtained from evidence samples and of profiles used to identify missing persons. In this study, the East Asian haplogroup patterns in the SWGDAM data sets were analyzed in a phylogenetic context to determine relevant single

Marc W Allard; Mark R Wilson; Keith L Monson; Bruce Budowle



Complementation of DNA repair in xeroderma pigmentosum group A cell extracts by a protein with affinity for damaged DNA.  


Complementation group A of xeroderma pigmentosum (XP) represents one of the most prevalent and serious forms of this cancer-prone disorder. Because of a marked defect in DNA excision repair, cells from individuals with XP-A are hypersensitive to the toxic and mutagenic effects of ultraviolet light and many chemical agents. We report here the isolation of the XP-A DNA repair protein by complementation of cell extracts from a repair-defective human XP-A cell line. XP-A protein purified from calf thymus migrates on denaturing gel electrophoresis as a doublet of 40 and 42 kilodaltons. The XP-A protein binds preferentially to ultraviolet light-irradiated DNA, with a preference for damaged over nondamaged nucleotides of approximately 10(3). This strongly suggests that the XP-A protein plays a direct role in the recognition of and incision at lesions in DNA. We further show that this protein corresponds to the product encoded by a recently isolated gene that can restore excision repair to XP-A cells. Thus, excision repair of plasmid DNA by cell extracts sufficiently resembles genomic repair in cells to reveal accurately the repair defect in an inherited disease. The general approach described here can be extended to the identification and isolation of other human DNA repair proteins. PMID:1935910

Robins, P; Jones, C J; Biggerstaff, M; Lindahl, T; Wood, R D



Cockayne syndrome group B protein promotes mitochondrial DNA stability by supporting the DNA repair association with the mitochondrial membrane  

PubMed Central

Cockayne syndrome (CS) is a human premature aging disorder associated with severe developmental deficiencies and neurodegeneration, and phenotypically it resembles some mitochondrial DNA (mtDNA) diseases. Most patients belong to complementation group B, and the CS group B (CSB) protein plays a role in genomic maintenance and transcriptome regulation. By immunocytochemistry, mitochondrial fractionation, and Western blotting, we demonstrate that CSB localizes to mitochondria in different types of cells, with increased mitochondrial distribution following menadione-induced oxidative stress. Moreover, our results suggest that CSB plays a significant role in mitochondrial base excision repair (BER) regulation. In particular, we find reduced 8-oxo-guanine, uracil, and 5-hydroxy-uracil BER incision activities in CSB-deficient cells compared to wild-type cells. This deficiency correlates with deficient association of the BER activities with the mitochondrial inner membrane, suggesting that CSB may participate in the anchoring of the DNA repair complex. Increased mutation frequency in mtDNA of CSB-deficient cells demonstrates functional significance of the presence of CSB in the mitochondria. The results in total suggest that CSB plays a direct role in mitochondrial BER by helping recruit, stabilize, and/or retain BER proteins in repair complexes associated with the inner mitochondrial membrane, perhaps providing a novel basis for understanding the complex phenotype of this debilitating disorder.—Aamann, M. D., Sorensen, M. M., Hvitby, C., Berquist, B. R., Muftuoglu, M., Tian, J., de Souza-Pinto, N. C., Scheibye-Knudsen, M., Wilson, D. M., III, Stevnsner, T., Bohr, V. A. Cockayne syndrome group B protein promotes mitochondrial DNA stability by supporting the DNA repair association with the mitochondrial membrane.

Aamann, Maria D.; Sorensen, Martin M.; Hvitby, Christina; Berquist, Brian R.; Muftuoglu, Meltem; Tian, Jingyan; de Souza-Pinto, Nadja C.; Scheibye-Knudsen, Morten; Wilson, David M.; Stevnsner, Tinna; Bohr, Vilhelm A.



Mitochondrial DNA genetic diversity among four ethnic groups in Sierra Leone.  


Although there are numerous ethnic groups in Sierra Leone, the Mende and Temne together account for approximately 60% of the total population. To see if genetic differences could be observed among ethnic groups in Sierra Leone, the nucleotide sequence of the hypervariable 1 (HV1) region of mitochondrial DNA (mtDNA) was determined from samples of the two major ethnic groups, the Mende (n=59) and Temne (n=121), and of two minor ethnic groups, the Loko (n=29) and Limba (n=67). Among these 276 HV1 sequences, 164 individual haplotypes were observed. An analysis of molecular variance indicated that the distribution of these haplotypes within the Limba sample was significantly different from that of the other ethnic groups. No significant genetic variation was seen between the Mende, Temne, and Loko. These results indicate that distinguishing genetic differences can be observed among ethnic groups residing in historically close proximity to one another. Furthermore, we observed some mitochondrial DNA haplotypes that are common among the Sierra Leone ethnic groups but that have not been observed in other published studies of West African ethnic groups. Therefore, we may have evidence for mtDNA lineages that are unique to this region of West Africa. PMID:15761855

Jackson, Bruce A; Wilson, Jamie Lee; Kirbah, Salwa; Sidney, Sheree S; Rosenberger, Joshua; Bassie, Larry; Alie, Joe A D; McLean, David C; Garvey, W Timothy; Ely, Bert



Xeroderma Pigmentosum Group F Caused by a Defect in a Structure-Specific DNA Repair Endonuclease  

Microsoft Academic Search

Nucleotide excision repair, which is defective in xeroderma pigmentosum (XP), involves incision of a DNA strand on each side of a lesion. We isolated a human gene homologous to yeast Rad1 and found that it corrects the repair defects of XP group F as well as rodent groups 4 and 11. Causative mutations and strongly reduced levels of encoded protein

Anneke M Sijbers; Wouter L de Laat; Rafael R Ariza; Maureen Biggerstaff; Ying-Fei Wei; Jonathan G Moggs; Kenneth C Carter; Brenda K Shell; Elizabeth Evans; Mariska C de Jong; Suzanne Rademakers; Johan de Rooij; Nicolaas G. J Jaspers; Jan H. J Hoeijmakers; Richard D Wood



Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family.  

PubMed Central

A new family of protein domains consisting of 50-80 amino acid residues is described. It is composed of nearly 40 members, including domains encoded by plastid and phage group I introns; mitochondrial, plastid, and bacterial group II introns; eubacterial genomes and plasmids; and phages. The name "EX1HH-HX3H" was coined for both domain and family. It is based on 2 most prominent amino acid sequence motifs, each encompassing a pair of highly conserved histidine residues in a specific arrangement: EX1HH and HX3H. The "His" motifs often alternate with amino- and carboxy-terminal motifs of a new type of Zn-finger-like structure CX2,4CX29-54[CH]X2,3[CH]. The EX1HH-HX3H domain in eubacterial E2-type bacteriocins and in phage RB3 (wild variant of phage T4) product of the nrdB group I intron was reported to be essential for DNA endonuclease activity of these proteins. In other proteins, the EX1HH-HX3H domain is hypothesized to possess DNase activity as well. Presumably, this activity promotes movement (rearrangement) of group I and group II introns encoding the EX1HH-HX3H domain and other gene targets. In the case of Escherichia coli restrictase McrA and possibly several related proteins, it appears to mediate the restriction of alien DNA molecules.

Gorbalenya, A. E.



Control of DNA minor groove width and Fis protein binding by the purine 2-amino group.  


The width of the DNA minor groove varies with sequence and can be a major determinant of DNA shape recognition by proteins. For example, the minor groove within the center of the Fis-DNA complex narrows to about half the mean minor groove width of canonical B-form DNA to fit onto the protein surface. G/C base pairs within this segment, which is not contacted by the Fis protein, reduce binding affinities up to 2000-fold over A/T-rich sequences. We show here through multiple X-ray structures and binding properties of Fis-DNA complexes containing base analogs that the 2-amino group on guanine is the primary molecular determinant controlling minor groove widths. Molecular dynamics simulations of free-DNA targets with canonical and modified bases further demonstrate that sequence-dependent narrowing of minor groove widths is modulated almost entirely by the presence of purine 2-amino groups. We also provide evidence that protein-mediated phosphate neutralization facilitates minor groove compression and is particularly important for binding to non-optimally shaped DNA duplexes. PMID:23661683

Hancock, Stephen P; Ghane, Tahereh; Cascio, Duilio; Rohs, Remo; Di Felice, Rosa; Johnson, Reid C



Control of DNA minor groove width and Fis protein binding by the purine 2-amino group  

PubMed Central

The width of the DNA minor groove varies with sequence and can be a major determinant of DNA shape recognition by proteins. For example, the minor groove within the center of the Fis–DNA complex narrows to about half the mean minor groove width of canonical B-form DNA to fit onto the protein surface. G/C base pairs within this segment, which is not contacted by the Fis protein, reduce binding affinities up to 2000-fold over A/T-rich sequences. We show here through multiple X-ray structures and binding properties of Fis–DNA complexes containing base analogs that the 2-amino group on guanine is the primary molecular determinant controlling minor groove widths. Molecular dynamics simulations of free-DNA targets with canonical and modified bases further demonstrate that sequence-dependent narrowing of minor groove widths is modulated almost entirely by the presence of purine 2-amino groups. We also provide evidence that protein-mediated phosphate neutralization facilitates minor groove compression and is particularly important for binding to non-optimally shaped DNA duplexes.

Hancock, Stephen P.; Ghane, Tahereh; Cascio, Duilio; Rohs, Remo; Di Felice, Rosa; Johnson, Reid C.



DNA duplex-supported artificial esterase mimicking by cooperative grafting functional groups.  


The molecular structures of enzyme mimics may be modified to optimize their catalytic properties. In this study, to generate artificial enzyme mimics, Watson-Crick base paired DNA duplexes were designed as scaffolds which were assembled by nucleotides modified with specific functional groups. This process allowed various functional groups to be precisely assembled at different sites on the duplexes. By using this strategy, the 5-[2-(1H-imidazolyl-4)-(E)-ethylene]-2'-deoxythymidine (1) analog with the 5-substituted imidazolyl group was incorporated into single strands of DNA. Upon DNA duplex formation, several combinations of the imidazolyl group were formed. Using p-nitrophenyl acetate as the substrate of the catalytic reaction, we evaluated the hydrolysis capabilities of the imidazolyl assemblies. The catalytic ability was closely related to the distribution of imidazolyl groups in the DNA duplex. The most effective catalytic center was that of the duplex O5-O6 construct with three imidazolyl groups. This construct displayed bell-shaped pH-dependent and Mg(2+)-independent kinetic curves, which are typical characteristics of imidazolyl-mediated catalytic reactions. PMID:23583410

Xu, Liang; Ji, Chuanshi; Bai, Yu; He, Junlin; Liu, Keliang



Group II introns designed to insert into therapeutically relevant DNA target sites in human cells.  


Mobile group II intron RNAs insert directly into DNA target sites and are then reverse-transcribed into genomic DNA by the associated intron-encoded protein. Target site recognition involves modifiable base-pairing interactions between the intron RNA and a >14-nucleotide region of the DNA target site, as well as fixed interactions between the protein and flanking regions. Here, we developed a highly efficient Escherichia coli genetic assay to determine detailed target site recognition rules for the Lactococcus lactis group II intron Ll.LtrB and to select introns that insert into desired target sites. Using human immunodeficiency virus-type 1 (HIV-1) proviral DNA and the human CCR5 gene as examples, we show that group II introns can be retargeted to insert efficiently into virtually any target DNA and that the retargeted introns retain activity in human cells. This work provides the practical basis for potential applications of targeted group II introns in genetic engineering, functional genomics, and gene therapy. PMID:10903206

Guo, H; Karberg, M; Long, M; Jones, J P; Sullenger, B; Lambowitz, A M



Impact of pyrophosphate and O-ethyl-substituted pyrophosphate groups on DNA structure.  


Design of novel DNA probes to inhibit specific repair pathways is important for basic science applications and for use as therapeutic agents. As shown previously, single pyrophosphate (PP) and O-ethyl-substituted pyrophosphate (SPP) modifications can inhibit the DNA glycosylase activities on damaged DNA. To understand the structural basis of this inhibition, the influence of the PP and SPP internucleotide groups on the helical parameters and geometry of a double-stranded DNA was studied by using molecular modeling tools including molecular dynamics and quantum mechanical-molecular mechanical (QM/MM) approaches. Native and locally modified PP- and SPP-containing DNA duplexes of dodecanucleotide d(C1G2C3G4A5A6T7T8C9G10C11G12) were simulated in aqueous solution. The energies and forces were computed by using the PBE0/6-31+G** approach in the QM part and the AMBER force-field parameters in the MM part. Analysis of the local base-pair helical parameters, internucleotide distances, and overall global structure at the located stationary points revealed a close similarity of the initial and modified duplexes, with only torsion angles of the main chain being altered in the vicinity of introduced chemical modification. Results show that the PP and SPP groups are built into a helix structure without elongation of the internucleotide distance due to flipping-out of phosphate group from the sugar-phosphate backbone. The mechanism of such embedding has only a minor impact on the base pairs stacking and Watson-Crick interactions. Biochemical studies revealed that the PP and SPP groups immediately 5', but not 3', to the 8-oxoguanosine (8oxodG) inhibit translesion synthesis by a DNA polymerase in vitro. These results suggest that subtle perturbations of the DNA backbone conformation influence processing of base lesions. PMID:17214495

Rogacheva, Maria V; Bochenkova, Anastasia V; Kuznetsova, Svetlana A; Saparbaev, Murat K; Nemukhin, Alexander V



Haplotype diversity in mitochondrial DNA hypervariable region I, II and III in a Korean ethnic group from northeast China  

Microsoft Academic Search

Sequence polymorphism of the mitochondrial DNA (mtDNA) control region, hypervariable regions HVR I, II and III, from 55 unrelated Korean ethnic group individuals from northeast China (YanBian area) were determined by PCR amplification and cycle sequencing.

YongJi Zhang; QingSong Xu; Hong Cui; Yan Cui; HaiYu Lin; KiBeom Kim; JungBin Lee



Y-STR analysis on DNA mixture samples--results of a collaborative project of the ENFSI DNA Working Group.  


The ENFSI (European Network of Forensic Science Institutes) DNA Working Group undertook a collaborative project on Y-STR typing of DNA mixture samples that were centrally prepared and thoroughly tested prior to the shipment. Four commercial Y-STR typing kits (Y-Filer, Applied Biosystems, Foster City, CA, USA; Argus Y Nonaplex, Biotype, Dresden, Germany; Powerplex Y, Promega, Madison, WI, USA; and DYSplex-3, SERAC, Bad Homburg, Germany) were used for the amplification of the mixture samples. The results of the study showed a striking inter-laboratory difference of kit performance as determined from the peak heights of the obtained Y-STR genotypes. Variation in quantity and quality of the shipped DNA can be excluded as reason for the observed differences because both samples and shipping conditions were found to be reproducible in an earlier study. The results suggest that in some cases a laboratory-specific optimization process is indicated to reach a comparable sensitivity for the analysis of minute amounts of DNA. PMID:19083827

Parson, Walther; Niederstätter, Harald; Lindinger, Alexandra; Gill, Peter



DNA barcoding of Schistosoma haematobium on Zanzibar reveals substantial genetic diversity and two major phylogenetic groups.  


To shed light on the genetic diversity of Schistosoma haematobium on Zanzibar a DNA barcoding study was performed on parasite material isolated from different time-points 4 years apart. Substantive sequence variation was found within the mitochondrial cytochrome oxidase subunit I (cox1) and the NADH-dehydrogenase subunit 1 (nad1) with 27 and 22 unique haplotypes identified respectively and 38 when both gene regions were considered. Upon phylogenetic analysis and comparison with other S. haematobium isolates, haplotypes or barcode types partitioned into two discrete major groups, designated Group 1 and Group 2. Whilst Group 1 isolates were recovered from both Zanzibar and the African mainland, Group 2 isolates were exclusive to Zanzibar. A mixture of Group 1 and 2 parasites were recovered from individual children with no child shedding parasites of a single group haplotype alone. Whilst changes in general levels of genetic diversity between the two parasite isolation time-points were observed, no obvious change in genetic diversity was detected, despite large-scale drug distribution of praziquantel during the intervening period and there was no biased of Group 1 or 2 parasites persisting at the different time-points. To assist in future genetic screening of schistosome larval stages e.g. eggs, miracidia or cercariae, two new DNA-typing assays based on group-specific PCR primers and SNaPshot™ probes have been developed to distinguish Group 1 and 2 haplotypes. PMID:22721826

Webster, Bonnie L; Culverwell, C Lorna; Khamis, I Simba; Mohammed, Khalfan A; Rollinson, David; Stothard, J Russell



Retrotransposition of the Ll.LtrB group II intron proceeds predominantly via reverse splicing into DNA targets.  


Catalytic group II introns are mobile retroelements that invade cognate intronless genes via retrohoming, where the introns reverse splice into double-stranded DNA (dsDNA) targets. They can also retrotranspose to ectopic sites at low frequencies. Whereas our previous studies with a bacterial intron, Ll.LtrB, supported frequent use of RNA targets during retrotransposition, recent experiments with a retrotransposition indicator gene indicate that DNA, rather than RNA, is a prominent target, with both dsDNA and single-stranded DNA (ssDNA) as possibilities. Thus retrotransposition occurs in both transcriptional sense and antisense orientations of target genes, and is largely independent of homologous DNA recombination and of the endonuclease function of the intron-encoded protein, LtrA. Models based on both dsDNA and ssDNA targeting are presented. Interestingly, retrotransposition is biased toward the template for lagging-strand DNA synthesis, which suggests the possibility of the replication folk as a source of ssDNA. Consistent with some use of ssDNA targets, many retrotransposition sites lack nucleotides critical for the unwinding of target duplex DNA. Moreover, in vitro the intron reverse spliced into ssDNA more efficiently than dsDNA substrates for some of the retrotransposition sites. Furthermore, many bacterial group II introns reside on the lagging-strand template, hinting at a role for DNA replication in intron dispersal in nature. PMID:12453213

Ichiyanagi, Kenji; Beauregard, Arthur; Lawrence, Stacey; Smith, Dorie; Cousineau, Benoit; Belfort, Marlene



Evolutionary differentiation of bimaculatus group anoles based on analyses of mtDNA and microsatellite data  

Microsoft Academic Search

The bimaculatus group of anoles inhabit the northern Lesser Antilles, as far south as Dominica. This study uses 1005 base pairs (bp) of mitochondrial DNA sequence data from two genes, cytochrome b (521bp) and cytochrome oxidase subunit I (484bp) to reconstruct phylogenetic relationships between species and populations of anoles from all islands banks. Allele frequency data from nuclear microsatellite loci

Andrew G. Stenson; Roger S. Thorpe; Anita Malhotra



Design of specific DNA primers to detect the Bacillus cereus group species  

Microsoft Academic Search

One of the most prevalent pathogens that cause foodborne outbreaks is the Bacillus cereus (B. cereus) group species (spp.) generally found in different types of food. Recently many researchers are focusing towards the progress of rapid methods to detect foodborne pathogens. Every year many innovative methodologies for bacterial detection are being developed to improve sensitivity and speed of detection. DNA

Catherine Adley; Khalil Arshak; Camila Molnar; Kamila Oliwa; Vijayalakshmi Velusamy



Genetic diversity of Fusarium moniliforme detected by vegetative compatibility groups and random amplified polymorphic DNA markers  

Microsoft Academic Search

Genetic diversity among Fusarium moniliformeisolates was analysed using vegetative compatibility group (VCG) and random amplified polymorphic DNA (RAPD) techniques. In the first experiment, RAPD was used to analyse a set of 43 isolates collected from different corn growing areas in Israel and the US. The isolates were assigned to 27 different VCGs. Thirty-two RAPD haplotypes were also detected by analysing




Large stabilization of a DNA duplex by the deoxyadenosine derivatives tethering an aromatic hydrocarbon group.  


Novel deoxyadenosine derivatives tethering a phenyl or naphthyl group by means of an amido linker have been synthesized, and these derivatives, stacking on the 5' end of a DNA duplex, provide free energy contributions equal to or greater than that of the Watson-Crick A/T base pair. PMID:12837062

Nakano, Shu-ichi; Uotani, Yuuki; Nakashima, Shoji; Anno, Yosuke; Fujii, Masayuki; Sugimoto, Naoki



A bridging model for persistence of a Polycomb Group protein complex through DNA replication in vitro  

PubMed Central

SUMMARY Epigenetic regulation may involve heritable chromatin states but how chromatin features can be inherited through DNA replication is incompletely understood. We address this question using cell free replication of chromatin. Previously, we showed that a Polycomb Group complex, PRC1, remains continuously associated with chromatin through DNA replication. Here we investigate the mechanism of persistence. We find that a single PRC1 subunit, Posterior Sex Combs (PSC) can reconstitute persistence through DNA replication. PSC binds nucleosomes and self-interacts, bridging nucleosomes into a stable, oligomeric structure. Within these structures, individual PSC-chromatin contacts are dynamic. Stable association of PSC with chromatin, including through DNA replication, depends on PSC-PSC interactions. Our data suggest labile individual PSC-chromatin contacts allow passage of the DNA replication machinery while PSC-PSC interactions prevent PSC from dissociating, allowing it to rebind to replicated chromatin. This mechanism may allow inheritance of chromatin proteins including PRC1 through DNA replication to maintain chromatin states.

Lo, Stanley M.; Follmer, Nicole E.; Lengsfeld, Bettina M.; Madamba, Egbert V.; Seong, Samuel; Grau, Daniel J.; Francis, Nicole J.



NMR spin grouping and correlation exchange analysis. Application to low hydration NaDNA paracrystals.  

PubMed Central

The NMR spin-grouping technique is applied to low hydration oriented fibers of NaDNA to study the role of exchange in determining the apparent (observed) spin relaxation of the system. The analysis proceeds in three steps: first, the apparent proton relaxation is measured at high fields, with both selective and nonselective inversion pulse sequences, and in the rotating frame. The spin-grouping technique is used in all spin-lattice relaxation measurements to provide the optimum apparent relaxation characterization of the sample. Next, all apparent results are analyzed for exchange. In this analysis the results from the high field and rotating frame experiments (which probe the exchange at two different time scales) are correlated to determine the inherent (or true) spin relaxation parameters of each of the proton groups in the system. The results of selective inversion T1 measurements are also incorporated into the exchange analysis. Finally, the dynamics of each spin group are inferred from the inherent relaxation characterization. The low hydration NaDNA structure is such that the exchange between the protons on the water and those on the NaDNA is limited, a priori, to dipolar mixing. The results of the exchange analysis indicate that the dipolar mixing between water and NaDNA protons is faster than the spin diffusion within the NaDNA proton group itself. The spin-diffusion on the macromolecule is the bottleneck for the exchange between the water protons and the NaDNA protons. The water protons serve as the relaxation sink both at high fields and in the rotating frame for the total NaDNA-water spin bath. The inherent relaxation of the water is characteristic of water undergoing anisotropic motion with a fast reorientational correlation time about one axis (5 X 10(-10) less than or equal to tau r less than or equal to 8 X 10(-9)S) which is about three orders of magnitude slower than that of water in the bulk; and a slow tumbling correlation time for this axis (1.5 x 10(-7) less than or equal to tau t less than or equal to 8 x 10(-7)S) which is two orders of magnitude slower yet. Images FIGURE 4 FIGURE 6

Schreiner, L J; MacTavish, J C; Pintar, M M; Rupprecht, A



UV damage-specific DNA-binding protein in xeroderma pigmentosum complementation group E  

SciTech Connect

The gel mobility shift assay method revealed a specifically ultraviolet (UV) damage recognizing, DNA-binding protein in nuclear extracts of normal human cells. The resulted DNA/protein complexes caused the two retarded mobility shifts. Four xeroderma pigmentosum complementation group E (XPE) fibroblast strains derived from unrelated Japanese families were not deficient in such a DNA damage recognition/binding protein because of the normal complex formation and gel mobility shifts, although we confirmed the reported lack of the protein in the European XPE (XP2RO and XP3RO) cells. Thus, the absence of this binding protein is not always commonly observed in all the XPE strains, and the partially repair-deficient and intermediately UV-hypersensitive phenotype of XPE cells are much similar whether or not they lack the protein.

Kataoka, H.; Fujiwara, Y. (Kobe Univ. School of Medicine, (Japan))



Origin of Caucasoid-Specific Mitochondrial DNA Lineages in the Ethnic Groups of the Altai–Sayan Region  

Microsoft Academic Search

The data on sequence variation in the first hypervariable segment (HVSI) of human mitochondrial DNA (mtDNA) representing Caucasoid mtDNA lineages in the gene pools of Altaians and Khakassians are presented. Identification of the subgroups of Caucasoid mtDNA lineages found in the gene pools of the ethnic groups of the Altai–Sayan region and the adjacent territories, Altaians, Khakassians, Tuvinians, Buryats, and

M. V. Derenko; B. A. Malyarchuk; I. A. Zakharov



Sequence variation of the rDNA ITS regions within and between anastomosis groups in Rhizoctonia solani  

Microsoft Academic Search

Sequence analysis of the rDNA region containing the internal transcribed spacer (ITS) regions and the 5.8s rDNA coding sequence was used to evaluate the genetic diversity of 45 isolates within and between anastomosis groups (AGs)\\u000a in Rhizoctonia solani. The 5.8s rDNA sequence was completely conserved across all the AGs examined, whereas the ITS rDNA sequence was found to be highly

Shiro Kuninaga; Tomohide Natsuaki; Toru Takeuchi; Ryozo Yokosawa



DNA content in nine species of Nematocera with special reference to the sibling species of the Anopheles maculipennis group and the Culex pipiens group  

Microsoft Academic Search

DNA values were determined for the nine species: Telmatoscopus meridionalis (family Psychodidae), Dixa obscura (family Dixidae), and Culiseta litorea, Culex pipiens, Aedes caspius, Anopheles labranchiae, Anopheles atroparvus, Anopheles stephensi, and Anopheles freeborni (family Culicidae). The DNA content indicated that the species could be divided into three categories: The Culex group with Culex pipiens, Culiseta litorea and Aedes caspius containing 1.02,

Erich Jost; Marco Mameli



Relatedness between major taxonomic groups of fungi based on the measurement of DNA nucleotide sequence homology  

Microsoft Academic Search

Summary A procedure for the isolation of highly purified labeled and unlabeled DNAs from fungi representing three major groups has been described. The yield of DNA per g weight of freeze-dried mycelia is always higher inNeurospora crassa thanCoprinus lagopus andMucor azygospora. Thermal melting profiles show that theN. crassa andC. lagopus DNAs have one low G+C (32 mole percent) and another

S. K. Dutta; M. Ojha



The DNA helicase BRIP1 is defective in Fanconi anemia complementation group J  

Microsoft Academic Search

The protein predicted to be defective in individuals with Fanconi anemia complementation group J (FA-J), FANCJ, is a missing component in the Fanconi anemia pathway of genome maintenance. Here we identify pathogenic mutations in eight individuals with FA-J in the gene encoding the DEAH-box DNA helicase BRIP1, also called FANCJ. This finding is compelling evidence that the Fanconi anemia pathway

Marieke Levitus; Quinten Waisfisz; Barbara C Godthelp; Yne de Vries; Shobbir Hussain; Wouter W Wiegant; Elhaam Elghalbzouri-Maghrani; Jûrgen Steltenpool; Martin A Rooimans; Gerard Pals; Fré Arwert; Christopher G Mathew; Ma?gorzata Z Zdzienicka; Kevin Hiom; Johan P De Winter; Hans Joenje



Expression cloning of a human DNA repair gene involved in xeroderma pigmentosum group C  

Microsoft Academic Search

XERODERMA pigmentosum (XP) is a rare human autosomal recessive disease characterized by solar sensitivity, high predisposition for developing cancers on areas exposed to sunlight, and, in some cases, neurological abnormalities1,2. XP cells are defective in DNA repair3, and complementation of this defect has been used to identify eight genetic groups (A-G and variant)4. We have developed a simple, highly efficient

Randy Legerski; Carolyn Peterson



Restriction fragment length polymorphism of 195 bp repeated satellite dna of Trypanosoma cruzi supports the existence of two phylogenetic groups  

Microsoft Academic Search

Hinf I) and high molecular weight DNA (Hae III), while group 2 presents a ladder profile for each enzyme, which is a characteristic of tandemly repeated DNA. The two groups, respectively, clustered stocks pertaining to the two principal lineages evidenced by isoenzyme and RAPD markers. The congruence among these three independent genomic markers corroborates the existence of two real phylogenetic

Brigitte Bastrenta; Marie France Bosseno; Christian Barnabé; Michel Tibayrenc; Simone Frédérique Brenière



Differentiation and Genetic Position of Slavs among Eurasian Ethnic Groups as Inferred from Variation in Mitochondrial DNA  

Microsoft Academic Search

The distribution of identical and similar (phylogenetically related) types of hypervariable segment 1 (HVS1) of the mitochondrial DNA (mtDNA) was studied in human populations belonging to three Slavonic groups and nine ethnogeographic groups of Eurasia (total sample size 2772 people). The results testified to a common origin of West, South, and East Slavs and revealed a central place of West

B. A. Malyarchuk



Conservation of DNA photolyase genes in group II nucleopolyhedroviruses infecting plusiine insects.  


DNA photolyase genes (phr) encode photoreactive enzymes, which are involved in the repair of UV-damaged DNA. Cyclobutane pyrimidine dimer (CPD) specific photolyase genes are present in nucleopolyhedroviruses isolated from Chrysodeixis chalcites (ChchNPV) and Trichoplusia ni (TnSNPV), insects belonging to the Plusiinae (Noctuidae). To better understand the occurrence and evolution of these genes in baculoviruses, we investigated their possible conservation in other group II NPVs, which infect plusiine insects. A PCR based strategy using degenerate phr-specific primers was designed to detect and analyze possible photolyase genes. Six additional Plusiinae-infecting NPVs were analyzed and all, except Thysanoplusia oricalcea NPV A28-1, which is a group I NPV, contained one or more phr-like sequences. Phylogenetic analysis revealed that all photolyase genes of the tested Plusiinae-infecting baculoviruses group in a single clade, separated into three subgroups. The phylogeny of the polyhedrin sequences of these viruses confirmed that the analyzed viruses also formed a single clade in group II NPVs. We hypothesize that all plusiine group II NPVs contain one or more photolyase genes and that these have a common ancestor. PMID:18513819

Xu, Fang; Vlak, Just M; van Oers, Monique M



Relationship of the Xeroderma Pigmentosum Group E DNA Repair Defect to the Chromatin and DNA Binding Proteins UV-DDB and Replication Protein A  

Microsoft Academic Search

Cells from complementation groups A through G of the heritable sun-sensitive disorder xeroderma pigmen- tosum (XP) show defects in nucleotide excision repair of damaged DNA. Proteins representing groups A, B, C, D, F, and G are subunits of the core recognition and incision machinery of repair. XP group E (XP-E) is the mildest form of the disorder, and cells generally




Mitochondrial DNA polymorphisms in Gelao ethnic group residing in Southwest China.  


Gelao ethnic group, an aboriginal population residing in southwest China, has undergone a long and complex evolutionary process. To investigate the genetic structure of this ancient ethnic group, mitochondrial DNA (mtDNA) polymorphisms of 102 Gelao individuals were collected and analyzed in this study. With the aid of the information extracted from control-region hypervariable segments (HVSs) I and II as well as some necessary coding-region segments, phylogenetic status of all mtDNAs under study were determined by means of classifying into various defined haplogroups. The southern-prevalent haplogroups B, R9, and M7 account for 45.1% of the gene pool, whereas northern-prevalent haplogroups A, D, G, N9, and M8 consist of 39.2%. Haplogroup distribution indicates that the Gelao bears signatures of southern populations and possesses some regional characters. In the PC map, Gelao clusters together with populations with Bai-Yue tribe origin as well as the local Han and the Miao. The results demonstrate the complexity of Gelao population and the data can well supplement the China mtDNA database. PMID:20494640

Liu, Chang; Wang, Sha-Yan; Zhao, Mian; Xu, Zhi-Yong; Hu, Yu-Hua; Chen, Feng; Zhang, Ruan-Zhang; Gao, Guo-Feng; Yu, Yue-Sheng; Kong, Qing-Peng



Somatic mosaicism for DNA repair capacity in fibroblasts derived from a group A xeroderma pigmentosum patient  

SciTech Connect

A female Japanese xeroderma pigmentosum (XP) patient with severe skin lesions and various neurologic abnormalities was assigned to complementation group A by conventional cell fusion studies. Ultraviolet (UV)-irradiated skin fibroblasts showed a biphasic survival curve, as measured by colony-forming ability. The surviving fraction decreased rapidly up to 2 J/m2 of UV, with a steep slope of D(O) (mean lethal dose) = 0.95 J/m2. At much higher doses it decreased more slowly, with D(O) = 3.5 J/m2. To elucidate the cause of this unique survival response, we isolated a large number of independent clones from single colonies and measured their responses to UV. Of 81 clones analyzed, ten showed a marked resistance to killing by UV, which was only slightly more sensitive than normal cells, and these clones had a rate of unscheduled DNA synthesis (UDS) that was about 45% of normal cells. By contrast, the remaining 71 clones were extremely sensitive to UV, typical of XP group A strains, and had a UDS level 1%-3% of normals. Analysis of restriction fragment length polymorphism using seven polymorphic DNA probes indicated that the UV-resistant clones were derived from the same individual as the UV-sensitive clones. These results clearly demonstrate that this patient's fibroblast cells consist of two types with differing responses to UV, and provide direct evidence of somatic mosaicism for DNA repair capacity in an XP patient.

Chang, H.R.; Ishizaki, K.; Sasaki, M.S.; Toguchida, J.; Kato, M.; Nakamura, Y.; Kawamura, S.; Moriguchi, T.; Ikenaga, M. (Kyoto Univ. (Japan))



Conserved primary sequences of the DNA terminal proteins of five different human adenovirus groups.  


The 31 human adenoviruses (Ad) from five groups (A-E) whose DNAs are <20% homologous by molecular hybridization. Ad5 (group C) DNA contains a 55,000-dalton protein probably covalently bound to each 5' terminus. This covalently bound protein may be analogous to polypeptides found in other viral and nonviral systems that are covalently bound to genomic DNAs or RNAs and that are thought to function in DNA or RNA replication. Because of the importance of proteins linked to nucleic acids, we have investigated whether DNAs from all five groups of human adenoviruses have terminal proteins, as well as the peptide relationships among the different terminal proteins. We show here that DNAs from Ad12, 7, 2, 19, and 4, representing Ad groups A-E, respectively, all contain covalently bound proteins of about 55,000 daltons. To investigate the peptide relatedness among the terminal proteins, we prepared microgram quantities of covalently bound protein from Ads in groups A-E and compared their chymotryptic and tryptic (125)I-labeled peptide maps. We find that the covalently bound protein maps of the five Ad groups are highly related and possibly identical. On the other hand, the tryptic and chymotryptic peptide maps of the major virion protein II and the core proteins V and VII of groups B, C, and E Ads show considerable heterology. Assuming that the covalently bound protein is virally coded, the conserved primary sequence of these proteins suggests a major functional role for the protein in Ad replication. Because the genetic origin of the Ad covalently bound proteins is not established, our data are also consistent with the possibility that the protein is coded by a cellular gene. PMID:228297

Green, M; Brackmann, K; Wold, W S; Cartas, M; Thornton, H; Elder, J H



Conserved primary sequences of the DNA terminal proteins of five different human adenovirus groups  

PubMed Central

The 31 human adenoviruses (Ad) from five groups (A-E) whose DNAs are <20% homologous by molecular hybridization. Ad5 (group C) DNA contains a 55,000-dalton protein probably covalently bound to each 5? terminus. This covalently bound protein may be analogous to polypeptides found in other viral and nonviral systems that are covalently bound to genomic DNAs or RNAs and that are thought to function in DNA or RNA replication. Because of the importance of proteins linked to nucleic acids, we have investigated whether DNAs from all five groups of human adenoviruses have terminal proteins, as well as the peptide relationships among the different terminal proteins. We show here that DNAs from Ad12, 7, 2, 19, and 4, representing Ad groups A-E, respectively, all contain covalently bound proteins of about 55,000 daltons. To investigate the peptide relatedness among the terminal proteins, we prepared microgram quantities of covalently bound protein from Ads in groups A-E and compared their chymotryptic and tryptic 125I-labeled peptide maps. We find that the covalently bound protein maps of the five Ad groups are highly related and possibly identical. On the other hand, the tryptic and chymotryptic peptide maps of the major virion protein II and the core proteins V and VII of groups B, C, and E Ads show considerable heterology. Assuming that the covalently bound protein is virally coded, the conserved primary sequence of these proteins suggests a major functional role for the protein in Ad replication. Because the genetic origin of the Ad covalently bound proteins is not established, our data are also consistent with the possibility that the protein is coded by a cellular gene. Images

Green, Maurice; Brackmann, Karl; Wold, William S. M.; Cartas, Maria; Thornton, Helen; Elder, John H.



Complex evolutionary history of the Aeromonas veronii group revealed by host interaction and DNA sequence data.  


Aeromonas veronii biovar sobria, Aeromonas veronii biovar veronii, and Aeromonas allosaccharophila are a closely related group of organisms, the Aeromonas veronii Group, that inhabit a wide range of host animals as a symbiont or pathogen. In this study, the ability of various strains to colonize the medicinal leech as a model for beneficial symbiosis and to kill wax worm larvae as a model for virulence was determined. Isolates cultured from the leech out-competed other strains in the leech model, while most strains were virulent in the wax worms. Three housekeeping genes, recA, dnaJ and gyrB, the gene encoding chitinase, chiA, and four loci associated with the type three secretion system, ascV, ascFG, aexT, and aexU were sequenced. The phylogenetic reconstruction failed to produce one consensus tree that was compatible with most of the individual genes. The Approximately Unbiased test and the Genetic Algorithm for Recombination Detection both provided further support for differing evolutionary histories among this group of genes. Two contrasting tests detected recombination within aexU, ascFG, ascV, dnaJ, and gyrB but not in aexT or chiA. Quartet decomposition analysis indicated a complex recent evolutionary history for these strains with a high frequency of horizontal gene transfer between several but not among all strains. In this study we demonstrate that at least for some strains, horizontal gene transfer occurs at a sufficient frequency to blur the signal from vertically inherited genes, despite strains being adapted to distinct niches. Simply increasing the number of genes included in the analysis is unlikely to overcome this challenge in organisms that occupy multiple niches and can exchange DNA between strains specialized to different niches. Instead, the detection of genes critical in the adaptation to specific niches may help to reveal the physiological specialization of these strains. PMID:21359176

Silver, Adam C; Williams, David; Faucher, Joshua; Horneman, Amy J; Gogarten, J Peter; Graf, Joerg



Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data  

PubMed Central

Aeromonas veronii biovar sobria, Aeromonas veronii biovar veronii, and Aeromonas allosaccharophila are a closely related group of organisms, the Aeromonas veronii Group, that inhabit a wide range of host animals as a symbiont or pathogen. In this study, the ability of various strains to colonize the medicinal leech as a model for beneficial symbiosis and to kill wax worm larvae as a model for virulence was determined. Isolates cultured from the leech out-competed other strains in the leech model, while most strains were virulent in the wax worms. Three housekeeping genes, recA, dnaJ and gyrB, the gene encoding chitinase, chiA, and four loci associated with the type three secretion system, ascV, ascFG, aexT, and aexU were sequenced. The phylogenetic reconstruction failed to produce one consensus tree that was compatible with most of the individual genes. The Approximately Unbiased test and the Genetic Algorithm for Recombination Detection both provided further support for differing evolutionary histories among this group of genes. Two contrasting tests detected recombination within aexU, ascFG, ascV, dnaJ, and gyrB but not in aexT or chiA. Quartet decomposition analysis indicated a complex recent evolutionary history for these strains with a high frequency of horizontal gene transfer between several but not among all strains. In this study we demonstrate that at least for some strains, horizontal gene transfer occurs at a sufficient frequency to blur the signal from vertically inherited genes, despite strains being adapted to distinct niches. Simply increasing the number of genes included in the analysis is unlikely to overcome this challenge in organisms that occupy multiple niches and can exchange DNA between strains specialized to different niches. Instead, the detection of genes critical in the adaptation to specific niches may help to reveal the physiological specialization of these strains.

Faucher, Joshua; Horneman, Amy J.; Gogarten, J. Peter; Graf, Joerg



The Polycomb Group Protein EZH2 Impairs DNA Repair in Breast Epithelial Cells1  

Microsoft Academic Search

The Polycomb group protein EZH2 is a transcriptional repressor involved in controlling cellular memory and has been linked to aggressive and metastatic breast cancer. Here we report that EZH2 decreased the ex- pression of five RAD51 paralog proteins involved in homologous recombination (HR) repair of DNA double- strand breaks (RAD51B\\/RAD51L1, RAD51C\\/RAD51L2, RAD51D\\/RAD51L3, XRCC2, and XRCC3), but did not affect the

Michael Zeidler; Sooryanarayana Varambally; Qi Cao; Arul M. Chinnaiyan; David O. Ferguson; Sofia D. Merajver; Celina G. Kleer


Conducting polymer based DNA biosensor for the detection of the Bacillus cereus group species  

NASA Astrophysics Data System (ADS)

Biosensor designs are emerging at a significant rate and play an increasingly important role in foodborne pathogen detection. Conducting polymers are excellent tools for the fabrication of biosensors and polypyrrole has been used in the detection of biomolecules due to its unique properties. The prime intention of this paper was to pioneer the design and fabrication of a single-strand (ss) DNA biosensor for the detection of the Bacillus cereus (B.cereus) group species. Growth of B. cereus, results in production of several highly active toxins. Therefore, consumption of food containing >106 bacteria/gm may results in emetic and diarrhoeal syndromes. The most common source of this bacterium is found in liquid food products, milk powder, mixed food products and is of particular concern in the baby formula industry. The electrochemical deposition technique, such as cyclic voltammetry, was used to develop and test a model DNA-based biosensor on a gold electrode electropolymerized with polypyrrole. The electrically conducting polymer, polypyrrole is used as a platform for immobilizing DNA (1?g) on the gold electrode surface, since it can be more easily deposited from neutral pH aqueous solutions of pyrrolemonomers. The average current peak during the electrodeposition event is 288?A. There is a clear change in the current after hybridization of the complementary oligonucleotide (6.35?A) and for the noncomplementary oligonucleotide (5.77?A). The drop in current after each event was clearly noticeable and it proved to be effective.

Velusamy, Vijayalakshmi; Arshak, Khalil; Korostynska, Olga; Oliwa, Kamila; Adley, Catherine



A Randomly Amplified Polymorphic DNA Marker Specific for the Bacillus cereus Group Is Diagnostic for Bacillus anthracis  

Microsoft Academic Search

Aiming to develop a DNA marker specific for Bacillus anthracis and able to discriminate this species from Bacillus cereus, Bacillus thuringiensis, and Bacillus mycoides, we applied the randomly amplified polymorphic DNA (RAPD) fingerprinting technique to a collection of 101 strains of the genus Bacillus, including 61 strains of the B. cereus group. An 838-bp RAPD marker (SG-850) specific for B.




Male and Female Mitochondrial DNA Lineages in the Blue Mussel (Mytilus edulis) Species Group  

Microsoft Academic Search

In blue mussels of the Mytilus edulis species complex, mitochondrial DNA (mtDNA) inheritance is coupled with gender. Females receive their mother's mtDNA and pass it on to both their daughters and sons. In addition, males receive mtDNA from their father and transmit this male mtDNA to their sons. If this pattern of \\

Donald T. Stewart; Carlos Saavedra; Rebecca R. Stanwood; Eleftherios Zouros


Differential characteristics of catalase-positive campylobacters correlated with DNA homology groups.  


Eighty-four strains of catalase-positive campylobacters could be placed into seven distinct DNA homology groups (species), corresponding to Campylobacter fetus, "C. hyointestinalis," C. jejuni, C. coli, "C. laridis," "C. fecalis," and aerotolerant campylobacters. The biochemical and physiological characteristics of the strains were examined for their correlation with the homology groups. The characterization tests that provided the most reliable differentiation at the species and subspecies level were growth at 25 and 42 degrees C, sensitivity to cephalothin and nalidixic acid, growth in semisolid media containing 1% glycine and 3.5% NaCl, growth on plates containing 1.5% NaCl, growth in a semisolid minimal medium, anaerobic growth in the presence of 0.1% trimethylamine-N-oxide, hydrogen sulfide production in SIM medium and triple-sugar iron agar, hippurate hydrolysis, nitrite reduction, and growth on plates under an air atmosphere. PMID:6478314

Roop, R M; Smibert, R M; Johnson, J L; Krieg, N R



Mobile group II introns of yeast mitochondrial DNA are novel site-specific retroelements.  


Group II introns aI1 and aI2 of the yeast mitochondrial COXI gene are mobile elements that encode an intron-specific reverse transcriptase (RT) activity. We show here that the introns of Saccharomyces cerevisiae ID41-6/161 insert site specifically into intronless alleles. The mobility is accompanied by efficient, but highly asymmetric, coconversion of nearby flanking exon sequences. Analysis of mutants shows that the aI2 protein is required for the mobility of both aI1 and aI2. Efficient mobility is dependent on both the RT activity of the aI2-encoded protein and a separate function, a putative DNA endonuclease, that is associated with the Zn2+ finger-like region of the intron reading frame. Surprisingly, there appear to be two mobility modes: the major one involves cDNAs reverse transcribed from unspliced precursor RNA; the minor one, observed in two mutants lacking detectable RT activity, appears to involve DNA level recombination. A cis-dominant splicing-defective mutant of aI2 continues to synthesize cDNAs containing the introns but is completely defective in both mobility modes, indicating that the splicing or the structure of the intron is required. Our results demonstrate that the yeast group II intron aI2 is a retroelement that uses novel mobility mechanisms. PMID:7537853

Moran, J V; Zimmerly, S; Eskes, R; Kennell, J C; Lambowitz, A M; Butow, R A; Perlman, P S



Mitochondrial DNA polymorphisms in nine aboriginal groups of Taiwan: implications for the population history of aboriginal Taiwanese  

Microsoft Academic Search

Mitochondrial DNA (mtDNA) polymorphisms in the D-loop region and the intergenic COII\\/tRNALys 9-bp deletion were examined in 180 individuals from all nine aboriginal Taiwanese groups: Atayal, Saisiat, Bunun, Tsou, Rukai, Paiwan, Ami, Puyuma, and Yami. A comparison of 563-bp sequences showed that there were 61 different sequence types, of which 42 types were specific to respective aboriginal groups. D-loop sequence

Atsushi Tajima; Cheih-Shan Sun; I-Hung Pan; Takafumi Ishida; Naruya Saitou; Satoshi Horai



Molecular Cloning of a Mouse DNA Repair Gene that Complements the Defect of Group-A Xeroderma Pigmentosum  

Microsoft Academic Search

For isolation of the gene reponsible for xeroderma pigmentosum (XP) complementation group A, plasmid pSV2gpt and genomic DNA from a mouse embryo were cotransfected into XP2OSSV cells, a group-A XP cell line. Two primary UV-resistant XP transfectants were isolated from about 1.6 × 105 pSV2gpt-transformed XP colonies. pSV2gpt and genomic DNA from the primary transfectants were again cotransfected into XP2OSSV

Kiyoji Tanaka; Ichiro Satokata; Zenzaburo Ogita; Tsuyoshi Uchida; Yoshio Okada



Preparation of DNA Containing 5-Hydroxymethyl-2?-Deoxycytidine Modification Through Phosphoramidites with TBDMS as 5-Hydroxymethyl Protecting Group  

PubMed Central

This unit describes procedures for preparation of two phosphoramidite building blocks III and IV, both containing a TBDMS as 5-CH2OH-protecting group. Phosphoramidites III and IV allow efficient incorporation of 5-hmC into DNA and a “one-step” deprotection procedure to cleanly remove all the protecting groups. A “two-step” deprotection strategy is compatible with ultramild DNA synthesis, which enables the synthesis of 5hmC-containing DNA with additional modifications. Methods are also presented for their incorporation into oligonucleotides by solid-phase synthesis, subsequent deprotection, and HPLC analysis.

Dai, Qing; He, Chuan



Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor  

PubMed Central

We determined the crystal structure of a bifunctional group I intron splicing factor and homing endonuclease, termed the I-AniI maturase, in complex with its DNA target at 2.6 Å resolution. The structure demonstrates the remarkable structural conservation of the ?-sheet DNA-binding motif between highly divergent enzyme subfamilies. DNA recognition by I-AniI was further studied using nucleoside deletion and DMS modification interference analyses. Correlation of these results with the crystal structure provides information on the relative importance of individual nucleotide contacts for DNA recognition. Alignment and modeling of two homologous maturases reveals conserved basic surface residues, distant from the DNA-binding surface, that might be involved in RNA binding. A point mutation that introduces a single negative charge in this region uncouples the maturase and endonuclease functions of the protein, inhibiting RNA binding and splicing while maintaining DNA binding and cleavage.

Bolduc, Jill M.; Spiegel, P. Clint; Chatterjee, Piyali; Brady, Kristina L.; Downing, Maureen E.; Caprara, Mark G.; Waring, Richard B.; Stoddard, Barry L.



Identification of a group-I intron within the 25S rDNA from the yeast Arxula adeninivorans.  


The 25S rDNA of the yeast Arxula adeninivorans LS3 has been closed from a genomic library and sequenced. This DNA could be localized on chromosome 1 from A. adeninivorans and comprised 3790 bp. The DNA sequence from this rDNA of the strain LS3 is very similar to the 25S rDNA of Candida albicans (91.7%), Saccharomyces cerevisiae (90.5%), Schizosaccharomyces pombe (83.8%) and Mucor racemosus (79.2%). Additionally a 411 bp insertion could be localized within the 25S rDNA. This intervening sequence, which is devoid of any long open reading frame, is a group-IC intron as revealed from its site of insertion, predicted secondary structure, and its self-splicing capability. The Arxula intron is intermediate in structure and sequence between the ribosomal introns of Tetrahymena thermophila and C. albicans. PMID:8905924

Rösel, H; Kunze, G



Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility.  


Eukaryotic High-Mobility Group B (HMGB) proteins alter DNA elasticity while facilitating transcription, replication and DNA repair. We developed a new single-molecule method to probe non-specific DNA interactions for two HMGB homologs: the human HMGB2 box A domain and yeast Nhp6Ap, along with chimeric mutants replacing neutral N-terminal residues of the HMGB2 protein with cationic sequences from Nhp6Ap. Surprisingly, HMGB proteins constrain DNA winding, and this torsional constraint is released over short timescales. These measurements reveal the microscopic dissociation rates of HMGB from DNA. Separate microscopic and macroscopic (or local and non-local) unbinding rates have been previously proposed, but never independently observed. Microscopic dissociation rates for the chimeric mutants (~10 s(-1)) are higher than those observed for wild-type proteins (~0.1-1.0 s(-1)), reflecting their reduced ability to bend DNA through short-range interactions, despite their increased DNA-binding affinity. Therefore, transient local HMGB-DNA contacts dominate the DNA-bending mechanism used by these important architectural proteins to increase DNA flexibility. PMID:23143110

McCauley, Micah J; Rueter, Emily M; Rouzina, Ioulia; Maher, L James; Williams, Mark C



DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar  

PubMed Central

The role of DNA barcoding as a tool to accelerate the inventory and analysis of diversity for hyperdiverse arthropods is tested using ants in Madagascar. We demonstrate how DNA barcoding helps address the failure of current inventory methods to rapidly respond to pressing biodiversity needs, specifically in the assessment of richness and turnover across landscapes with hyperdiverse taxa. In a comparison of inventories at four localities in northern Madagascar, patterns of richness were not significantly different when richness was determined using morphological taxonomy (morphospecies) or sequence divergence thresholds (Molecular Operational Taxonomic Unit(s); MOTU). However, sequence-based methods tended to yield greater richness and significantly lower indices of similarity than morphological taxonomy. MOTU determined using our molecular technique were a remarkably local phenomenon—indicative of highly restricted dispersal and/or long-term isolation. In cases where molecular and morphological methods differed in their assignment of individuals to categories, the morphological estimate was always more conservative than the molecular estimate. In those cases where morphospecies descriptions collapsed distinct molecular groups, sequence divergences of 16% (on average) were contained within the same morphospecies. Such high divergences highlight taxa for further detailed genetic, morphological, life history, and behavioral studies.

Smith, M. Alex; Fisher, Brian L; Hebert, Paul D.N



Correlation of 16S Ribosomal DNA Signature Sequences with Temperature-Dependent Growth Rates of Mesophilic and Psychrotolerant Strains of the Bacillus cereus Group  

Microsoft Academic Search

Sequences of the 16S ribosomal DNA (rDNA) from psychrotolerant and mesophilic strains of the Bacillus cereus group revealed signatures which were specific for these two thermal groups of bacteria. Further analysis of the genomic DNA from a wide range of food and soil isolates showed that B. cereus group strains have between 6 and 10 copies of 16S rDNA. Moreover,




A deficiency in a 230 kDa DNA repair protein in fanconi anemia complementation group A cells is corrected by the FANCA cDNA.  


Cells from individuals with the cancer-prone, inherited disorder Fanconi anemia (FA) are hypersensitive to DNA interstrand cross-linking agents and this hypersensitivity correlates with a defect in ability to repair this type of damage to their DNA. We have isolated a DNA endonuclease complex from the nuclei of normal human cells which is involved in repair of DNA interstrand cross-links and have shown that in FA complementation group A (FA-A) cells there is a defect in ability of this complex to incise DNA containing interstrand cross-links. In order to identify the specific protein(s) in this complex which is defective in FA-A cells, monoclonal antibodies (mAbs) were developed against proteins in the normal complex. One of these mAbs, which is against a protein with a molecular weight of approximately 230 kDa, completely inhibited the ability of the normal complex to incise cross-linked DNA. Western blot analysis has shown that there is a deficiency in this protein in FA-A cells. Electophoretic analysis has also indicated that there are reduced levels of this protein in FA-A compared with normal cells. Studies carried out utilizing FA-A cells which have been stably transduced with a retroviral vector expressing the FANCA cDNA have shown that the DNA repair defect in these cells has been corrected; levels of unscheduled DNA synthesis are at least as great as those of normal human cells. In addition, in the transduced cells the deficiency in the 230 kDa protein has been corrected, as determined by both western blot and electrophoretic analysis. These results indicate that the FANCA gene plays a role in the expression or stability of the 230 kDa protein. PMID:10469633

Brois, D W; McMahon, L W; Ramos, N I; Anglin, L M; Walsh, C E; Lambert, M W



Increased UV resistance in xeroderma pigmentosum group A cells after transformation with a human genomic DNA clone  

SciTech Connect

Xeroderma pigmentosum (XP) is an autosomal recessive disease in which the major clinical manifestation is a 2,000-fold enhanced probability of developing sunlight-induced skin tumors, and the molecular basis for the disease is a defective DNA excision repair system. To clone the gene defective XP complementation group A (XP-A), cDNA clones were isolated by a competition hybridization strategy in which the corresponding mRNAs were more abundant in cells of the obligately heterozygous parents relative to cells to the homozygous proband affected with the disease. In this report, a human genomic DNA clone that contains this cDNA was transformed into two independent homozygous XP-A cell lines, and these transformants displayed partial restoration of resistance to the killing effects of UV irradiation. The abundance of mRNA corresponding to this cDNA appears to correlate well with the observed UV cell survival. The results of unscheduled DNA synthesis after UV exposure indicate that the transformed cells are repair proficient relative to that of the control XP-A cells. However, using this same genomic DNA, transformation of an XP-F cell line did not confer any enhancement of UV survival or promote unscheduled DNA synthesis after UV exposure.

Rinaldy, A.; Bellew, T.; Egli, E.; Lloyd, R.S. (Vanderbilt Univ., Nashville, TN (USA))



mtDNA variation in East Africa unravels the history of Afro-Asiatic groups.  


East Africa (EA) has witnessed pivotal steps in the history of human evolution. Due to its high environmental and cultural variability, and to the long-term human presence there, the genetic structure of modern EA populations is one of the most complicated puzzles in human diversity worldwide. Similarly, the widespread Afro-Asiatic (AA) linguistic phylum reaches its highest levels of internal differentiation in EA. To disentangle this complex ethno-linguistic pattern, we studied mtDNA variability in 1,671 individuals (452 of which were newly typed) from 30 EA populations and compared our data with those from 40 populations (2970 individuals) from Central and Northern Africa and the Levant, affiliated to the AA phylum. The genetic structure of the studied populations--explored using spatial Principal Component Analysis and Model-based clustering--turned out to be composed of four clusters, each with different geographic distribution and/or linguistic affiliation, and signaling different population events in the history of the region. One cluster is widespread in Ethiopia, where it is associated with different AA-speaking populations, and shows shared ancestry with Semitic-speaking groups from Yemen and Egypt and AA-Chadic-speaking groups from Central Africa. Two clusters included populations from Southern Ethiopia, Kenya and Tanzania. Despite high and recent gene-flow (Bantu, Nilo-Saharan pastoralists), one of them is associated with a more ancient AA-Cushitic stratum. Most North-African and Levantine populations (AA-Berber, AA-Semitic) were grouped in a fourth and more differentiated cluster. We therefore conclude that EA genetic variability, although heavily influenced by migration processes, conserves traces of more ancient strata. PMID:23283748

Boattini, Alessio; Castrì, Loredana; Sarno, Stefania; Useli, Antonella; Cioffi, Manuela; Sazzini, Marco; Garagnani, Paolo; De Fanti, Sara; Pettener, Davide; Luiselli, Donata



Group-specific primers for DNA-based detection of springtails (Hexapoda: Collembola) within predator gut contents.  


Group-specific, degenerate polymerase chain reaction primers for DNA-based detection of springtails (Hexapoda: Collembola) within predator gut contents have been developed for the first time. Primers were designed from 18S rDNA and amplified fragments of 272 bp and 177 bp from 17 springtail species collected in agricultural habitats. Specificity tests against 41 nontarget species revealed no cross-reactivity. Group-specific polymerase chain reaction is advantageous when working in species-rich habitats and these primers could facilitate studies of trophic links between springtails and generalist arthropod predators worldwide. PMID:21585869

Kuusk, A K; Agustí, N



Reproducibility of mtDNA analysis between laboratories: a report of the European DNA profiling group (EDNAP)  

Microsoft Academic Search

The aim of this collaborative exercise was to determine whether uniformity of mtDNA sequencing results could be achieved among different EDNAP laboratories. Laboratories were asked to sequence mtDNAHV1 region (16024–16365) from three bloodstains, proceeding in accordance with the protocol and strategies currently used in each individual laboratory. Cycle sequencing was used by 11 laboratories and solid phase single stranded sequencing

A. Carracedo; E. D'Aloja; B. Dupuy; A. Jangblad; M. Karjalainen; C. Lambert; W. Parson; H. Pfeiffer; H. Pfitzinger; M. Sabatier; D. Syndercombe Court; C. Vide



Molecular cloning of a mouse DNA repair gene that complements the defect of group-A xeroderma pigmentosum  

SciTech Connect

For isolation of the gene responsible for xeroderma pigmentosum (XP) complementation group A, plasmid pSV2gpt and genomic DNA from a mouse embryo were cotransfected into XP2OSSV cells, a group-A XP cell line. Two primary UV-resistant XP transfectants were isolated from about 1.6 X 10(5) pSV2gpt-transformed XP colonies. pSV2gpt and genomic DNA from the primary transfectants were again cotransfected into XP2OSSV cells and a secondary UV-resistant XP transfectant was obtained by screening about 4.8 X 10(5) pSV2gpt-transformed XP colonies. The secondary transfectant retained fewer mouse repetitive sequences. A mouse gene that complements the defect of XP2OSSV cells was cloned into an EMBL3 vector from the genome of a secondary transfectant. Transfections of the cloned DNA also conferred UV resistance on another group-A XP cell line but not on XP cell lines of group C, D, F, or G. Northern blot analysis of poly(A)+ RNA with a subfragment of cloned mouse DNA repair gene as the probe revealed that an approximately 1.0 kilobase mRNA was transcribed in the donor mouse embryo and secondary transfectant, and approximately 1.0- and approximately 1.3-kilobase mRNAs were transcribed in normal human cells, but none of these mRNAs was detected in three strains of group-A XP cells. These results suggest that the cloned DNA repair gene is specific for group-A XP and may be the mouse homologue of the group-A XP human gene.

Tanaka, K.; Satokata, I.; Ogita, Z.; Uchida, T.; Okada, Y.



Threonine phosphorylation prevents promoter DNA binding of the Group B Streptococcus response regulator CovR  

PubMed Central

Summary All living organisms communicate with the external environment for their survival and existence. In prokaryotes, communication is achieved by two-component systems (TCS) comprising histidine kinases and response regulators. In eukaryotes, signalling is accomplished by serine/threonine and tyrosine kinases. Although TCS and serine/threonine kinases coexist in prokaryotes, direct cross-talk between these families was first described in Group B Streptococcus (GBS).Aserine/threonine kinase (Stk1) and a TCS (CovR/CovS) co-regulate toxin expression in GBS. Typically, promoter binding of regulators like CovR is controlled by phosphorylation of the conserved active site aspartate (D53). In this study, we show that Stk1 phosphorylates CovR at threonine 65. The functional consequence of threonine phosphorylation of CovR in GBS was evaluated using phosphomimetic and silencing substitutions. GBS encoding the phosphomimetic T65E allele are deficient for CovR regulation unlike strains encoding the non-phosphorylated T65A allele. Further, compared with wild-type or T65A CovR, the T65E CovR is unable to bind promoter DNA and is decreased for phosphorylation at D53, similar to Stk1-phosphorylated CovR. Collectively, we provide evidence for a novel mechanism of response regulator control that enables GBS (and possibly other prokaryotes) to fine-tune gene expression for environmental adaptation.

Lin, Wan-Jung; Walthers, Don; Connelly, James E.; Burnside, Kellie; Jewell, Kelsea A.; Kenney, Linda J.; Rajagopal, Lakshmi



Fanconi anemia group J mutation abolishes its DNA repair function by uncoupling DNA translocation from helicase activity or disruption of protein-DNA complexes  

PubMed Central

Fanconi anemia (FA) is a genetic disease characterized by congenital abnormalities, bone marrow failure, and susceptibility to leukemia and other cancers. FANCJ, one of 13 genes linked to FA, encodes a DNA helicase proposed to operate in homologous recombination repair and replicational stress response. The pathogenic FANCJ-A349P amino acid substitution resides immediately adjacent to a highly conserved cysteine of the iron-sulfur domain. Given the genetic linkage of the FANCJ-A349P allele to FA, we investigated the effect of this particular mutation on the biochemical and cellular functions of the FANCJ protein. Purified recombinant FANCJ-A349P protein had reduced iron and was defective in coupling adenosine triphosphate (ATP) hydrolysis and translocase activity to unwinding forked duplex or G-quadruplex DNA substrates or disrupting protein-DNA complexes. The FANCJ-A349P allele failed to rescue cisplatin or telomestatin sensitivity of a FA-J null cell line as detected by cell survival or ?-H2AX foci formation. Furthermore, expression of FANCJ-A349P in a wild-type background exerted a dominant-negative effect, indicating that the mutant protein interferes with normal DNA metabolism. The ability of FANCJ to use the energy from ATP hydrolysis to produce the force required to unwind DNA or destabilize protein bound to DNA is required for its role in DNA repair.

Wu, Yuliang; Sommers, Joshua A.; Suhasini, Avvaru N.; Leonard, Thomas; Deakyne, Julianna S.; Mazin, Alexander V.; Shin-ya, Kazuo; Kitao, Hiroyuki



Pyramidal and Chiral Groupings of Gold Nanocrystals Assembled Using DNA Scaffolds  

SciTech Connect

Nanostructures constructed from metal and semiconductor nanocrystals conjugated to, and organized by DNA are an emerging class of material with collective optical properties. We created discrete pyramids of DNA with gold nanocrystals at the tips. By taking small angle X-ray scattering (SAXS) measurments from solutions of these pyramids we confirmed that this pyramidal geometry creates structures which are more rigid in solution than linear DNA. We then took advantage of the tetrahedral symmetry to demonstrate construction of chiral nanostructures.

Mastroianni, Alexander; Claridge, Shelley; Alivisatos, A. Paul



DNA conformation is determined by economics in the hydration of phosphate groups  

Microsoft Academic Search

Mixed sequence DNA can exist in two right-handed and one left-handed double helical conformations-A, B and Z1-3. Under conditions of high water activity the B conformation prevails. If the water activity is reduced on addition of salt or organic solvents, transformation occurs to A-DNA or, in DNAs with alternating purine-pyrimidine sequences, to the left-handed Z-DNA. In crystal structure analyses of

Wolfram Saenger; William N. Hunter; Olga Kennard



p53 and DNA damage-inducible expression of the xeroderma pigmentosum group C gene  

Microsoft Academic Search

The p53 tumor suppressor gene product is a transcription factor involved in cell-cycle regulation, apoptosis, and DNA repair. We and others have shown that p53 is required for efficient nucleotide excision repair (NER) of UV-induced DNA lesions. p53-deficient cells are defective in the repair of UV photoproducts in genomic DNA but proficient for transcription-coupled repair. Therefore, we examined whether p53

Shanthi Adimoolam; James M. Ford



Transforming Region of Group A, B, and C Adenoviruses: DNA Homology Studies with Twenty-Nine Human Adenovirus Serotypes  

PubMed Central

The 31 human adenovirus (Ad) serotypes form five groups based upon DNA genome homologies: group A (Ad12, 18, 31), group B (Ad3, 7, 11, 14, 16, 21), group C (Ad1, 2, 5, 6), group D (Ad8, 9, 10, 13, 15, 17, 19, 20, 22-30), and group E (Ad4) (M. Green, J. Mackey, W. Wold, and P. Rigden, Virology, in press). Group A Ads are highly oncogenic in newborn hamsters, group B Ads are weakly oncogenic, and other Ads are nononcogenic. However, most or all Ads transform cultured cells. We have studied the homology of Ad5, Ad7, and Ad12 transforming restriction endonuclease DNA fragments with DNAs of 29 Ad types. Ad5 HindIII-G (map position 0-7.3), Ad7 XhoI-C (map position 0-10.8), and Ad12 (strain Huie) EcoRI-C (map position 0-16) and SalI-C (map position 0-10.6) fragments were purified, labeled in vitro (nick translation), and annealed with DNAs of Ad1 to Ad16, Ad18 to Ad24, and Ad26 to Ad31. Hybrids were assayed by using hydroxylapatite. Ad5 HindIII-G hybridized 98 to 100% with DNAs of group C Ads, but only 1 to 15% with DNAs of other types. Ad7 XhoI-C fragment hybridized 85 to 99% with DNAs of group B Ads, but only 6 to 21% with DNAs of other types. Ad12 (Huie) EcoRI-C hybridized 53 to 68% with DNAs of five other Ad12 strains, 53% with Ad18 DNA, 56% with Ad31 DNA, but only 3 to 13% with DNAs of other types. In vitro-labeled Ad12 (Huie) SalI-C hybridized 35 to 71% with DNAs of 6 other Ad12 strains, 44% with Ad18 DNA, 52% with Ad31 DNA, but only 2 to 7% with DNAs Ad7, Ad2, Ad26, or Ad4. When assayed using S-1 nuclease, SalI-C annealed 17 to 44% with DNAs of group A Ads. The melting temperatures of the hybrids of Ad5 HindIII-G with all group C Ad DNAs were 84°C in 0.12 M sodium phosphate (pH 6.8). The melting temperature of the Ad12 (Huie) EcoRI-C hybrid with Ad12 (Huie) DNA was 83°C, but was only 71 to 77°C with DNAs of other group A Ads. Thus, group C and group B Ads both have very homologous transforming regions that are not represented in DNAs of non-group C Ads or non-group B Ads, respectively. Similarily, group A Ads have unique but less homologous transforming regions. These different transforming nucleotide sequences may be reflected in the different oncogenic properties of group A, B, and C Ads. Images

Mackey, Jesse K.; Wold, William S. M.; Rigden, Patricia; Green, Maurice



DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar  

Microsoft Academic Search

The role of DNA barcoding as a tool to accelerate the inventory and analysis of diversity for hyperdiverse arthropods is tested using ants in Madagascar. We demonstrate how DNA barcoding helps address the failure of current inventory methods to rapidly respond to pressing biodiversity needs, specifically in the assessment of richness and turnover across landscapes with hyperdiverse taxa. In a

M. Alex Smith; Brian L. Fisher; Paul D. N. Hebert



Highly selective binding of naphthyridine with a trifluoromethyl group to cytosine opposite an abasic site in DNA duplexes.  


We report on highly selective binding of a naphthyridine derivative with a trifluoromethyl group to cytosine opposite an abasic site in DNA duplexes; the binding-induced fluorescence quenching is applicable to the analysis of a C-related single-base mutation in DNAs amplified by PCR. PMID:22526917

Sato, Yusuke; Zhang, Yushuang; Seino, Takehiro; Sugimoto, Takashi; Nishizawa, Seiichi; Teramae, Norio



Phylogeny of the Mexican coastal leopard frogs of the Rana berlandieri group based on mtDNA sequences  

Microsoft Academic Search

Phylogenetic relationships among specimens from 25 different locations for the six Mexican coastal leopard frog species of the Rana berlandieri species group were investigated using 797bp of the mitochondrial 12S rDNA gene. Relationships among the haplotypes obtained were recovered using maximum parsimony and Bayesian analyses. Most of the clades recovered by both tree building methods are strongly supported, but conflicting

Alejandro Zald??var-Riverón; Virginia León-Regagnon; Adrián Nieto-Montes de Oca



Complementation of the DNA repair defect in xeroderma pigmentosum group G cells by a human cDNA related to yeast RAD2  

Microsoft Academic Search

DEFECTS in human DNA repair proteins can give rise to the autosomal recessive disorders xeroderma pigmentosum (XP) and Cockayne's syndrome (CS), sometimes even together1-3. Seven XP and three CS complementation groups have been identified that are thought to be due to mutations in genes from the nucleotide excision repair pathway2,3. Here we isolate frog and human complementary DNAs that encode

Daniel Scherly; Thierry Nouspikel; Janine Corlet; Catherine Ucla; Amos Bairoch; Stuart G. Clarkson



Evidence for two genetically distinct DNA primase activities specified by plasmids of the B and I incompatibility groups.  

PubMed Central

Plasmid ColIb-P9 of the I alpha incompatibility group is known to encode a DNA primase that acts in the conjugal transfer of the plasmid and can substitute for mutant dnaG gene product in vegetative replication of the Escherichia coli chromosome. The relevant genetic determinant (sog) has previously been cloned into a small multicopy vector plasmid. Prototype IncB plasmid R16 also suppresses host dnaG mutations. The equivalent gene(s) (pri) of R16 was cloned into plasmid pBR325 and shown by filter hybridization studies to be different from the ColI primase gene(s). The cloned fragment carrying the pri determinant encoded an enzyme which could initiate DNA synthesis in vitro on single-stranded phage M13 DNA template, but which was antigenically distinct from ColI primase. We used the cloned primase genes as probes in colony hybridization screening of strains carrying plasmids of the IncI complex and IncB group. Plasmids R64, R144 (I alpha), R621a (I gamma), RIP72, and R864a (B) contained nucleotide sequences homologous with the cloned ColI sog genes. Plasmids R805 (I xi), R724, (I delta), TP125, and PLG101 (B) showed sequence homology with the R16 pri determinant. Images

Dalrymple, B P; Boulnois, G J; Wilkins, B M; Orr, E; Williams, P H



Differentiation and grouping of isolates of the Ganoderma lucidum complex by random amplified polymorphic DNA-PCR compared with grouping on the basis of internal transcribed spacer sequences.  

PubMed Central

Laccate polypores of the Ganoderma lucidum species complex are widespread white rot fungi of economic importance, but isolates cannot be identified by traditional taxonomic methods. Parsimony analysis of nucleotide sequences from the internal transcribed spacers (ITS) of the ribosomal gene (rDNA) distinguished six lineages in this species complex. Each ITS lineage may represent one or more putative species. While some isolates have identical ITS sequences, all of them could be clearly differentiated by genetic fingerprinting using random amplified polymorphic DNA (RAPD). To investigate the suitability of RAPD markers for taxonomic identification and grouping of isolates of the G. lucidum complex, RAPD fragments (RAPDs) were used as phenotypic characters in numerical and parsimony analyses. Results show that data from RAPDS do not distinguish the same clades as ITS data do. Groupings based on analysis of RAPD data were very sensitive to the choice of the grouping method used, and no consistent grouping of isolates could be proposed. However, analysis with RAPDs did resolve several robust terminal clades containing putatively conspecific isolates, suggesting that RAPDs might be helpful for systematics at the lower taxonomic levels that are unresolved by ITS sequence data. The limitations of RAPDs for systematics are briefly discussed. The conclusion of this study is that ITS sequences can be used to identify isolates of the G. lucidum complex, whereas RAPDs can be used to differentiate between isolates having identical ITS sequences. The practical implications of these results are briefly illustrated.

Hseu, R S; Wang, H H; Wang, H F; Moncalvo, J M



Remarkable stabilization of antiparallel DNA triplexes by strong stacking effects of consecutively modified nucleobases containing thiocarbonyl groups.  


The consecutive arrangement of 2'-deoxy-6-thioguanosines (s(6)Gs) and 4-thiothymidines (s(4)Ts) in antiparallel triplex-forming oligonucleotides (TFOs) considerably stabilized the resulting antiparallel triplexes with high base recognition ability by the strong stacking effects of thiocarbonyl groups. This result was remarkable because chemical modifications of the sugar moieties and nucleobases of antiparallel TFOs generally destabilize triplex structures. Moreover, in comparison with unmodified TFOs, it was found that TFOs containing s(6)Gs and s(4)Ts could selectively bind to the complementary DNA duplex but not to mismatched DNA duplexes or single-stranded RNA. PMID:23287737

Yamada, Kenji; Hattori, Yusaku; Inde, Takeshi; Kanamori, Takashi; Ohkubo, Akihiro; Seio, Kohji; Sekine, Mitsuo



Sequence-length variation of mtDNA HVS-I C-stretch in Chinese ethnic groups  

Microsoft Academic Search

The purpose of this study was to investigate mitochondrial DNA (mtDNA) hypervariable segment-I (HVS-I) C-stretch variations\\u000a and explore the significance of these variations in forensic and population genetics studies. The C-stretch sequence variation\\u000a was studied in 919 unrelated individuals from 8 Chinese ethnic groups using both direct and clone sequencing approaches. Thirty\\u000a eight C-stretch haplotypes were identified, and some novel

Feng Chen; Yong-hui Dang; Chun-xia Yan; Yan-ling Liu; Ya-jun Deng; David J. R. Fulton; Teng Chen



Crystal structure of the trithorax group protein ASH2L reveals a forkhead-like DNA binding domain  

SciTech Connect

Absent, small or homeotic discs-like 2 (ASH2L) is a trithorax group (TrxG) protein and a regulatory subunit of the SET1 family of lysine methyltransferases. Here we report that ASH2L binds DNA using a forkhead-like helix-wing-helix (HWH) domain. In vivo, the ASH2L HWH domain is required for binding to the {beta}-globin locus control region, histone H3 Lys4 (H3K4) trimethylation and maximal expression of the {beta}-globin gene (Hbb-1), validating the functional importance of the ASH2L DNA binding domain.

Sarvan, Sabina; Avdic, Vanja; Tremblay, Véronique; Chaturvedi, Chandra-Prakash; Zhang, Pamela; Lanouette, Sylvain; Blais, Alexandre; Brunzelle, Joseph S; Brand, Marjorie; Couture, Jean-François (Ottawa Hosp.); (Ottawa); (NWU)



Crystal structure of the trithorax group protein ASH2L reveals a forkhead-like DNA binding domain.  


Absent, small or homeotic discs-like 2 (ASH2L) is a trithorax group (TrxG) protein and a regulatory subunit of the SET1 family of lysine methyltransferases. Here we report that ASH2L binds DNA using a forkhead-like helix-wing-helix (HWH) domain. In vivo, the ASH2L HWH domain is required for binding to the ?-globin locus control region, histone H3 Lys4 (H3K4) trimethylation and maximal expression of the ?-globin gene (Hbb-1), validating the functional importance of the ASH2L DNA binding domain. PMID:21642971

Sarvan, Sabina; Avdic, Vanja; Tremblay, Véronique; Chaturvedi, Chandra-Prakash; Zhang, Pamela; Lanouette, Sylvain; Blais, Alexandre; Brunzelle, Joseph S; Brand, Marjorie; Couture, Jean-François



Cloning and analysis of the mouse Fanconi anemia group A cDNA and an overlapping penta zinc finger cDNA.  


Despite the cloning of four disease-associated genes for Fanconi anemia (FA), the molecular pathogenesis of FA remains largely unknown. To study FA complementation group A using the mouse as a model system, we cloned and characterized the mouse homolog of the human FANCA cDNA. The mouse cDNA (Fanca) encodes a 161-kDa protein that shares 65% amino acid sequence identity with human FANCA. Fanca is located at the distal region of mouse chromosome 8 and has a ubiquitous pattern of expression in embryonic and adult tissues. Expression of the mouse cDNA in human FA-A cells restores the cellular drug sensitivity to normal levels. Thus, the expression pattern, protein structure, chromosomal location, and function of FANCA are conserved in the mouse. We also isolated a novel zinc finger protein, Zfp276, which has five C(2)H(2) domains. Interestingly, Zfp276 is situated in the Fanca locus, and the 3'UTR of its cDNA overlaps with the last four exons of Fanca in a tail-to-tail manner. Zfp276 is expressed in the same tissues as Fanca, but does not complement the mitomycin C (MMC)-sensitive phenotype of FA-A cells. The overlapping genomic organization between Zfp276 and Fanca may have relevance to the disease phenotype of FA. PMID:10936049

Wong, J C; Alon, N; Norga, K; Kruyt, F A; Youssoufian, H; Buchwald, M



New epistasis group for the repair of DNA damage in bacteriophage T4: replication repair  

SciTech Connect

The gene 32 mutation amA453 sensitizes bacteriophage T4 to the lethal effects of ultraviolet (UV) irradiation, methyl methanesulfonate and angelicin-mediated photodynamic irradiation when treated particles are plated on amber-suppressing host cells. The increased UV sensitivity caused by amA453 is additive to that caused by mutations in both the T4 excision repair (denV) and recombination repair (uvsWXY) systems, suggesting the operation of third kind of repair system. The mutation uvs79, with many similarities to amA453 but mapping in gene 41, is largely epistatic to amA453. The mutation mms1, also with many similarities to amA453, maps close to amA453 within gene 32 and is largely epistatic to uvs79. Neither amA453 nor uvs79 affect the ratio of UV-induced mutational to lethal hits, nor does amA453 affect spontaneous or UV-enhanced recombination frequencies. Gene 32 encode the major T4 ssDNA-binding protein (the scaffolding of the DNA replication) and gene 41 encodes a DNA helicase, both being required for T4 DNA replication. The authors conclude that a third repair process operates in phage T4 and suggest that it acts during rather than before of after DNA replication.

Wachsman, J.T.; Drake, J.W.



Immobilization of DNA via oligonucleotides containing an aldehyde or carboxylic acid group at the 5' terminus.  

PubMed Central

A general method for the immobilization of DNA through its 5'-end has been developed. A synthetic oligonucleotide, modified at its 5'-end with an aldehyde or carboxylic acid, was attached to latex microspheres containing hydrazide residues. Using T4 polynucleotide ligase and an oligonucleotide splint, a single stranded 98mer was efficiently joined to the immobilized synthetic fragment. After impregnation of the latex microspheres with the fluorescent dye, Nile Red and attachment of an aldehyde 16mer, 5 X 10(5) bead-DNA conjugates could be detected with a conventional fluorimeter. Images

Kremsky, J N; Wooters, J L; Dougherty, J P; Meyers, R E; Collins, M; Brown, E L



The DNA polymerase genes of several HMU-bacteriophages have similar group I introns with highly divergent open reading frames.  

PubMed Central

A previous report described the discovery of a group I, self-splicing intron in the DNA polymerase gene of the Bacillus subtilis bacteriophage SPO1 (1). In this study, the DNA polymerase genes of three close relatives of SPO1: SP82, 2C and phi e, were also found to be interrupted by an intron. All of these introns have group I secondary structures that are extremely similar to one another in primary sequence. Each is interrupted by an open reading frame (ORF) that, unlike the intron core or exon sequences, are highly diverged. Unlike the relatives of Escherichia coli bacteriophage T4, most of which do not have introns (2), this intron seems to be common among the relatives of SPO1. Images

Goodrich-Blair, H; Shub, D A



Analysis of body fluid mixtures by mtDNA sequencing: An inter-laboratory study of the GEP-ISFG working group  

Microsoft Academic Search

The mitochondrial DNA (mtDNA) working group of the GEP-ISFG (Spanish and Portuguese Group of the International Society for Forensic Genetics) carried out an inter-laboratory exercise consisting of the analysis of mtDNA sequencing patterns in mixed stains (saliva\\/semen and blood\\/semen). Mixtures were prepared with saliva or blood from a female donor and three different semen dilutions (pure, 1:10 and 1:20) in

M. Montesino; A. Salas; M. Crespillo; C. Albarrán; A. Alonso; V. Álvarez-Iglesias; J. A. Cano; M. Carvalho; D. Corach; C. Cruz; A. Di Lonardo; R. Espinheira; M. J. Farfán; S. Filippini; J. García-Hirschfeld; A. Hernández; G. Lima; C. M. López-Cubría; M. López-Soto; S. Pagano; M. Paredes; M. F. Pinheiro; A. M. Rodríguez-Monge; A. Sala; S. Sóñora; D. R. Sumita; M. C. Vide; M. R. Whittle; A. Zurita; L. Prieto



Suppression of a DNA polymerase ? mutation by the absence of the high mobility group protein Hmo1 in Saccharomyces cerevisiae  

Microsoft Academic Search

The deletion of the gene encoding the high mobility group protein Hmo1 suppresses the growth retardation of the DNA pol ?\\u000a mutation, pol3-14, at the restrictive temperature. pol3-14 mutant cells undergo cell cycle arrest, and hmo1? alleviates the arrest permitting continual division of the double mutant. Bypass of cell cycle control occurs with an increased\\u000a rate of mutation. Both pol3-14

Haeyoung Kim; Dennis M. Livingston



Analysis of a human DNA excision repair gene involved in group A xeroderma pigmentosum and containing a zinc-finger domain  

Microsoft Academic Search

XERODERMA pigmentosum (XP) is an autosomal recessive disease, characterized by a high incidence of sunlight-induced skin cancer. Cells from people with this condition are hypersensitive to ultraviolet because of a defect in DNA repair. There are nine genetic complementation groups of XP, groups A-H and a variant. We have cloned the mouse DNA repair gene that complements the defect of

Kiyoji Tanaka; Naoyuki Miura; Ichiro Satokata; Iwai Miyamoto; Michihiro C. Yoshida; Yoshiaki Satoh; Seiji Kondo; Akira Yasui; Hiroto Okayama; Yoshio Okada



Different patterns of evolution for duplicated DNA repair genes in bacteria of the Xanthomonadales group  

Microsoft Academic Search

BACKGROUND: DNA repair genes encode proteins that protect organisms against genetic damage generated by environmental agents and by-products of cell metabolism. The importance of these genes in life maintenance is supported by their high conservation, and the presence of duplications of such genes may be easily traced, especially in prokaryotic genomes. RESULTS: The genome sequences of two Xanthomonas species were

Marinalva Martins-Pinheiro; Rodrigo S Galhardo; Claudia Lage; Keronninn M Lima-Bessa; Karina A Aires; Carlos FM Menck



Repair of 8-oxoguanine in DNA is deficient in Cockayne syndrome group B cells  

Microsoft Academic Search

The incision of the 8-oxoguanine in DNA by normal and Cockayne Syndrome (CS) cell extracts has been investigated. The incision in extracts derived from CS cells was ~50% of the incision level compared with extracts prepared from normal cells. In contrast, the incision rate of uracil and thymine glycol was not defective in CS cells. The deficiency in 8-oxoguanine incision

Grigory Dianov; Claus Bischoff; Morten Sunesen; Vilhelm A. Bohr




Microsoft Academic Search

In this paper we continue the study ofalg 1 (S) for minimal surfaces of general type S satisfying K2 S < 3?(S). We show that, if K 2 S = 3?(S) 1 and |?alg 1 (S)| = 8, then S is a Campedelli surface. In view of the results of (MP1) and (MP2), this implies that the fundamental group of



Lay perceptions of predictive testing for diabetes based on DNA test results versus family history assessment: a focus group study  

PubMed Central

Background This study assessed lay perceptions of issues related to predictive genetic testing for multifactorial diseases. These perceived issues may differ from the "classic" issues, e.g. autonomy, discrimination, and psychological harm that are considered important in predictive testing for monogenic disorders. In this study, type 2 diabetes was used as an example, and perceptions with regard to predictive testing based on DNA test results and family history assessment were compared. Methods Eight focus group interviews were held with 45 individuals aged 35-70 years with (n = 3) and without (n = 1) a family history of diabetes, mixed groups of these two (n = 2), and diabetes patients (n = 2). All interviews were transcribed and analysed using Atlas-ti. Results Most participants believed in the ability of a predictive test to identify people at risk for diabetes and to motivate preventive behaviour. Different reasons underlying motivation were considered when comparing DNA test results and a family history risk assessment. A perceived drawback of DNA testing was that diabetes was considered not severe enough for this type of risk assessment. In addition, diabetes family history assessment was not considered useful by some participants, since there are also other risk factors involved, not everyone has a diabetes family history or knows their family history, and it might have a negative influence on family relations. Respect for autonomy of individuals was emphasized more with regard to DNA testing than family history assessment. Other issues such as psychological harm, discrimination, and privacy were only briefly mentioned for both tests. Conclusion The results suggest that most participants believe a predictive genetic test could be used in the prevention of multifactorial disorders, such as diabetes, but indicate points to consider before both these tests are applied. These considerations differ with regard to the method of assessment (DNA test or obtaining family history) and also differ from monogenic disorders.



Microinjection of partially purified protein factor restores DNA damage specifically in group A of xeroderma pigmentosum cells  

SciTech Connect

Microinjection of cell extracts prepared from both human placenta and HeLa cells into xeroderma pigmentosum (XP) cells of complementation group A restores unscheduled DNA synthesis (UDS) in these cells after UV irradiation. These cells also showed normal resistance to UV irradiation. The half-life of the factors in the cell extracts corresponding to the UDS activity (factor A) was 14 hr in XP cells of group A, and the maximal level of UDS was exerted 2 hr after microinjection. The factors were sensitive to protease treatment but not to RNase treatment and were found to be approx. = 160 and approx. = 90 kDa by gel filtration. These two fractions of the factor(s) acted specifically in XP cells of complementation group A among complementation groups A, B, C, D, F, G, and probably E and H.

Yamaizumi, M.; Sugano, T.; Asahina, H.; Okada, Y.; Uchida, T.



The effect of amino groups on the stability of DNA duplexes and triplexes based on purines derived from inosine  

PubMed Central

The effect of amino groups attached at positions 2 and 8 of the hypoxanthine moiety in the structure, reactivity and stability of DNA duplexes and triplexes is studied by means of quantum mechanical calculations, as well as extended molecular dynamics (MD) and thermodynamic integration (MD/TI) simulations. Theoretical estimates of the change in stability related to 2?-deoxyguanosine (G) ? 2?-deoxyinosine (I) ? 8-amino-2?-deoxyinosine (8AI) mutations have been experimentally verified, after synthesis of the corresponding compounds. An amino group placed at position 2 stabilizes the duplex, as expected, and surprisingly also the triplex. The presence of an amino group at position 8 of the hypoxanthine moiety stabilizes the triplex but, surprisingly, destabilizes the duplex. The subtle electronic redistribution occurring upon the introduction of an amino group on the purine seems to be responsible for this surprising behavior. Interesting ‘universal base’ properties are found for 8AI.

Cubero, Elena; Guimil-Garcia, Ramon; Luque, F. Javier; Eritja, Ramon; Orozco, Modesto



A Fuzzy Classifier to Taxonomically Group DNA Fragments within a Metagenome  

Microsoft Academic Search

Extracting microorganisms from their natural en- vironment has become a popular technique. These metagenomic fragments lack enough information that can mark them into taxonomic groups. In this paper, we implement a fuzzy k- means classifier to separate fragments into taxonomic groups present in a metagenomic data set. The fuzzy classifier is used to group shotgun sequence fragments as small as

Sara Nasser; Adrienne Breland; Frederick C. Harris Jr; Monica Nicolescu



Multiple group I introns in the small-subunit rDNA of Botryosphaeria dothidea: implication for intraspecific genetic diversity.  


Botryosphaeria dothidea is a widespread and economically important pathogen on various fruit trees, and it often causes die-back and canker on limbs and fruit rot. In characterizing intraspecies genetic variation within this fungus, group I introns, rich in rDNA of fungi, may provide a productive region for exploration. In this research, we analysed complete small subunit (SSU) ribosomal DNA (rDNA) sequences of 37 B. dothidea strains, and found four insertions, designated Bdo.S943, Bdo.S1199-A, Bdo.S1199-B and Bdo.S1506, at three positions. Sequence analysis and structure prediction revealed that both Bdo.S943 and Bdo.S1506 belonged to subgroup IC1 of group I introns, whereas Bdo.S1199-A and Bdo.S1199-B corresponded to group IE introns. Moreover, Bdo.S1199-A was found to host an open reading frame (ORF) for encoding the homing endonuclease (HE), whereas Bdo.S1199-B, an evolutionary descendant of Bdo.S1199-A, included a degenerate HE. The above four introns were novel, and were the first group I introns observed and characterized in this species. Differential distribution of these introns revealed that all strains could be separated into four genotypes. Genotype III (no intron) and genotype IV (Bdo.S1199-B) were each found in only one strain, whereas genotype I (Bdo.S1199-A) and genotype II (Bdo.S943 and Bdo.S1506) occurred in 95% of the strains. There is a correlation between B. dothidea genotypes and hosts or geographic locations. Thus, these newly discovered group I introns can help to advance understanding of genetic differentiation within B. dothidea. PMID:23844098

Xu, Chao; Wang, Chunsheng; Sun, Xinyao; Zhang, Rong; Gleason, Mark L; Eiji, Tanaka; Sun, Guangyu



DNA barcoding reveals both known and novel taxa in the Albitarsis Group (Anopheles: Nyssorhynchus) of Neotropical malaria vectors  

PubMed Central

Background Mosquitoes belonging to the Albitarsis Group (Anopheles: Nyssorhynchus) are of importance as malaria vectors across the Neotropics. The Group currently comprises six known species, and recent studies have indicated further hidden biodiversity within the Group. DNA barcoding has been proposed as a highly useful tool for species recognition, although its discriminatory utility has not been verified in closely related taxa across a wide geographic distribution. Methods DNA barcodes (658 bp of the mtDNA Cytochrome c Oxidase - COI) were generated for 565 An. albitarsis s.l. collected in Argentina, Brazil, Colombia, Paraguay, Trinidad and Venezuela over the past twenty years, including specimens from type series and type localities. Here we test the utility of currently advocated barcoding methodologies, including the Kimura-two-parameter distance model (K2P) and Neighbor-joining analysis (NJ), for determining species delineation within mosquitoes of the Neotropical Albitarsis Group of malaria vectors (Anopheles: Nyssorhynchus), and compare results with Bayesian analysis. Results Species delineation through barcoding analysis and Bayesian phylogenetic analysis, fully concur. Analysis of 565 sequences (302 unique haplotypes) resolved nine NJ tree clusters, with less than 2% intra-node variation. Mean intra-specific variation (K2P) was 0.009 (range 0.002 - 0.014), whereas mean inter-specific divergence were several-fold higher at 0.041 (0.020 - 0.056), supporting the reported "barcoding gap". These results show full support for separate species status of the six known species in the Albitarsis Group (An. albitarsis s.s., An. albitarsis F, An. deaneorum, An. janconnae, An. marajoara and An. oryzalimnetes), and also support species level status for two previously detected lineages - An. albitarsis G &An. albitarsis I (designated herein). In addition, we highlight the presence of a unique mitochondrial lineage close to An. deaneorum and An. marajoara (An. albitarsis H) from Rondônia and Mato Grosso in southwestern Brazil. Further integrated studies are required to confirm the status of this lineage. Conclusions DNA barcoding provides a reliable means of identifying both known and undiscovered biodiversity within the closely related taxa of the Albitarsis Group. We advocate its usage in future studies to elucidate the vector competence and respective distributions of all eight species in the Albitarsis Group and the novel mitochondrial lineage (An. albitarsis H) recovered in this study.



Complex interactions of the Eastern and Western Slavic populations with other European groups as revealed by mitochondrial DNA analysis.  


Mitochondrial DNA sequence variation was examined by the control region sequencing (HVS I and HVS II) and RFLP analysis of haplogroup-diagnostic coding region sites in 570 individuals from four regional populations of Poles and two Russian groups from northwestern part of the country. Additionally, sequences of complete mitochondrial genomes representing K1a1b1a subclade in Polish and Polish Roma populations have been determined. Haplogroup frequency patterns revealed in Poles and Russians are similar to those characteristic of other Europeans. However, there are several features of Slavic mtDNA pools seen on the level of regional populations which are helpful in the understanding of complex interactions of the Eastern and Western Slavic populations with other European groups. One of the most important is the presence of subhaplogroups U5b1b1, D5, Z1 and U8a with simultaneous scarcity of haplogroup K in populations of northwestern Russia suggesting the participation of Finno-Ugrian tribes in the formation of mtDNA pools of Russians from this region. The results of genetic structure analyses suggest that Russians from Velikii Novgorod area (northwestern Russia) and Poles from Suwalszczyzna (northeastern Poland) differ from all remaining Polish and Russian samples. Simultaneously, northwestern Russians and northeastern Poles bear some similarities to Baltic (Latvians) and Finno-Ugrian groups (Estonians) of northeastern Europe, especially on the level of U5 haplogroup frequencies. The occurrence of K1a1b1a subcluster in Poles and Polish Roma is one of the first direct proofs of the presence of Ashkenazi-specific mtDNA lineages in non-Jewish European populations. PMID:19083745

Grzybowski, Tomasz; Malyarchuk, Boris A; Derenko, Miroslava V; Perkova, Maria A; Bednarek, Jaros?aw; Wo?niak, Marcin



A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses  

PubMed Central

Background Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis. Results Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence and circular configuration of the complete virus genome was confirmed by inverse PCR amplification from native DNA extracted from lake sediment. The virus genome appears to be the result of a RNA-DNA recombination event between two ostensibly unrelated virus groups. Environmental sequence databases were examined for homologous genes arranged in similar configurations and three similar putative virus genomes from marine environments were identified. This result indicates the existence of a widespread but previously undetected group of viruses. Conclusions This unique viral genome carries implications for theories of virus emergence and evolution, as no mechanism for interviral RNA-DNA recombination has yet been identified, and only scant evidence exists that genetic exchange occurs between such distinct virus lineages. Reviewers This article was reviewed by EK, MK (nominated by PF) and AM. For the full reviews, please go to the Reviewers' comments section.



A polycomb group protein, PHF1, is involved in the response to DNA double-strand breaks in human cell  

PubMed Central

DNA double-strand breaks (DSBs) represent the most toxic DNA damage arisen from endogenous and exogenous genotoxic stresses and are known to be repaired by either homologous recombination or nonhomologous end-joining processes. Although many proteins have been identified to participate in either of the processes, the whole processes still remain elusive. Polycomb group (PcG) proteins are epigenetic chromatin modifiers involved in gene silencing, cancer development and the maintenance of embryonic and adult stem cells. By screening proteins responding to DNA damage using laser micro-irradiation, we found that PHF1, a human homolog of Drosophila polycomb-like, Pcl, protein, was recruited to DSBs immediately after irradiation and dissociated within 10 min. The accumulation at DSBs is Ku70/Ku80-dependent, and knockdown of PHF1 leads to X-ray sensitivity and increases the frequency of homologous recombination in HeLa cell. We found that PHF1 interacts physically with Ku70/Ku80, suggesting that PHF1 promotes nonhomologous end-joining processes. Furthermore, we found that PHF1 interacts with a number of proteins involved in DNA damage responses, RAD50, SMC1, DHX9 and p53, further suggesting that PHF1, besides the function in PcG, is involved in genome maintenance processes.

Hong, Zehui; Jiang, Jie; Lan, Li; Nakajima, Satoshi; Kanno, Shin-ichiro; Koseki, Haruhiko; Yasui, Akira



Promising genomic transfectant into Xeroderma pigmentosum group A with highly amplified mouse DNA and intermediate UV resistance turns revertant  

SciTech Connect

Following transfection of genomic mouse DNA into an SV40 transformed fibroblast cell line from a patient with Xeroderma pigmentosum (complementation group A, XPA), a single UV resistant cell clone was isolated out of a total of 10(4) independent transfectants. The recipient XPA cell line has as yet not produced spontaneous revertants among 2.2 x 10(8) cells. The isolated cell clone contains 50-70 kb of mouse sequences which are heavily amplified (500-fold), and has acquired both intermediate resistance to UV killing and intermediate unscheduled DNA synthesis (UDS) capacity. By continued passage without selective pressure, cells were generated, which had lost both the dominant marker gene and repetitive mouse sequences. Single colonies of these cells were still intermediately resistant to UV suggesting that either undetected unique mouse DNA had segregated from the bulk of repetitive DNA, or, more likely, that the initially isolated transfectant was a spontaneous revertant. This documents that a persuasive clone isolated can still be a false positive (spontaneous revertant) and that an extremely laborious approach may lead into a dead end.

Blum, M.; Baumann, I.; Lohrer, H.; Rahmsdorf, H.J.; Herrlich, P.



Molecular Renormalization Group Coarse-Graining of Polymer Chains: Application to Double-Stranded DNA  

Microsoft Academic Search

Coarse-graining of atomistic force fields allows us to investigate complex biological problems, occurring at long timescales and large length scales. In this work, we have developed an accurate coarse-grained model for double-stranded DNA chain, derived systematically from atomistic simulations. Our approach is based on matching correlators obtained from atomistic and coarse-grained simulations, for observables that explicitly enter the coarse-grained Hamiltonian.

Alexey Savelyev; Garegin A. Papoian



Preparation of carboxyl group-modified palladium nanoparticles in an aqueous solution and their conjugation with DNA  

NASA Astrophysics Data System (ADS)

The use of nanomaterials in biomolecular labeling and their corresponding detection has been attracting much attention, recently. There are currently very few studies on palladium nanoparticles (Pd NPs) due to their lack of appropriate surface functionalities for conjugation with DNA. In this paper, we thus firstly present an approach to prepare carboxyl group-modified Pd NPs (with an average size of 6 nm) by the use of 11-mercaptoundecanoic acid (MUDA) as a stabilizer in the aqueous solution. The effect of the various reducing reaction conditions on the morphology of the Pd NPs was investigated. The particles were further characterized by TEM, UV-vis, FT-IR and XPS techniques. DNA was finally covalently conjugated to the surface of the Pd NPs through the activation of the carboxyl group, which was confirmed by agarose gel electrophoresis and fluorescence analysis. The resulting Pd NPs-DNA conjugates show high single base pair mismatch discrimination capabilities. This work therefore sets a good foundation for further applications of Pd NPs in bio-analytical research.

Wang, Zhifei; Li, Hongying; Zhen, Shuang; He, Nongyue



Three Group-I introns in 18S rDNA of Endosymbiotic Algae of Paramecium bursaria from Japan  

NASA Astrophysics Data System (ADS)

In the nuclear encoded small subunit ribosomal DNA (18S rDNA) of symbiotic alga of Paramecium bursaria (F36 collected in Japan) possesses three intron-like insertions (Hoshina et al., unpubl. data, 2003). The present study confirmed these exact lengths and insertion sites by reverse transcription-PCR. Two of them were inserted at Escherichia coli 16S rRNA genic position 943 and 1512 that are frequent intron insertion positions, but another insertion position (nearly 1370) was the first finding. Their secondary structures suggested they belong to Group-I intron; one belongs to subgroup IE, others belong to subgroup IC1. Similarity search indicated these introns are ancestral ones.

Hoshina, Ryo; Kamako, Shin-Ichiro; Imamura, Nobutaka



Results of a collaborative study of the EDNAP group regarding mitochondrial DNA heteroplasmy and segregation in hair shafts.  


A collaborative exercise was carried out by the European DNA Profiling Group (EDNAP) in order to evaluate the distribution of mitochondrial DNA (mtDNA) heteroplasmy amongst the hairs of an individual who displays point heteroplasmy in blood and buccal cells. A second aim of the exercise was to study reproducibility of mtDNA sequencing of hairs between laboratories using differing chemistries, further to the first mtDNA reproducibility study carried out by the EDNAP group. Laboratories were asked to type 2 sections from each of 10 hairs, such that each hair was typed by at least two laboratories. Ten laboratories participated in the study, and a total of 55 hairs were typed. The results showed that the C/T point heteroplasmy observed in blood and buccal cells at position 16234 segregated differentially between hairs, such that some hairs showed only C, others only T and the remainder, C/T heteroplasmy at varying ratios. Additionally, differential segregation of heteroplasmic variants was confirmed in independent extracts at positions 16093 and the poly(C) tract at 302-309, whilst a complete A-G transition was confirmed at position 16129 in one hair. Heteroplasmy was observed at position 16195 on both strands of a single extract from one hair segment, but was not observed in the extracts from any other segment of the same hair. Similarly, heteroplasmy at position 16304 was observed on both strands of a single extract from one hair. Additional variants at positions 73, 249 and the HVII poly(C) region were reported by one laboratory; as these were not confirmed in independent extracts, the possibility of contamination cannot be excluded. Additionally, the electrophoresis and detection equipment used by this laboratory was different to those of the other laboratories, and the discrepancies at position 249 and the HVII poly(C) region appear to be due to reading errors that may be associated with this technology. The results, and their implications for forensic mtDNA typing, are discussed in the light of the biology of hair formation. PMID:15013160

Tully, G; Barritt, S M; Bender, K; Brignon, E; Capelli, C; Dimo-Simonin, N; Eichmann, C; Ernst, C M; Lambert, C; Lareu, M V; Ludes, B; Mevag, B; Parson, W; Pfeiffer, H; Salas, A; Schneider, P M; Staalstrom, E



Rapid plant identification using species- and group-specific primers targeting chloroplast DNA.  


Plant identification is challenging when no morphologically assignable parts are available. There is a lack of broadly applicable methods for identifying plants in this situation, for example when roots grow in mixture and for decayed or semi-digested plant material. These difficulties have also impeded the progress made in ecological disciplines such as soil- and trophic ecology. Here, a PCR-based approach is presented which allows identifying a variety of plant taxa commonly occurring in Central European agricultural land. Based on the trnT-F cpDNA region, PCR assays were developed to identify two plant families (Poaceae and Apiaceae), the genera Trifolium and Plantago, and nine plant species: Achillea millefolium, Fagopyrum esculentum, Lolium perenne, Lupinus angustifolius, Phaseolus coccineus, Sinapis alba, Taraxacum officinale, Triticum aestivum, and Zea mays. These assays allowed identification of plants based on size-specific amplicons ranging from 116 bp to 381 bp. Their specificity and sensitivity was consistently high, enabling the detection of small amounts of plant DNA, for example, in decaying plant material and in the intestine or faeces of herbivores. To increase the efficacy of identifying plant species from large number of samples, specific primers were combined in multiplex PCRs, allowing screening for multiple species within a single reaction. The molecular assays outlined here will be applicable manifold, such as for root- and leaf litter identification, botanical trace evidence, and the analysis of herbivory. PMID:22253728

Wallinger, Corinna; Juen, Anita; Staudacher, Karin; Schallhart, Nikolaus; Mitterrutzner, Evi; Steiner, Eva-Maria; Thalinger, Bettina; Traugott, Michael



Rapid Plant Identification Using Species- and Group-Specific Primers Targeting Chloroplast DNA  

PubMed Central

Plant identification is challenging when no morphologically assignable parts are available. There is a lack of broadly applicable methods for identifying plants in this situation, for example when roots grow in mixture and for decayed or semi-digested plant material. These difficulties have also impeded the progress made in ecological disciplines such as soil- and trophic ecology. Here, a PCR-based approach is presented which allows identifying a variety of plant taxa commonly occurring in Central European agricultural land. Based on the trnT-F cpDNA region, PCR assays were developed to identify two plant families (Poaceae and Apiaceae), the genera Trifolium and Plantago, and nine plant species: Achillea millefolium, Fagopyrum esculentum, Lolium perenne, Lupinus angustifolius, Phaseolus coccineus, Sinapis alba, Taraxacum officinale, Triticum aestivum, and Zea mays. These assays allowed identification of plants based on size-specific amplicons ranging from 116 bp to 381 bp. Their specificity and sensitivity was consistently high, enabling the detection of small amounts of plant DNA, for example, in decaying plant material and in the intestine or faeces of herbivores. To increase the efficacy of identifying plant species from large number of samples, specific primers were combined in multiplex PCRs, allowing screening for multiple species within a single reaction. The molecular assays outlined here will be applicable manifold, such as for root- and leaf litter identification, botanical trace evidence, and the analysis of herbivory.

Staudacher, Karin; Schallhart, Nikolaus; Mitterrutzner, Evi; Steiner, Eva-Maria; Thalinger, Bettina; Traugott, Michael



Fanconi anemia group J helicase and MRE11 nuclease interact to facilitate the DNA damage response.  


FANCJ mutations are linked to Fanconi anemia (FA) and increase breast cancer risk. FANCJ encodes a DNA helicase implicated in homologous recombination (HR) repair of double-strand breaks (DSBs) and interstrand cross-links (ICLs), but its mechanism of action is not well understood. Here we show with live-cell imaging that FANCJ recruitment to laser-induced DSBs but not psoralen-induced ICLs is dependent on nuclease-active MRE11. FANCJ interacts directly with MRE11 and inhibits its exonuclease activity in a specific manner, suggesting that FANCJ regulates the MRE11 nuclease to facilitate DSB processing and appropriate end resection. Cells deficient in FANCJ and MRE11 show increased ionizing radiation (IR) resistance, reduced numbers of ?H2AX and RAD51 foci, and elevated numbers of DNA-dependent protein kinase catalytic subunit foci, suggesting that HR is compromised and the nonhomologous end-joining (NHEJ) pathway is elicited to help cells cope with IR-induced strand breaks. Interplay between FANCJ and MRE11 ensures a normal response to IR-induced DSBs, whereas FANCJ involvement in ICL repair is regulated by MLH1 and the FA pathway. Our findings are discussed in light of the current model for HR repair. PMID:23530059

Suhasini, Avvaru N; Sommers, Joshua A; Muniandy, Parameswary A; Coulombe, Yan; Cantor, Sharon B; Masson, Jean-Yves; Seidman, Michael M; Brosh, Robert M



Detection and differentiation of grapevine yellows phytoplasmas belonging to the elm yellows group and to the stolbur subgroup by PCR amplification of non-ribosomal DNA  

Microsoft Academic Search

Primer pairs were designed from a cloned DNA probe of a strain of flavescence dorée (FD) phytoplasma and from a cloned DNA probe of a strain of stolbur phytoplasma. Among an array of reference phytoplasma strains maintained in periwinkle, pair FD9f\\/r amplified a 1.3 kb DNA fragment only with phytoplasma strains of elm yellows (EY) group, i.e. two strains of

X. Daire; D. Clair; W. Reinert; E. Boudon-Padieu



Complementation of DNA repair defect in xeroderma pigmentosum cells of group C by the transfer of human chromosome 5  

SciTech Connect

Complementation of DNA excision repair defect in xeroderma pigmentosum cells of group C (XP-C) has been achieved by the transfer of human chromosome 5. Individual human chromosomes tagged with a selectable marker were transferred to XP-C cells by microcell fusion from mouse-human hybrid cell lines each bearing a single different human chromosome. Analysis of the chromosome transfer clones revealed that introduction of chromosome 5 into XP-C cells corrected the DNA repair defect as well as UV-sensitive phenotypes, while chromosomes 2, 6, 7, 9, 13, 15, 17, and 21 failed to complement. The introduced chromosome 5 in complemented UV[sup r] clones was distinguished from the parental XP-C chromosomes by polymorphism for dinucleotide (CA)[sub n] repeats at two loci, D5S117 and D5S209. In addition, an intact marked chromosome 5 was rescued into mouse cells from a complemented UV[sup r] clone by microcell fusion. Five subclones of a complemented clone that had lost the marked chromosome 5 exhibited UV-sensitive and repair-deficient phenotypes identical to parental XP-C cells. Concordant loss of the transferred chromosome and reappearance of XP-C phenotype further confirmed the presence of a DNA repair gene on human chromosome 5. 38 refs., 7 figs., 1 tab.

Kaur, G.P.; Athwal, R.S. (New Jersey Medical School, Newark (United States))



Molecular phylogeny of Australian Helicarionidae, Euconulidae and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA.  


The delineation and phylogenetic relationships of the pulmonate family Helicarionidae are currently poorly understood. We have undertaken a phylogenetic analysis of Australian members of Helicarionidae. Three consecutive mitochondrial genes (COI, tRNA-val and 16S rRNA) were sequenced for 36 species from Helicarionidae and related groups. Helicarionidae grouped with Ariophantidae and Urocyclidae with good support in all trees, as did Microcystinae with Trochomorphidae, corresponding to the results of a previous morphological study, but the relationships of Euconulinae and Limacidae could not be resolved. Cystopeltidae never grouped with Helicarionidae and should be regarded as a separate family. The position of tRNA-val in the mitochondrial genome provided a new synapomorphy for Microcystinae. In addition, the COI and 16S rRNA sequences showed a high degree of compositional heterogeneity and incompatibility of phylogenetic signals, highlighting the importance of testing for the decay of the historical signal prior to the phylogenetic analysis. PMID:17951078

Hyman, Isabel T; Ho, Simon Y W; Jermiin, Lars S




ERIC Educational Resources Information Center

|This history for molecular genetics and its explanation of DNA begins with an analysis of the Golden Jubilee essay papers, 1955. The paper ends stating that the higher nervous system is the one major frontier of biological inquiry which still offers some romance of research. (Author/VW)|

Stent, Gunther S.



Group I introns in small subunit ribosomal DNA of several Phaeosphaeria species  

Technology Transfer Automated Retrieval System (TEKTRAN)

In a study of small subunit ribosomal RNA (SSU-rRNA) gene sequences in Phaeosphaeria species, group I introns were found in 9 of 10 P. avenaria f.sp. avenaria (Paa) isolates, 1 of 2 Phaeosphaeria sp. (P-rye) isolates from Polish rye (Sn48-1), 1 Phaeosphaeria sp. from dallis grass (P-dg) (S-93-48) an...


DNA polymerase gene sequences indicate western and forest tent caterpillar viruses form a new taxonomic group within baculoviruses.  


Baculoviruses infect larval lepidopterans, and thus have potential value as microbial controls of agricultural and forest pests. Understanding their genetic relatedness and host specificity is relevant to the risk assessment of viral insecticides if non-target impacts are to be avoided. DNA polymerase gene sequences have been demonstrated to be useful for inferring genetic relatedness among dsDNA viruses. We have adopted this approach to examine the relatedness among natural isolates of two uncharacterized caterpillar-infecting baculoviruses, Malacosoma californicum pluviale nucleopolyhedrovirus (McplMNPV) and Malacosoma disstria nucleopolyhedrovirus (MadiMNPV), which infect two closely related host species with little to no cross-infectivity. We designed two degenerate primers (BVP1 and BVP2) based on protein motifs conserved among baculoviruses. McplMNPV and MadiMNPV viral DNA was obtained from naturally infected caterpillars collected from geographically distinct sites in the Southern Gulf Islands and Prince George regions of British Columbia, Canada. Sequencing of 0.9 kb PCR amplicons from six McplMNPV and six MadiMNPV isolates obtained from a total of eight sites, revealed very low nucleotide variation among McplMNPV isolates (99.2-100% nucleotide identity) and among MadiMNPV isolates (98.9-100% nucleotide identity). Greater nucleotide variation was observed between viral isolates from the two different caterpillar species (only 84.7-86.1% nucleotide identity). Both maximum parsimony and maximum likelihood phylogenetic analyses support placement of McplMNPV and MadiMNPV in a clade that is distinct from other groups of baculoviruses. PMID:12507483

Nielsen, Cydney B; Cooper, Dawn; Short, Steven M; Myers, Judith H; Suttle, Curtis A



Organization of the BcgI restriction-modification protein for the transfer of one methyl group to DNA  

PubMed Central

The Type IIB restriction–modification protein BcgI contains A and B subunits in a 2:1 ratio: A has the active sites for both endonuclease and methyltransferase functions while B recognizes the DNA. Like almost all Type IIB systems, BcgI needs two unmethylated sites for nuclease activity; it cuts both sites upstream and downstream of the recognition sequence, hydrolyzing eight phosphodiester bonds in a single synaptic complex. This complex may incorporate four A2B protomers to give the eight catalytic centres (one per A subunit) needed to cut all eight bonds. The BcgI recognition sequence contains one adenine in each strand that can be N6-methylated. Although most DNA methyltransferases operate at both unmethylated and hemi-methylated sites, BcgI methyltransferase is only effective at hemi-methylated sites, where the nuclease component is inactive. Unlike the nuclease, the methyltransferase acts at solitary sites, functioning catalytically rather than stoichiometrically. Though it transfers one methyl group at a time, presumably through a single A subunit, BcgI methyltransferase can be activated by adding extra A subunits, either individually or as part of A2B protomers, which indicates that it requires an assembly containing at least two A2B units.

Smith, Rachel M.; Jacklin, Alistair J.; Marshall, Jacqueline J. T.; Sobott, Frank; Halford, Stephen E.



Multiscale modeling of double-helical DNA and RNA: a unification through Lie groups.  


Several different mechanical models of double-helical nucleic-acid structures that have been presented in the literature are reviewed here together with a new analysis method that provides a reconciliation between these disparate models. In all cases, terminology and basic results from the theory of Lie groups are used to describe rigid-body motions in a coordinate-free way, and when necessary, coordinates are introduced in a way in which simple equations result. We consider double-helical DNAs and RNAs which, in their unstressed referential state, have backbones that are either straight, slightly precurved, or bent by the action of a protein or other bound molecule. At the coarsest level, we consider worm-like chains with anisotropic bending stiffness. Then, we show how bi-rod models converge to this for sufficiently long filament lengths. At a finer level, we examine elastic networks of rigid bases and show how these relate to the coarser models. Finally, we show how results from molecular dynamics simulation at full atomic resolution (which is the finest scale considered here) and AFM experimental measurements (which is at the coarsest scale) relate to these models. PMID:22676719

Wolfe, Kevin C; Hastings, Whitney A; Dutta, Samrat; Long, Andrew; Shapiro, Bruce A; Woolf, Thomas B; Guthold, Martin; Chirikjian, Gregory S



The application of multiplex PCR to detect seven different DNA targets in group B streptococci.  


Group B Streptococcus (GBS) causes severe infections in infants and in immunocompromised adults. GBS pathogenicity varies between and within serotypes, with considerable variation in genetic content between strains. For this reason, it is important to be able to carry out immediate and comprehensive diagnostics of these infections. Seven genes important for screening of GBS infection were detected: cfb gene encoding the CAMP factor presented in every GBS; the cps operon genes such as cps1aH, cps1a/2/3IJ, and cps5O specific for capsular polysaccharide types Ia, III, and V, respectively; macrolide resistance genes ermB and mefA/E; and the gbs2018 S10 region specific for ST17 hypervirulent clone. Standardization of multiplex PCR with the use of seven primer pairs was performed on 81 bacterial strains representing different GBS isolates (n = 75) and other Gram-positive cocci (n = 10). Multiplex PCR can be used as an effective screening method to detect different sequences important for the screening of GBS infection. PMID:22407941

Gosiewski, Tomasz; Brzychczy-W?och, Monika; Heczko, Piotr B



Mitochondrial DNA diversity in two ethnic groups in southeastern Kenya: perspectives from the northeastern periphery of the Bantu expansion.  


The Bantu languages are widely distributed throughout sub-Saharan Africa. Genetic research supports linguists and historians who argue that migration played an important role in the spread of this language family, but the genetic data also indicates a more complex process involving substantial gene flow with resident populations. In order to understand the Bantu expansion process in east Africa, mtDNA hypervariable region I variation in 352 individuals from the Taita and Mijikenda ethnic groups was analyzed, and we evaluated the interactions that took place between the Bantu- and non-Bantu-speaking populations in east Africa. The Taita and Mijikenda are Bantu-speaking agropastoralists from southeastern Kenya, at least some of whose ancestors probably migrated into the area as part of Bantu migrations that began around 3,000 BCE. Our analyses indicate that they show some distinctive differences that reflect their unique cultural histories. The Taita are genetically more diverse than the Mijikenda with larger estimates of genetic diversity. The Taita cluster with other east African groups, having high frequencies of haplogroups from that region, while the Mijikenda have high frequencies of central African haplogroups and cluster more closely with central African Bantu-speaking groups. The non-Bantu speakers who lived in southeastern Kenya before Bantu speaking groups arrived were at least partially incorporated into what are now Bantu-speaking Taita groups. In contrast, gene flow from non-Bantu speakers into the Mijikenda was more limited. These results suggest a more complex demographic history where the nature of Bantu and non-Bantu interactions varied throughout the area. PMID:23382080

Batai, Ken; Babrowski, Kara B; Arroyo, Juan Pablo; Kusimba, Chapurukha M; Williams, Sloan R



A Gynecologic Oncology Group Study of Platinum-DNA Adducts and Excision Repair Cross-Complementation Group 1 Expression in Optimal, Stage III Epithelial Ovarian Cancer Treated with Platinum-Taxane Chemotherapy  

Microsoft Academic Search

To determine whether platinum-DNA adducts and\\/or mRNA expression of the excision nuclease excision repair cross- complementation group 1 (ERCC1) from peripheral blood leukocytes (PBL) were associated with clinical outcome in women with epithelial ovarian cancer (EOC), participants that had previously untreated, optimally resected, stage III EOC were randomized to paclitaxel plus cisplatin or carboplatin. DNA and RNA were extracted from

Kathleen M. Darcy; Chunqiao Tian; Eddie Reed


Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region.  


The Philippines is a strategic point in the Asia-Pacific region for the study of human diversity, history and origins, as it is a cross-road for human migrations and consequently exhibits enormous ethnolinguistic diversity. Following on a previous in-depth study of Y-chromosome variation, here we provide new insights into the maternal genetic history of Filipino ethnolinguistic groups by surveying complete mitochondrial DNA (mtDNA) genomes from a total of 14 groups (11 groups in this study and 3 groups previously published) including previously published mtDNA hypervariable segment (HVS) data from Filipino regional center groups. Comparison of HVS data indicate genetic differences between ethnolinguistic and regional center groups. The complete mtDNA genomes of 14 ethnolinguistic groups reveal genetic aspects consistent with the Y-chromosome, namely: diversity and heterogeneity of groups, no support for a simple dichotomy between Negrito and non-Negrito groups, and different genetic affinities with Asia-Pacific groups that are both ancient and recent. Although some mtDNA haplogroups can be associated with the Austronesian expansion, there are others that associate with South Asia, Near Oceania and Australia that are consistent with a southern migration route for ethnolinguistic group ancestors into the Asia-Pacific, with a timeline that overlaps with the initial colonization of the Asia-Pacific region, the initial colonization of the Philippines and a possible separate post-colonization migration into the Philippine archipelago.European Journal of Human Genetics advance online publication, 12 June 2013; doi:10.1038/ejhg.2013.122. PMID:23756438

Delfin, Frederick; Min-Shan Ko, Albert; Li, Mingkun; Gunnarsdóttir, Ellen D; Tabbada, Kristina A; Salvador, Jazelyn M; Calacal, Gayvelline C; Sagum, Minerva S; Datar, Francisco A; Padilla, Sabino G; De Ungria, Maria Corazon A; Stoneking, Mark



MtDNA phylogeny and biogeography of Copelatinae, a highly diverse group of tropical diving beetles (Dytiscidae).  


Copelatinae is a diverse lineage of diving beetles (Dytiscidae) frequently encountered in wet tropical and subtropical forests, but phylogenetic relationships are very poorly understood. We performed a phylogenetic and biogeographic analysis of this worldwide distributed group based on 50 species including a representative sample of major taxonomic groups and biogeographical regions. DNA sequences were obtained for the mitochondrial genes cytochrome oxidase I, cytochrome b, and 16S rRNA, for a total of 1575 aligned nucleotide positions. We found Copelatinae to be monophyletic, placed in a derived position and not sister to all remaining dytiscids, as had been suggested by earlier authors. The largest genus, Copelatus with some 460 known species was paraphyletic with respect to the smaller genera Lacconectus and Aglymbus. Among the major lineages of Copelatus, the subgenus Papuadytes was consistently recovered as sister to all other species (including Lacconectus and Aglymbus) with the possible exception of two western Palearctic taxa. We propose that the subgenus Papuadytes is removed from Copelatus and assigned generic status. Likewise, the two western Palearctic Copelatus are removed from this genus, and assigned the available genus name Liopterus. Our best phylogenetic hypothesis retrieved Afrotropical and New Guinean plus Australian species of Copelatus as monophyletic. Asian species were paraphyletic with respect to a species from Sulawesi which grouped with the species from New Guinea. Asian species were also paraphyletic with respect to Oriental Lacconectus, which was grouped with a clade of Neotropical species. Neotropical Copelatus form at least two separate lineages. The biogeographical evolution of Papuadytes is consistent with the relative age of the landmasses in the Austral region. Basal species are Australian, and successively derived ones are from New Caledonia and New Guinea. One species apparently dispersed from New Caledonia to China. Assuming a molecular clock and using a standard calibration of 2% divergence/MY the origin of Copelatinae is estimated to be between 85 and 95 MY. PMID:15288062

Balke, Michael; Ribera, Ignacio; Vogler, Alfried P



Sensitive non-radioactive dot-blot hybridization using DNA probes labelled with chelate group substituted psoralen and quantitative detection by europium ion fluorescence.  

PubMed Central

A new labelling method for cloned DNA probes used in hybridization assays is described. The DNA insert of recombinant plasmid DNA was made partially single-stranded for the labelling reaction by a restriction enzyme digest, followed by a controlled exonuclease III incubation. A thiol-containing psoralen derivative was covalently bound through irradiation with UV-light to the remaining double-stranded region of the plasmid DNA. The psoralen-SH groups were labelled with a large number of metal chelators (diethylentriamine pentaacetic acid, DTPA) using poly-L-lysine as a macromolecular carrier. The main advantage of the labelling procedure is that a high degree of labelling is achieved without modification of the single-stranded DNA hybridizing sequences. The specific hybrids were labelled after filter hybridization with europium ions through the chelating groups of DTPA. The europium ions were quantitatively detected by time-resolved fluorometry. The sensitivity of the assay for target DNA detection was in the low picogram range, comparable to radioactively labelled DNA probes.

Oser, A; Roth, W K; Valet, G



Sensitive non-radioactive dot-blot hybridization using DNA probes labelled with chelate group substituted psoralen and quantitative detection by europium ion fluorescence.  


A new labelling method for cloned DNA probes used in hybridization assays is described. The DNA insert of recombinant plasmid DNA was made partially single-stranded for the labelling reaction by a restriction enzyme digest, followed by a controlled exonuclease III incubation. A thiol-containing psoralen derivative was covalently bound through irradiation with UV-light to the remaining double-stranded region of the plasmid DNA. The psoralen-SH groups were labelled with a large number of metal chelators (diethylentriamine pentaacetic acid, DTPA) using poly-L-lysine as a macromolecular carrier. The main advantage of the labelling procedure is that a high degree of labelling is achieved without modification of the single-stranded DNA hybridizing sequences. The specific hybrids were labelled after filter hybridization with europium ions through the chelating groups of DTPA. The europium ions were quantitatively detected by time-resolved fluorometry. The sensitivity of the assay for target DNA detection was in the low picogram range, comparable to radioactively labelled DNA probes. PMID:3344204

Oser, A; Roth, W K; Valet, G



Redefinition of hypervariable region I in mitochondrial DNA control region and comparing its diversity among various ethnic groups.  


The hypervariable region I (HVR-I) of the mitochondrial DNA control region described in the literature is variable in its 5'and 3' ends as well as in its length, causing a problem when data from different ethnic groups are to be compared. To redefine HVR-I, which should be highly polymorphic yet relatively short in length, we analyzed 1437 reported sequences distributed among 11 geographic areas in the world. The results showed that the 237-bp (nts 16126-16362) redefined HVR-I (rHVR-I) had a global genetic diversity of 0.9905 and the 154-bp (nts 16209-16362) short HVR-I (sHVR-I) had a global diversity of 0.9735. Being flanked by a stretch of highly conservative sequences, both rHVR-I and sHVR-I can be produced by PCR, even if extracted from badly degraded specimens. Comparing the genetic diversity among 3870 sequences from 25 countries, we found that the genetic diversity of rHVR-I was 0.9869+/-0.0133 in Asian countries, 0.9685+/-0.0193 in African countries, 0.9299+/-0.0664 in European countries, and 0.8477+/-0.1857 in American countries, whereas that of sHVR-I was 0.9689+/-0.0284 in Asian countries, 0.9504+/-0.0334 in African countries, 0.8721+/-0.0911 in European countries, and 0.8230+/-0.1693 in American countries. The difference in genetic diversity among these countries is consistent with the notion that genetic diversity roughly reflects the genetic history of a given ethnic group. Our results indicate that a polymorphic, short, and PCR-producible HVR-I can be defined, making the comparison among various ethnic groups possible. PMID:18248776

Tzen, Jessica M; Hsu, Hsiu-Jun; Wang, Man-Ning



DNA-binding properties and antitumour activity of monofunctional alkylating groups attached to the DNA-intercalating chromophore phenanthridine: n-bromoalkylphenanthridinium bromides.  


We have synthesised an homologous series of n-bromoalkylphenanthridinium bromides and studied their DNA-binding and antitumour properties. Each of these compounds has the capacity both to intercalate and alkylate DNA. Dialysis measurements reveal a relatively high affinity for calf thymus DNA, being about 10(5) M-1 at ionic strength 0.01. Incubating calf thymus DNA-ligand complexes having a ligand-to-basepair ratio of 0.4 at 37 degrees C for 18 h leads to maximum alkylation levels of about one ligand molecule bound irreversibly per 40 basepairs. The reactivity of these compounds towards DNA is chain-length dependent, the n-decyl compound, for example, requiring about 10-times the ligand-to-basepair input ratio of the n-hexyl derivative to reach the same level of alkylation. The limited degree of alkylation is a consequence of conversion of the alkylbromides to the less reactive alkylchlorides in the buffer medium. The results of DNA sequencing experiments indicate that the n-hexyl derivative alkylates at guanines occurring in 5'-GT-3' sequences and in runs of guanines [(Gp)n]. The corresponding n-decyl compound, on the other hand, is highly selective for guanines in 5'-GT-3' sequences only and also reacts weakly with some adenines. None of the phenanthridinium compounds showed significant antitumour activity in the P388 murine leukaemia test system. PMID:2015276

Wickham, G; Prakash, A S; Wakelin, L P; McFadyen, W D



A novel phylogenetic group within Thozetella (Chaetosphaeriaceae): a new taxon based on morphology and DNA sequence analyses.  


A new species, Thozetella pinicola, was isolated from leaf litter of Pinus elliottii Engelm. in Hong Kong. This taxon is described and compared with existing species in the genus. It occurs on the substrate as creamy white sporodochia and has short black conidiophores. Morphological characters are typical of Thozetella and it most closely resembles Thozetella falcata, Thozetella gigantea and Thozetella nivea, but may be distinguished by its distinct microawns and different conidial size. To gain further taxonomic insight into the phylogenetic relationships of our new taxon and its allies, we sequenced and analysed 6 different regions of 3 genes (ribosomal DNA and protein coding genes: RNA polymerase II largest subunit (RBP2) and b-tubulin). Resulting phylogenies are compared with existing morphological information. Molecular data support the relationship between Thozetella species and the Chaetosphaeriaceae (Chaetosphaeriales, Sordariomycetes). In addition, we recovered a new phylogenetic lineage (or group) within the existing phylogenetic framework of Thozetella as previously proposed. In particular, there is a close association between T. pinicola and T. nivea, which is strongly supported. The affinities of these 2 newly sequenced taxa are discussed in light of morphological and molecular characters. PMID:19767838

Jeewon, R; Yeung, S Y Q; Hyde, K D



Comparative analysis of the influence of the high-mobility group box 1 protein on DNA binding and transcriptional activation by the androgen, glucocorticoid, progesterone and mineralocorticoid receptors.  

PubMed Central

We performed a comparative analysis of the effect of high-mobility group box protein 1 (HMGB1) on DNA binding by the DNA-binding domains (DBDs) of the androgen, glucocorticoid, progesterone and mineralocorticoid receptors. The affinity of the DBDs of the different receptors for the tyrosine aminotransferase glucocorticoid response element, a classical high-affinity binding element, was augmented up to 7-fold by HMGB1. We found no major differences in the effects of HMGB1 on DNA binding between the different steroid hormone receptors. In transient transfection assays, however, HMGB1 significantly enhances the activity of the glucocorticoid and progesterone receptors but not the androgen or mineralocorticoid receptor. We also investigated the effect of HMGB1 on the binding of the androgen receptor DBD to a subclass of directly repeated response elements that is recognized exclusively by the androgen receptor and not by the glucocorticoid, progesterone or mineralocorticoid receptor. Surprisingly, a deletion of 26 amino acid residues from the C-terminal extension of the androgen receptor DBD does not influence DNA binding but destroys its sensitivity to HMGB1. Deletion of the corresponding fragment in the DBDs of the glucocorticoid, progesterone and mineralocorticoid receptor destroyed their DNA binding. This 26-residue fragment is therefore essential for the influence of HMGB1 on DNA recognition by all steroid hormone receptors that were tested. However, it is dispensable for DNA binding by the androgen receptor.

Verrijdt, Guy; Haelens, Annemie; Schoenmakers, Erik; Rombauts, Wilfried; Claessens, Frank



Determination and analysis of site-specific 125I decay-induced DNA double-strand break end-group structures.  


End groups contribute to the structural complexity of radiation-induced DNA double-strand breaks (DSBs). As such, end-group structures may affect a cell's ability to repair DSBs. The 3'-end groups of strand breaks caused by gamma radiation, or oxidative processes, under oxygenated aqueous conditions have been shown to be distributed primarily between 3'-phosphoglycolate and 3'-phosphate, with 5'-phosphate ends in both cases. In this study, end groups of the high-LET-like DSBs caused by 125I decay were investigated. Site-specific DNA double-strand breaks were produced in plasmid pTC27 in the presence or absence of 2 M DMSO by 125I-labeled triplex-forming oligonucleotide targeting. End-group structure was assessed enzymatically as a function of the DSB end to serve as a substrate for ligation and various forms of end labeling. Using this approach, we have demonstrated 3'-hydroxyl (3'-OH) and 3'-phosphate (3'-P) end groups and 5'-ends (> or = 42%) terminated by phosphate. A 32P postlabeling assay failed to detect 3'-phosphoglycolate in a restriction fragment terminated by the 125I-induced DNA double-strand break, and this is likely due to restricted oxygen diffusion during irradiation as a frozen aqueous solution. Even so, end-group structure and relative distribution varied as a function of the free radical scavenging capacity of the irradiation buffer. PMID:17390723

Datta, Kamal; Weinfeld, Michael; Neumann, Ronald D; Winters, Thomas A



Bacillus anthracis Diverges from Related Clades of the Bacillus cereus Group in 16S-23S Ribosomal DNA Intergenic Transcribed Spacers Containing tRNA Genes  

Microsoft Academic Search

Mung bean nuclease treatment of 16S-23S ribosomal DNA intergenic transcribed spacers (ITS) amplified from several strains of the six species of the Bacillus cereus group showed that B. anthracis Davis TE702 and B. mycoides G2 have other intermediate fragments in addition to the 220- and 550-bp homoduplex fragments typical of the B. cereus group. Long and intermediate homoduplex ITS fragments

Ameur Cherif; Sara Borin; Aurora Rizzi; Hadda Ouzari; Abdellatif Boudabous; Daniele Daffonchio



Morphology and DNA barcoding reveal three cryptic species within the Xylophanes neoptolemus and loelia species-groups (Lepidoptera: Sphingidae)  

Microsoft Academic Search

Two species complexes within the genus Xylophanes are addressed using a combination of morphological study and analysis of DNA barcode sequences. The existence of two and three cryptic species respectively within the X. loelia and X. neoptolemus complexes is revealed following consideration of both adult habitus and genital morphology, and the results of a phylogenetic analysis of partial COI sequences—DNA




Divergent DNA-binding specificities of a group of ETHYLENE RESPONSE FACTOR transcription factors involved in plant defense.  


Transcription factors (TFs) recognize target DNA sequences with distinct DNA-binding domains (DBDs). The DBD of Arabidopsis (Arabidopsis thaliana) ETHYLENE RESPONSE FACTOR1 (AtERF1) uses three consecutive ?-strands to recognize a GCC-containing sequence, but tobacco (Nicotiana tabacum) ERF189 and periwinkle (Catharanthus roseus) Octadecanoid-derivative Responsive Catharanthus AP2-domain protein3 (ORCA3) of the same TF subgroup appear to target similar but divergent DNA sequences. Here, we examined how DNA-binding specificities of these TFs have diverged in each plant lineage to regulate distinct defense metabolisms. Extensive mutational analyses of these DBDs suggest that two modes of protein-DNA interactions independently contribute to binding specificity and affinity. Substitution of a conserved arginine to lysine in the first ?-strand of ERF189 relaxes its interaction with the second GC pair of the GCC DNA sequence. By contrast, an increased number of basic amino acids in the first two ?-strands of ORCA3 allows this TF to recognize more than one GCC-related target, presumably via increased electrostatic interactions with the negatively charged phosphate backbone of DNA. Divergent DNA-binding specificities of the ERFs may have arisen through mutational changes of these amino acid residues. PMID:23629834

Shoji, Tsubasa; Mishima, Masaki; Hashimoto, Takashi



DNA Evidence on the Phylogenetic Systematics of New World Monkeys: Support for the Sister-Grouping of Cebus and Saimiri from Two Unlinked Nuclear Genes  

Microsoft Academic Search

Previous inferences from ?-globin gene sequences on cladistic relationships among the 16 extant genera of Ceboidea (the New World monkeys) were tested by strength of grouping and bootstrap values for the clades in the most parsimonious trees found: for this epsilon data set enlarged with additional Cebus and Saimiri orthologues; for another nuclear DNA sequence data set consisting of IRBP

M. L. Harada; H. Schneider; M. P. C. Schneider; I. Sampaio; J. Czelusniak; M. Goodman



DNA repair in human xeroderma pigmentosum group C cells involves a different distribution of damaged sites in confluent and growing cells.  

PubMed Central

Xeroderma pigmentosum is a human disease consisting of several complementation groups that are deficient in excision repair. Group C is one in which excision repair occurs at about 20-30% of normal levels. The distribution of mended sites in relation to unrepaired sites has been determined by cutting remaining unrepaired pyrimidine dimers with Microccocus luteus UV endonuclease. The mended sites have been found clustered together in a fashion that depended on cell proliferation. In confluent group C cells, the mended sites were clustered in regions where dimer excision was as efficient as excision in the DNA of normal cells. In proliferating group C cells, however, mended sites were randomly dispersed. The total amount of repair replication was the same in confluent and proliferating cells. Since previous work has shown that confluent group C cells show more extensive recovery from the lethal effects of UV irradiation than some other groups, clustered repair may correlate with a more efficient mechanism of restoring cell viability. The different distribution of repaired sites during DNA replication may be the result of changes in the state of the substrate for repair or changes in the metabolic priorities of DNA polymerases.

Cleaver, J E



Display of amino groups on substrate surfaces by simple dip-coating of methacrylate-based polymers and its application to DNA immobilization.  


The implementation of a reactive functional group onto a material surface is of great importance. Reactive functional groups (e.g., an amino group and a hydroxyl group) are usually hydrophilic, which makes it difficult to display them on a dry polymer surface. We here propose a novel method for displaying amino groups on the surfaces of polymeric substrates through dip-coating of a methacrylate-based copolymer. We synthesized copolymers composed of methyl methacrylate and 2-aminoethyl methacrylate with different protecting groups or ion-complexes on their amino groups, then dip-coated the copolymers onto a poly(methyl methacrylate) (PMMA) substrate. Evaluation using a cleavable fluorescent compound, which was synthesized in the present study to quantify a small amount (pmol/cm(2)) of amino groups on a solid surface, revealed that the protection of amino groups affected their surface segregation in the copolymer coating. p-Toluenesulfonate ion-complex and tert-butoxycarbonyl (Boc) protection of amino groups were found to effectively display amino groups on the surface (more than 70 pmol/cm(2)). The density of amino groups displayed on a surface can be easily controlled by mixing the copolymer and PMMA before dip-coating. Dip-coating of the copolymer with Boc protection on various polymeric substrates also successfully displayed amino groups on their surfaces. Finally, we demonstrated that the amino groups displayed can be utilized for the immobilization of a DNA oligonucleotide on a substrate surface. PMID:23276150

Shimomura, Ayane; Nishino, Takashi; Maruyama, Tatsuo



The SRY high-mobility-group box recognizes DNA by partial intercalation in the minor groove: a topological mechanism of sequence specificity.  

PubMed Central

SRY, a putative transcription factor encoded by the sex-determining region of the human Y chromosome, regulates a genetic switch in male development. Impairment of this switch leads to intersex abnormalities of the newborn and is observed in association with mutations in the SRY DNA-binding domain [the high-mobility-group (HMG) box]. Here we show that the SRY HMG box exhibits a novel mechanism of DNA recognition: partial intercalation of a nonpolar side chain in the DNA minor groove. Base stacking (but not base pairing) is interrupted at the site of insertion. Sequence specificity reflects topological requirements of partial intercalation rather than direct readout of base-specific functional groups. Our results predict that the SRY HMG box inserts an alpha-helix into a widened minor groove at the center of a sharp DNA bend. A similar mechanism may underlie binding of SRY and homologous HMG proteins to four-way junctions (Holliday intermediates) and other noncanonical DNA structures. Images Fig. 1 Fig. 6

King, C Y; Weiss, M A



Nonenzymatic methylation of DNA by the intracellular methyl group donor S-adenosyl-L-methionine is a potentially mutagenic reaction.  

PubMed Central

Incubation of DNA with S-adenosyl-L-methionine (SAM) in neutral aqueous solution leads to base modification, with formation of small amounts of 7-methylguanine and 3-methyladenine. The products have been identified by high performance liquid chromatography of DNA hydrolysates and by the selective release of free 3-methyladenine from SAM-treated DNA by a specific DNA glycosylase. We conclude that SAM acts as a weak DNA-alkylating agent. Several control experiments including extensive purification of [3H-methyl]SAM preparations and elimination of the alkylating activity by pretreatment of SAM with a phage T3-induced SAM cleaving enzyme, have been performed to determine that the activity observed was due to SAM itself and not to a contaminating substance. We estimate that SAM, at an intracellular concentration of 4 X 10(-5) M, causes DNA alkylation at a level similar to that expected from continuous exposure of cells to 2 X 10(-8) M methyl methane-sulphonate. This ability of SAM to act as a methyl donor in a nonenzymatic reaction could result in a background of mutagenesis and carcinogenesis. The data provide an explanation for the apparently universal occurrence of multiple DNA repair enzymes specific for methylation damage.

Rydberg, B; Lindahl, T



dnaJ gene sequence-based assay for species identification and phylogenetic grouping in the genus Staphylococcus  

Microsoft Academic Search

In the last few years, many attempts have been made to use conserved gene sequences for identification and for phylogenetic studies of Staphylococcus species. In an effort to identify a more reliable approach, a dnaJ gene sequence-based database was created. In this study, an approximately 883 bp portion of the dnaJ gene sequence from 45 staphylococcal type strains was compared

Mohammad Monir Shah; Hirotoshi Iihara; Makiko Noda; S. X. Song; Pham Hong Nhung; Kiyofumi Ohkusu; Yoshiaki Kawamura; Takayuki Ezaki



A Drosophila single-strand DNA/RNA-binding factor contains a high-mobility-group box and is enriched in the nucleolus.  

PubMed Central

We have isolated a Drosophila melanogaster cDNA encoding a high-mobility-group (HMG) box-containing protein. This protein shares 50% amino acid identity with the human putative structure-specific recognition protein, hSSRP. The gene encoding the D. melanogaster homolog, DssRP, is developmentally regulated and is expressed most abundantly in ovaries (nurse cells in particular). The protein is localized in nuclei and is particularly abundant in the nucleolus. In vitro binding studies using DssRP produced in bacteria showed that, despite expectation, the protein does not bind to structured DNA. Instead, it binds to single-stranded DNA and RNA, with highest affinity to nucleotides G and U. Images Fig. 2 Fig. 3 Fig. 4 Fig. 5

Hsu, T; King, D L; LaBonne, C; Kafatos, F C



EcI5, a group IIB intron with high retrohoming frequency: DNA target site recognition and use in gene targeting  

PubMed Central

We find that group II intron EcI5, a subclass CL/IIB1 intron from an Escherichia coli virulence plasmid, is highly active in retrohoming in E. coli. Both full-length EcI5 and an EcI5-?ORF intron with the intron-encoded protein expressed separately from the same donor plasmid retrohome into a recipient plasmid target site at substantially higher frequencies than do similarly configured Lactococcus lactis Ll.LtrB introns. A comprehensive view of DNA target site recognition by EcI5 was obtained from selection experiments with donor and recipient plasmid libraries in which different recognition elements were randomized. These experiments suggest that EcI5, like other mobile group II introns, recognizes DNA target sequences by using both the intron-encoded protein and base-pairing of the intron RNA, with the latter involving EBS1, EBS2, and EBS3 sequences characteristic of class IIB introns. The intron-encoded protein appears to recognize a small number of bases flanking those recognized by the intron RNA, but their identity is different than in previously characterized group II introns. A computer algorithm based on the empirically determined DNA recognition rules enabled retargeting of EcI5 to integrate specifically at 10 different sites in the chromosomal lacZ gene at frequencies up to 98% without selection. Our findings provide insight into modes of DNA target site recognition used by mobile group II introns. More generally, they show how the diversity of mobile group II introns can be exploited to provide a large variety of different target specificities and potentially other useful properties for gene targeting.

Zhuang, Fanglei; Karberg, Michael; Perutka, Jiri; Lambowitz, Alan M.



The Saccharomyces cerevisiae DNA recombination and repair functions of the RAD52 epistasis group inhibit Ty1 transposition.  

PubMed Central

RNA transcribed from the Saccharomyces cerevisiae retrotransposon Ty1 accumulates to a high level in mitotically growing haploid cells, yet transposition occurs at very low frequencies. The product of reverse transcription is a linear double-stranded DNA molecule that reenters the genome by either Ty1-integrase-mediated insertion or homologous recombination with one of the preexisting genomic Ty1 (or delta) elements. Here we examine the role of the cellular homologous recombination functions on Ty1 transposition. We find that transposition is elevated in cells mutated for genes in the RAD52 recombinational repair pathway, such as RAD50, RAD51, RAD52, RAD54, or RAD57, or in the DNA ligase I gene CDC9, but is not elevated in cells mutated in the DNA repair functions encoded by the RAD1, RAD2, or MSH2 genes. The increase in Ty1 transposition observed when genes in the RAD52 recombinational pathway are mutated is not associated with a significant increase in Ty1 RNA or proteins. However, unincorporated Ty1 cDNA levels are markedly elevated. These results suggest that members of the RAD52 recombinational repair pathway inhibit Ty1 post-translationally by influencing the fate of Ty1 cDNA.

Rattray, A J; Shafer, B K; Garfinkel, D J



Variation in ribosomal and mitochondrial DNA sequences demonstrates the existence of intraspecific groups in Paramecium multimicronucleatum (Ciliophora, Oligohymenophorea).  


This is the first phylogenetic study of the intraspecific variability within Paramecium multimicronucleatum with the application of two-loci analysis (ITS1-5.8S-ITS2-5'LSU rDNA and COI mtDNA) carried out on numerous strains originated from different continents. The species has been shown to have a complex structure of several sibling species within taxonomic species. Our analysis revealed the existence of 10 haplotypes for the rDNA fragment and 15 haplotypes for the COI fragment in the studied material. The mean distance for all of the studied P. multimicronucleatum sequence pairs was p=0.025/0.082 (rDNA/COI). Despite the greater variation of the COI fragment, the COI-derived tree topology is similar to the tree topology constructed on the basis of the rDNA fragment. P. multimicronucleatum strains are divided into three main clades. The tree based on COI fragment analysis presents a greater resolution of the studied P. multimicronucleatum strains. Our results indicate that the strains of P. multimicronucleatum that appear in different clades on the trees could belong to different syngens. PMID:22342870

Tarcz, Sebastian; Potekhin, Alexey; Rautian, Maria; Przybo?, Ewa



The dichotomy in the DNA-binding behaviour of ruthenium(II) complexes bearing benzoxazole and benzothiazole groups  

Microsoft Academic Search

The substituted tris(bipyridine)ruthenium(II) complexes {[Ru(bpy)2(4,4?-bbob)]2+ and [Ru(bpy)2(5,5?-bbob)]2+ [where bpy=2,2?-bipyridine and bbob=bis(benzoxazol-2-yl)-2,2?-bipyridine] have been prepared and compared to the previously studied complex [Ru(bpy)2(4,4?-bbtb)]2+ [where bbtb=bis(benzothiazol-2-yl)-2,2?-bipyridine]. From the UV\\/VIS titration studies, ?-[Ru(bpy)2(4,4?-bbob)]2+ displays a stronger association than the ?-isomer with calf-thymus DNA (ct-DNA). For [Ru(bpy)2(5,5?-bbob)]2+, there appears to be minimal interaction with ct-DNA. The results of fluorescence titration studies suggest that [Ru(bpy)2(4,4?-bbob)]2+

Catriona B. Spillane; Marième N. V. Dabo; Nicholas C. Fletcher; Joy L. Morgan; F. Richard Keene; Ihtshamul Haq; Niklaas J. Buurma



Establishment of a quality assurance program for human immunodeficiency virus type 1 DNA polymerase chain reaction assays by the AIDS Clinical Trials Group. ACTG PCR Working Group, and the ACTG PCR Virology Laboratories.  

PubMed Central

An independent quality assurance program has been established by the Virology Committee of the AIDS Clinical Trials Group in the Division of AIDS, National Institute of Allergy and Infectious Diseases, for monitoring polymerase chain reaction (PCR) assays for human immunodeficiency virus type 1 (HIV-1) DNA that are performed by 11 laboratories participating in multicenter clinical trials in the United States. To perform HIV-1 DNA PCR for patients in AIDS Clinical Trials Group protocols, each laboratory was initially certified by correctly testing a coded certification panel consisting of eight well-defined clinical whole-blood specimens and 30 cell pellets containing 0, 2, 5, 10, 20, or 50 8E5/LAV cells per 125,000 uninfected peripheral blood mononuclear cells. PCR was performed by one of two standardized commercial assays for amplification and nonisotopic detection of HIV-1 proviral DNA. For continuing certification, each laboratory must correctly test eight coded whole-blood samples per quarter and run three or four coded cell pellets and HIV-1 DNA copy standards with every PCR assay in real time. The PCR results for the coded pellets on each run are entered into an encrypted computer file, which immediately assesses the validity of the run. To date, 10 of 11 laboratories have correctly tested all HIV-1-positive and -negative samples in the initial certification panel on their first or second attempt. Subsequently, 9 of these 11 laboratories have continued to maintain their certified status. The use of commercial HIV-1 DNA PCR assays and an external quality assurance program have ensured that results from different laboratories are comparable and that problems with sensitivity and specificity are quickly identified.

Jackson, J B; Drew, J; Lin, H J; Otto, P; Bremer, J W; Hollinger, F B; Wolinsky, S M



[Genetic diversity and relatives of the goitered gazelle (Gazella subgutturosa) groups from Uzbekistan, Turkmenistan, and Azerbaijan: analysis of the D-loop of mitochondrial DNA].  


Polymorphism of the nucleotide sequence of a hypervariable fragment of the D-loop (985 bp) of mtDNA in 76 Goitered gazelles of subspecies Gazella subgutturosa subgutturosa from Uzbekistan, Turkmenistan, and Azerbaijan was studied. The genetic similarity of gazelles from Turkmenistan and Uzbekistan has been identified. The population of gazelles from Shirvanskaya steppe reserve (Azerbaijan) is unique and strictly isolated from other groups studied. A high haplotypic (H = 0.9649 +/- 0.0091) and relatively low nucleotide diversity (pi = 0.0212 +/- 0.0105) were noted for all investigated groups of gazelle based on this mtDNA fragment, which is probably related to ecological peculiarities of the species and the history of formation of regional populations. PMID:22292288

Sorokin, P A; Soldatova, N V; Lukarevski?, V S; Kholodova, M V


Analysis of body fluid mixtures by mtDNA sequencing: An inter-laboratory study of the GEP-ISFG working group.  


The mitochondrial DNA (mtDNA) working group of the GEP-ISFG (Spanish and Portuguese Group of the International Society for Forensic Genetics) carried out an inter-laboratory exercise consisting of the analysis of mtDNA sequencing patterns in mixed stains (saliva/semen and blood/semen). Mixtures were prepared with saliva or blood from a female donor and three different semen dilutions (pure, 1:10 and 1:20) in order to simulate forensic casework. All labs extracted the DNA by preferential lysis and amplified and sequenced the first mtDNA hypervariable region (HVS-I). Autosomal and Y-STR markers were also analysed in order to compare nuclear and mitochondrial results from the same DNA extracts. A mixed stain prepared using semen from a vasectomized individual was also analysed. The results were reasonably consistent among labs for the first fractions but not for the second ones, for which some laboratories reported contamination problems. In the first fractions, both the female and male haplotypes were generally detected in those samples prepared with undiluted semen. In contrast, most of the mixtures prepared with diluted semen only yielded the female haplotype, suggesting that the mtDNA copy number per cell is smaller in semen than in saliva or blood. Although the detection level of the male component decreased in accordance with the degree of semen dilution, it was found that the loss of signal was not consistently uniform throughout each electropherogram. Moreover, differences between mixtures prepared from different donors and different body fluids were also observed. We conclude that the particular characteristics of each mixed stain can deeply influence the interpretation of the mtDNA evidence in forensic mixtures (leading in some cases to false exclusions). In this sense, the implementation of preliminary tests with the aim of identifying the fluids involved in the mixture is an essential tool. In addition, in order to prevent incorrect conclusions in the interpretation of electropherograms we strongly recommend: (i) the use of additional sequencing primers to confirm the sequencing results and (ii) interpreting the results to the light of the phylogenetic perspective. PMID:16899347

Montesino, M; Salas, A; Crespillo, M; Albarrán, C; Alonso, A; Alvarez-Iglesias, V; Cano, J A; Carvalho, M; Corach, D; Cruz, C; Di Lonardo, A; Espinheira, R; Farfán, M J; Filippini, S; García-Hirschfeld, J; Hernández, A; Lima, G; López-Cubría, C M; López-Soto, M; Pagano, S; Paredes, M; Pinheiro, M F; Rodríguez-Monge, A M; Sala, A; Sóñora, S; Sumita, D R; Vide, M C; Whittle, M R; Zurita, A; Prieto, L



Mechanism of Promoter Melting by the Xeroderma Pigmentosum Complementation Group B Helicase of Transcription Factor IIH Revealed by Protein-DNA Photo-Cross-Linking  

Microsoft Academic Search

The p89\\/xeroderma pigmentosum complementation group B (XPB) ATPase-helicase of transcription factor IIH (TFIIH) is essential for promoter melting prior to transcription initiation by RNA polymerase II (RNA- PII). By studying the topological organization of the initiation complex using site-specific protein-DNA photo-cross-linking, we have shown that p89\\/XPB makes promoter contacts both upstream and downstream of the initiation site. The upstream contact,




The SRY High-Mobility-Group Box Recognizes DNA by Partial Intercalation in the Minor Groove: A Topological Mechanism of Sequence Specificity  

Microsoft Academic Search

SRY, a putative transcription factor encoded by the sex-determining region of the human Y chromosome, regulates a genetic switch in male development. Impairment of this switch leads to intersex abnormalities of the newborn and is observed in association with mutations in the SRY DNA-binding domain [the high-mobility-group (HMG) box]. Here we show that the SRY HMG box exhibits a novel

Chih-Yen King; Michael A. Weiss



A novel regulation mechanism of DNA repair by damage-induced and RAD23-dependent stabilization of xeroderma pigmentosum group C protein  

Microsoft Academic Search

Primary DNA damage sensing in mammalian global genome nucleotide excision repair (GG-NER) is performed by the xeroderma pigmentosum group C (XPC)\\/HR23B protein complex. HR23B and HR23A are human homologs of the yeast ubiquitin-domain repair factor RAD23, the function of which is unknown. Knockout mice revealed that mHR23A and mHR23B have a fully redundant role in NER, and a partially redundant

Jessica M. Y. Ng; Wim Vermeulen; Steven Bergink; Kaoru Sugasawa; Harry Vrieling; Jan H. J. Hoeijmakers



Quantifying male-biased dispersal among social groups in the collared peccary (Pecari tajacu) using analyses based on mtDNA variation.  


Recent advances in the statistical analysis of microsatellite data permit calculation of sex-specific dispersal rates through sex- and age-specific comparisons of genetic variation. This approach, developed for the analysis of data derived from co-dominant autosomal markers, should be applicable to a sex-specific marker such as mitochondrial DNA. To test this premise, we amplified a 449 bp control region DNA sequence from the mitochondrial genome of the collared peccary (Pecari tajacu), and estimated intra-class correlations among herds sampled from three Texas populations. Analyses on data partitioned by breeding group showed a clear signal of male-biased dispersal; sex-specific fixation indices associated with genetic variation among social groups within populations yielded values for females (F(GP)=0.91), which were significantly larger than values for males (F(GP)=0.24; P=0.0015). The same general pattern emerged when the analyses were conducted on age classes (albeit nonsignificantly), as well as categories of individuals that were predicted a posteriori to be dispersers (adult males) and philopatric (adult females and all immatures). By extending a previously published methodology based on biparentally inherited markers to matrilineally inherited haploid data, we calculated sex-specific rates of contemporary dispersal among social groups within populations (m(male symbol)=0.37). These results support the idea that mitochondrial DNA haplotype frequency data can be used to estimate sex-specific instantaneous dispersal rates in a social species. PMID:19639005

Cooper, J D; Vitalis, R; Waser, P M; Gopurenko, D; Hellgren, E C; Gabor, T M; DeWoody, J A



Growth and grazing rates of bacteria groups with different apparent DNA content in the Gulf of Mexico  

Microsoft Academic Search

Growth rates and grazing losses of bacterioplankton were assessed by serial dilution experiments in surface waters in the Mississippi River plume, the northern Gulf of Mexico, a Texas coastal lagoon (Laguna Madre), southeast Gulf of Mexico surface water, and the chlorophyll subsurface maximum layer in the southeast Gulf of Mexico. Bacteria were quantified by flow cytometry after DNA staining with

F. J. Jochem; P. J. Lavrentyev; M. R. First



The nicking homing endonuclease I-BasI is encoded by a group I intron in the DNA polymerase gene of the Bacillus thuringiensis phage Bastille.  


Here we describe the discovery of a group I intron in the DNA polymerase gene of Bacillus thuringiensis phage Bastille. Although the intron insertion site is identical to that of the Bacillus subtilis phages SPO1 and SP82 introns, the Bastille intron differs from them substantially in primary and secondary structure. Like the SPO1 and SP82 introns, the Bastille intron encodes a nicking DNA endonuclease of the H-N-H family, I-BasI, with a cleavage site identical to that of the SPO1-encoded enzyme I-HmuI. Unlike I-HmuI, which nicks both intron-minus and intron-plus DNA, I-BasI cleaves only intron-minus alleles, which is a characteristic of typical homing endonucleases. Interestingly, the C-terminal portions of these H-N-H phage endonucleases contain a conserved sequence motif, the intron-encoded endonuclease repeat motif (IENR1) that also has been found in endonucleases of the GIY-YIG family, and which likely comprises a small DNA-binding module with a globular betabetaalphaalphabeta fold, suggestive of module shuffling between different homing endonuclease families. PMID:12799434

Landthaler, Markus; Shub, David A



The Polycomb group protein MEDEA and the DNA methyltransferase MET1 interact to repress autonomous endosperm development in Arabidopsis.  


In flowering plants, double fertilization of the female gametes, the egg and the central cell, initiates seed development to give rise to a diploid embryo and the triploid endosperm. In the absence of fertilization, the FERTILIZATION-INDEPENDENT SEED Polycomb Repressive Complex 2 (FIS-PRC2) represses this developmental process by histone methylation of certain target genes. The FERTILIZATION-INDEPENDENT SEED (FIS) class genes MEDEA (MEA) and FERTILIZATION-INDEPENDENT ENDOSPERM (FIE) encode two of the core components of this complex. In addition, DNA methylation establishes and maintains the repression of gene activity, for instance via DNA METHYLTRANSFERASE1 (MET1), which maintains methylation of symmetric CpG residues. Here, we demonstrate that Arabidopsis MET1 interacts with MEA in vitro and in a yeast two-hybrid assay, similar to the previously identified interaction of the mammalian homologues DNMT1 and EZH2. MET1 and MEA share overlapping expression patterns in reproductive tissues before and after fertilization, a prerequisite for an interaction in vivo. Importantly, a much higher percentage of central cells initiate endosperm development in the absence of fertilization in mea-1/MEA; met1-3/MET1 as compared to mea-1/MEA mutant plants. In addition, DNA methylation at the PHERES1 and MEA loci, imprinted target genes of the FIS-PRC2, was affected in the mea-1 mutant compared with wild-type embryos. In conclusion, our data suggest a mechanistic link between two major epigenetic pathways involved in histone and DNA methylation in plants by physical interaction of MET1 with the FIS-PRC2 core component MEA. This concerted action is relevant for the repression of seed development in the absence of fertilization. PMID:23146178

Schmidt, Anja; Wöhrmann, Heike J P; Raissig, Michael T; Arand, Julia; Gheyselinck, Jacqueline; Gagliardini, Valeria; Heichinger, Christian; Walter, Joern; Grossniklaus, Ueli



Characterisation and Interpopulation Variability of a Complex HpaI Satellite DNA of Drosophila seriema (repleta Group)  

Microsoft Academic Search

A HpaI satellite DNA has been isolated and characterised from the genome of Drosophila seriema, a cactus-breeding species endemic to the rock fields of the Espinhaço Range in Brazil. The monomer sequences are slightly A + T rich (66%) and there is a significant variation of repetition length (343–391 bp). The length variability is mainly due to a 22 bp

Gustavo C. S. Kuhn; Fabio M. Sene



Identification, molecular characterization, and evolution of group I introns at the expansion segment D11 of 28S rDNA in Rhizoctonia species.  


The nuclear ribosomal DNA of Rhizoctonia species is polymorphic in terms of the nucleotide composition and length. Insertions of 349-410 nucleotides in length with characteristics of group I introns were detected at a single insertion point at the expansion segment D11 of 28S rDNA in 12 out of 64 isolates. Eleven corresponded to Rhizoctonia solani (teleomorph: Thanatephorous) and one (AG-Q) to Rhizoctonia spp. (teleomorph: Ceratobasidium). Sequence data showed that all but AG-Q contained conserved DNA catalytic core regions (P, Q, R, and S) essential for selfsplicing. The predicted secondary structure revealed that base-paired helices corresponded to subgroup IC1. Isolates from same anastomosis group and even subgroups within R. solani were variable with regard to possession of introns. Phylogenetic analyses indicated that introns were vertically transmitted. Unfortunately, sequence data from the conserved region from all 64 isolates were not useful for delimiting species. Analyses with IC1 introns at same insertion point, of both Ascomycota and Basidiomycota indicated the possibility of horizontal transfer at this site. The present study uncovered new questions on evolutionary pattern of change of these introns within Rhizoctonia species. PMID:24012302

González, Dolores



A complex array of DNA-binding proteins required for pairing-sensitive silencing by a polycomb group response element from the Drosophila engrailed gene.  

PubMed Central

Regulatory DNA from the Drosophila gene engrailed causes silencing of a linked reporter gene (mini-white) in transgenic Drosophila. This silencing is strengthened in flies homozygous for the transgene and has been called "pairing-sensitive silencing." The pairing-sensitive silencing activities of a large fragment (2.6 kb) and a small subfragment (181 bp) were explored. Since pairing-sensitive silencing is often associated with Polycomb group response elements (PREs), we tested the activities of each of these engrailed fragments in a construct designed to detect PRE activity in embryos. Both fragments were found to behave as PREs in a bxd-Ubx-lacZ reporter construct, while the larger fragment showed additional silencing capabilities. Using the mini-white reporter gene, a 139-bp minimal pairing-sensitive element (PSE) was defined. DNA mobility-shift assays using Drosophila nuclear extracts suggested that there are eight protein-binding sites within this 139-bp element. Mutational analysis showed that at least five of these sites are important for pairing-sensitive silencing. One of the required sites is for the Polycomb group protein Pleiohomeotic and another is GAGAG, a sequence bound by the proteins GAGA factor and Pipsqueak. The identity of the other proteins is unknown. These data suggest a surprising degree of complexity in the DNA-binding proteins required for PSE function.

Americo, Jeffrey; Whiteley, Mary; Brown, J Lesley; Fujioka, Miki; Jaynes, James B; Kassis, Judith A



[Gene pool of ethnic groups of the caucasus: results of integrated study of the Y chromosome and mitochondrial DNA and genome-wide data].  


Genetic diversity has been analyzed in 22 ethnic groups of the Caucasus on the basis of data on Y-chromosome and mitochondrial DNA (mtDNA) markers, as well as genome-wide data on autosomal single-nucleotide polymorphisms (SNPs). It has been found that the West Asian component is prevailing in all ethnic groups studied except for Nogays. This Near Eastern ancestral component has proved to be characteristic of Caucasian populations and almost entirely absent in their northern neighbors inhabiting the Eastern European Plain. Turkic-speaking populations, except Nogays, did not exhibit an increased proportion of Eastern Eurasian mtDNA or Y-chromosome haplogroups compared to some Abkhaz-Adyghe populations (Adygs and Kabardians). Genome-wide SNP analysis has also shown substantial differences of Nogays from all other Caucasian populations studied. However, the characteristic difference of Nogays from other populations of the Caucasus seems somewhat ambiguous in terms of the R1a1a-M17(M198) and R1b1b1-M73 haplogroups of the Y chromosome. The state of these haplogroups in Turkic-speaking populations of the Caucasus requires further study. PMID:22946333

Khusnutdinova, E K; Litvinov, S S; Kutuev, I A; Iunusbaev, B B; Khusainova, R I; Akhmetova, V L; Ahatova, F S; Metspalu, E; Rootsi, S; Villems, R



DNA repair in normal human and xeroderma pigmentosum group A fibroblasts following treatment with various methanesulfonates and the demonstration of a long-patch repair component  

SciTech Connect

Excision repair of DNA in normal and xeroderma pigmentosum complementation group A fibroblasts were examined following treatment with methyl-, ethyl-, and isopropyl methanesulfonate. Studies utilizing repair synthesis methods and inhibition with arabinofuranosyl cytosine revealed two distinct phases of repair; one commencing and terminating within the first 3-5 h after the treatment, and a second much longer phase extending from 9-35 h post-treatment. Both phases of repair have a long-patch component, which establishes for the first time the existence of this mode of repair in response to alkane sulfonate damage. While xeroderma cells display somewhat fewer alkaline labile sites in their DNA following alkylation treatment than do their normal counterparts, researchers are unable to demonstrate a deficiency of these cells in either of the two phases of repair.

Snyder, R.D.; Regan, J.D.



Mitochondrial DNA duplication\\/deletion events and polymorphism of the C group of male sterile maize cytoplasms  

Microsoft Academic Search

Five accessions of members of the C group of male sterile maize cytoplasms (BB, C, ES, PR, and RB) in two nuclear backgrounds (A619 and A632) were examined to elucidate the nature of mitochondrial genome diversity within a related group of cytoplasms. Cosmid and plasmid clones carrying single copy and recombinationally active sequences from N and S cytoplasms of maize

D. R. Pring; D. M. Lonsdale; V. E. Gracen; A. G. Smith



RAD25 (SSL2), the yeast homolog of the human xeroderma pigmentosum group B DNA repair gene, is essential for viability  

SciTech Connect

Xeroderma pigmentosum (XP) patients are extremely sensitive to ultraviolet (UV) light and suffer from a high incidence of skin cancers, due to a defect in nucleotide excision repair. The disease is genetically heterogeneous, and seven complementation groups, A-G, have been identified. Homologs of human excision repair genes ERCC1, XPDC/ERCC2, and XPAC have been identified in the yeast Saccharomyces cerevisiae. Since no homolog of human XPBC/ERCC3 existed among the known yeast genes, we cloned the yeast homolog by using XPBC cDNA as a hybridization probe. The yeast homolog, RAD25 (SSL2), encodes a protein of 843 amino acids (M[sub r] 95,356). The RAD25 (SSL2)- and XPCX-encoded proteins share 55% identical and 72% conserved amino acid residues, and the two proteins resemble one another in containing the conserved DNA helicase sequence motifs. A nonsense mutation at codon 799 that deletes the 45 C-terminal amino acid residues in RAD25 (SSL2) confers UV sensitivity. This mutation shows epistasis with genes in the excision repair group, whereas a synergistic increase in UN sensitivity occurs when it is combined with mutations in genes in other DNA repair pathways, indicating that RAD25 (SSL2) functions in excision repair but not in other repair pathways. We also show that RAD25 (SSL2) is an essential gene. A mutation of the Lys[sup 392] residue to arginine in the conserved Walker type A nucleotide-binding motif is lethal, suggesting an essential role of the putative RAD 25 (SSL2) ATPase/DNA helicase activity in viability. 40 refs., 3 figs., 1 tab.

Park, E.; Prakash, L. (Univ. of Rochester School of Medicine, NY (United States)); Guzder, S.N.; Prakash, S. (Univ. of Rochester, NY (United States)); Koken, M.H.M.; Jaspers-Dekker, I.; Weeda, G.; Hoeijmakers, H.J. (Erasmus Univ., Rotterdam (Netherlands))



Phylogenetic relationships of the downy mildews (Peronosporales) and related groups based on nuclear large subunit ribosomal DNA sequences  

Microsoft Academic Search

Abstract: In order,to investigate phylogenetic,rela- tionships of the Peronosporomycetes (Oomycetes), nuclear large subunit ribosomal,DNA sequences,con- taining the D1 and,D2 region,were,analyzed,of 92 species belonging to the orders Peronosporales, Py- thiales, Leptomitales, Rhipidiales, Saprolegniales and Sclerosporales. The,data,were,analyzed,applying methods,of neighbor-joining,as well as maximum,par- simony, both statistically supported using the boot- strap method. The results confirm,the major division between,the Pythiales and Peronosporales,on the one

A. Riethmu Ller; H. Voglmayr; M. Weiß; F. Oberwinkler


Restriction enzyme analysis of mitochondrial DNA of the Aspergillus flavus group: A. flavus, A. parasiticus, and A. nomius.  

PubMed Central

Mitochondrial DNA restriction fragment length polymorphisms were identified that clearly distinguish Aspergillus flavus, A. parasiticus, and A. nomius. Mitochondrial DNAs of A. flavus and A. parasiticus were found to be circular, and their size was estimated size to be 32 kilobases. A restriction map was constructed for the mitochondrial genome of an A. parasiticus isolate by using four restriction endonucleases. Four genes tested were found to have the same order as in the mitochondrial genome of A. nidulans. The mitochondrial genome of A. nomius was estimated to be 33 kilobases. Images

Moody, S F; Tyler, B M



Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China*  

PubMed Central

We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capillary electrophoresis, the PCR products of the 21 STR loci were separated and genotyped. A total of 161 alleles were observed in the Russian ethnic minority group, and corresponding allelic frequencies ranged from 0.0044 to 0.5965. The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population’s genetic background, for individual identification, and for paternity testing in forensic practice.

Wang, Hong-dan; Shen, Chun-mei; Liu, Wen-juan; Zhang, Yu-dang; Yang, Guang; Yan, Jiang-wei; Qin, Hai-xia; Zhu, Bo-feng



The group 10 allergen of Dermatophagoides farinae (Acari: Pyroglyphidae): cDNA cloning, sequence analysis, and expression in Escherichia coli BL21.  


Dermatophagoides farinae Hughes, American house dust mite, is highly allergenic, producing symptoms in people worldwide. Identifying and cloning the allergens in this species may enable better diagnostic and therapeutic approaches. Here, we cloned, sequenced, and expressed the full-length cDNA encoding D. farinae group 10 allergen (Der f 10) isolated from dust mites in China. Bioinformatic analysis indicated that the 888 bp sequence encoded a cytoskeleton protein 295 amino acids long, with a molecular weight of approximately equal 34 kDa. Sequence alignment with the group 10 allergens of Pyroglyphidae, Acaridae, and Glycyphagidae families revealed that the group 10 allergen from D. farinae is 95% similar to D. pteronyssinus Trouessart and Psoroptes ovis (Hering). These findings lay the groundwork for future studies, including large-scale production of recombinant Der f 10 allergen for diagnostic and therapeutic agents. PMID:23427671

Cui, Yubao; Zhou, Ying; Wang, Yungang; Ma, Guifang; Yang, Li



Improving the affinity of naphthalene diimide ligand to telomeric DNA by incorporating Zn²? ions into its dipicolylamine groups.  


N,N'-bis[3-[3-(2,2'-dipicolyl)methylaminopropyl]-methylaminopropyl]naphthalene-1,4,5,8-tetracarboxylic acid diimide, 1, and its complex with zinc ions, 2, were investigated against telomeric sequences, [TAGGG(TTAGGG)(3)] and [AGGG(TTAGGG)(3)], which reveal different G-quadruplex structures depending on the conditions. Spectrophotometric, SPR, and CD techniques revealed that both ligands showed large binding constants to hybrid-type G-quadruplexes formed in the presence of K(+) ions. Moreover, 2 revealed higher affinity to investigated oligonucleotides suggesting that complex of naphthalene diimide derivative with Zn(2+), comparing to 1, provided additional electrostatic or coordination interactions between positively charged zinc ions and condensed negative charged phosphate anions from G4 DNA. PMID:23021342

Czerwinska, Izabella; Sato, Shinobu; Takenaka, Shigeori



DNA Macrorestriction Analysis of Nontypeable Group B Streptococcal Isolates: Clonal Evolution of Nontypeable and Type V Isolates  

PubMed Central

Group B streptococci (GBS) are serotyped according to capsular polysaccharide (CPS) type (Ia to VIII); an isolate is classified as nontypeable (NT) if no detectable CPS is found. Surface-localized protein antigens (?, ?, R1, and R4) serve as additional markers to classify GBS isolates, which is particularly useful since NT isolates often express one or more of these proteins. To compare genetic resemblance among isolates with similar protein profiles, we studied 58 NT isolates digested with the SmaI macrorestriction enzyme prior to pulsed-field gel electrophoresis (PFGE). Of these 58, 15.5% expressed ? only, 20.7% expressed ?+?, 15.5% expressed R4, and 25.8% expressed R1,R4, while 22.4% of the isolates expressed no detectable proteins. The largest PFGE profile group, with 48% of the isolates, was group 4, composed primarily of isolates that expressed R1,R4 or no proteins. The second most common profiles were 3 and 32, each with 13.8% of the isolates. Since NT isolates in profile group 4 were highly related to type V isolates, as demonstrated by PFGE profiles, we investigated 45 type V isolates. Two-thirds of the type V isolates within profile group 4 were classified into subgroup 4a, compared to 28.2% of 39 NT isolates. Only 11% of the V/R1,R4 isolates were identical to the prototype group 4 profile, in contrast to 75% of the NT/R1,R4 isolates. A shift of type V isolates into profile 4 subgroups may be indicative of a genetic change over time. PFGE is a valuable approach for comparison of GBS isolate relatedness and for monitoring of NT and typeable GBS isolates for potential clonal divergence.

Amundson, Nicole R.; Flores, Aurea E.; Hillier, Sharon L.; Baker, Carol J.; Ferrieri, Patricia



Translocation of Cockayne syndrome group A protein to the nuclear matrix: Possible relevance to transcription-coupled DNA repair  

Microsoft Academic Search

Transcription-coupled repair (TCR) efficiently removes a variety of lesions from the transcribed strand of active genes. By allowing rapid resumption of RNA synthesis, the process is of major importance for cellular resistance to transcription-blocking genotoxic damage. Mutations in the Cockayne syndrome group A or B (CSA or CSB) gene result in defective TCR. However, the exact mechanism of TCR in

Shinya Kamiuchi; Masafumi Saijo; Elisabetta Citterio; Martijn de Jager; Jan H. J. Hoeijmakers; Kiyoji Tanaka



The bcr1 DNA Repeat Element Is Specific to the Bacillus cereus Group and Exhibits Mobile Element Characteristics  

PubMed Central

Bacillus cereus strains ATCC 10987 and ATCC 14579 harbor a ?155-bp repeated element, bcr1, which is conserved in B. cereus, B. anthracis, B. thuringiensis, and B. mycoides but not in B. subtilis and B. licheniformis. In this study, we show by Southern blot hybridizations that bcr1 is present in all 54 B. cereus group strains tested but absent in 11 Bacillus strains outside the group, suggesting that bcr1 may be specific and ubiquitous to the B. cereus group. By comparative analysis of the complete genome sequences of B. cereus ATCC 10987, B. cereus ATCC 14579, and B. anthracis Ames, we show that bcr1 is exclusively present in the chromosome but absent from large plasmids carried by these strains and that the numbers of full-length bcr1 repeats for these strains are 79, 54, and 12, respectively. Numerous copies of partial bcr1 elements are also present in the three genomes (91, 128, and 53, respectively). Furthermore, the genomic localization of bcr1 is not conserved between strains with respect to chromosomal position or organization of gene neighbors, as only six full-length bcr1 loci are common to at least two of the three strains. However, the intergenic sequence surrounding a specific bcr1 repeat in one of the three strains is generally strongly conserved in the other two, even in loci where bcr1 is found exclusively in one strain. This finding indicates that bcr1 either has evolved by differential deletion from a very high number of repeats in a common ancestor to the B. cereus group or is moving around the chromosome. The identification of bcr1 repeats interrupting genes in B. cereus ATCC 10987 and ATCC 14579 and the presence of a flanking TTTAT motif in each end show that bcr1 exhibits features characteristic of a mobile element.

?kstad, Ole Andreas; Tourasse, Nicolas J.; Stabell, Fredrik B.; Sundfaer, Cathrine K.; Egge-Jacobsen, Wolfgang; Ris?en, Per Arne; Read, Timothy D.; Kolst?, Anne-Brit



Critical Effect of the N2 Amino Group on Structure, Dynamics, and Elasticity of DNA Polypurine Tracts  

Microsoft Academic Search

Unrestrained 5–20-ns explicit-solvent molecular dynamics simulations using the Cornell et al. force field have been carried out for d[GCG(N)11GCG]2 (N, purine base) considering guanine·cytosine (G·C), adenine·thymine (A·T), inosine·5-methyl-cytosine (I·mC), and 2-amino-adenine·thymine (D·T) basepairs. The simulations unambiguously show that the structure and elasticity of N-tracts is primarily determined by the presence of the amino group in the minor groove. Simulated A-,

Filip Lankaš; Thomas E. Cheatham III; Nad’a Špa?áková; Pavel Hobza; Jörg Langowski; Ji?í Šponer



Data mining of RNA expression and DNA genotype data: presentation group 5 contributions to Genetic Analysis Workshop 15.  


The complexity of data available in human genetics continues to grow at an explosive rate. With that growth, the challenges to understanding the meaning of the underlying information also grow. A currently popular approach to dissecting such information falls under the broad category of data mining. This can apply to any approach that tries to extract relevant information from large amounts of data, but often refers to methods that deal, in a non-linear fashion, with very large numbers of variables that cannot be simultaneously handled by more conventional statistical methods. To explore the usefulness of some of these approaches, 13 groups applied a variety of strategies to the first dataset provided to GAW 15 participants. With the extensive microarray and SNP data provided for 14 CEPH families, these groups explored multistage analyses, machine learning methods, network construction, and other techniques to try to answer questions about gene-gene interaction, functional similarities, co-regulated gene expression and the mapping of gene expression determinants, among others. In general, the methods offered strategies to provide a better understanding of the complex pathways involved in gene expression and function. These are still "works in progress," often exploratory in nature, but they provide insights into ways in which the data might be interpreted. Despite the still preliminary nature of some of these methods and the diversity of the approaches, some common themes emerged. The collection of papers and methods offer a starting point for further exploration of complex interactions in human genetic data now readily available. PMID:18046764

Falk, Catherine T; Finch, Stephen J; Kim, Wonkuk; Mukhopadhyay, Nitai D; Gong, Binsheng; Hinrichs, Anthony; Li, Xia; Liu, Xing; Malhotra, Alka; Mehta, Tapan; Page, Grier; Rao, Shaoqi; Saccone, Nancy; Shete, Sanjay; Yang, Yang; Yu, Robert; Zhao, Jing Hua; Zhou, Xiaojun



High-Mobility Group 1/2 Proteins Are Essential for Initiating Rolling-Circle-Type DNA Replication at a Parvovirus Hairpin Origin  

PubMed Central

Rolling-circle replication is initiated by a replicon-encoded endonuclease which introduces a single-strand nick into specific origin sequences, becoming covalently attached to the 5? end of the DNA at the nick and providing a 3? hydroxyl to prime unidirectional, leading-strand synthesis. Parvoviruses, such as minute virus of mice (MVM), have adapted this mechanism to amplify their linear single-stranded genomes by using hairpin telomeres which sequentially unfold and refold to shuttle the replication fork back and forth along the genome, creating a continuous, multimeric DNA strand. The viral initiator protein, NS1, then excises individual genomes from this continuum by nicking and reinitiating synthesis at specific origins present within the hairpin sequences. Using in vitro assays to study ATP-dependent initiation within the right-hand (5?) MVM hairpin, we have characterized a HeLa cell factor which is absolutely required to allow NS1 to nick this origin. Unlike parvovirus initiation factor (PIF), the cellular complex which activates NS1 endonuclease activity at the left-hand (3?) viral origin, the host factor which activates the right-hand hairpin elutes from phosphocellulose in high salt, has a molecular mass of around 25 kDa, and appears to bind preferentially to structured DNA, suggesting that it might be a member of the high-mobility group 1/2 (HMG1/2) protein family. This prediction was confirmed by showing that purified calf thymus HMG1 and recombinant human HMG1 or murine HMG2 could each substitute for the HeLa factor, activating the NS1 endonuclease in an origin-specific nicking reaction.

Cotmore, Susan F.; Tattersall, Peter



Synthesis and structure of a new tetracopper(II) complex bridged both by oxamido and phenolato groups: Cytotoxic activity, and reactivity towards DNA and BSA  

NASA Astrophysics Data System (ADS)

A new tetracopper(II) complex bridged both by oxamido and phenolato groups, namely [Cu4(chmpoxd)2(dabt)2](ClO4)2, where H3chmpoxd and dabt stand for N-(5-chloro-2-hydroxyl-phenyl)-N?-[3-(methylamino)propyl]oxamide and 2,2?-diamino-4,4?-bithiazole, respectively, has been synthesized and characterized by elemental analyses, molar conductance measurements, IR and electronic spectra studies, and single-crystal X-ray diffraction. The crystal structure reveals a centrosymmetric circular tetranuclear cation [Cu4(chmpoxd)2(dabt)2]2+ assembled by a pair of cis-oxamido-bridged bicopper(II) units via ?2-phenolato bridges, in which one copper(II) atom is located in a slightly distorted square-planar environment, while the other is in a square-pyramidal geometry. The Cu\\ctdot Cu separations through the oxamido and the phenolato bridges are 5.2217(12) and 3.7042(11) Å, respectively. In vitro cytotoxicity experiment shows that the tetracopper(II) complex exhibits cytotoxic activity against the SMMC7721 and A549 cell lines. The reactivities towards HS-DNA and protein BSA revealed that the tetracopper(II) complex can interact with HS-DNA in the mode of intercalation, and the complex binds to BSA responsible for quenching of tryptophan fluorescence by static quenching mechanism.

Xu, Xiao-Wen; Li, Xue-Jie; Zhan, Shu-Hui; Li, Yan-Tuan; Wu, Zhi-Yong; Yan, Cui-Wei



Correction of xeroderma pigmentosum complementation group D mutant cell phenotypes by chromosome and gene transfer: Involvement of the human ERCC2 DNA repair gene  

SciTech Connect

Cultured cells from individuals afflicted with the genetically heterogeneous autosomal recessive disorder xeroderma pigmentosum (XP) exhibit sensitivity to UV radiation and defective nucleotide excision repair. Complementation of these mutant phenotypes after the introduction of single human chromosomes from repair-proficient cells into XP cells has provided a means of mapping the genes involved in this disease. The authors now report the phenotypic correction of XP cells from genetic complementation group D (XP-D) by a single human chromosome designated Tneo. Detailed molecular characterization of Tneo revealed a rearranged structure involving human chromosomes 16 and 19, including the excision repair cross-complementing 2 (ERCC2) gene from the previously described human DNA repair gene cluster at 19q13.2-q13.3. Direct transfer of a cosmid bearing the ERCC2 gene conferred UV resistance to XP-D cells.

Flejter, W.L.; McDaniel, L.D.; Johns, D.; Schultz, R.A. (Univ. of Maryland, Baltimore (United States)); Friedberg, E.C. (Univ. of Texas, Dallas (United States))



Broad and Cross-Clade CD4+ T-Cell Responses Elicited by a DNA Vaccine Encoding Highly Conserved and Promiscuous HIV-1 M-Group Consensus Peptides  

PubMed Central

T-cell based vaccine approaches have emerged to counteract HIV-1/AIDS. Broad, polyfunctional and cytotoxic CD4+ T-cell responses have been associated with control of HIV-1 replication, which supports the inclusion of CD4+ T-cell epitopes in vaccines. A successful HIV-1 vaccine should also be designed to overcome viral genetic diversity and be able to confer immunity in a high proportion of immunized individuals from a diverse HLA-bearing population. In this study, we rationally designed a multiepitopic DNA vaccine in order to elicit broad and cross-clade CD4+ T-cell responses against highly conserved and promiscuous peptides from the HIV-1 M-group consensus sequence. We identified 27 conserved, multiple HLA-DR-binding peptides in the HIV-1 M-group consensus sequences of Gag, Pol, Nef, Vif, Vpr, Rev and Vpu using the TEPITOPE algorithm. The peptides bound in vitro to an average of 12 out of the 17 tested HLA-DR molecules and also to several molecules such as HLA-DP, -DQ and murine IAb and IAd. Sixteen out of the 27 peptides were recognized by PBMC from patients infected with different HIV-1 variants and 72% of such patients recognized at least 1 peptide. Immunization with a DNA vaccine (HIVBr27) encoding the identified peptides elicited IFN-? secretion against 11 out of the 27 peptides in BALB/c mice; CD4+ and CD8+ T-cell proliferation was observed against 8 and 6 peptides, respectively. HIVBr27 immunization elicited cross-clade T-cell responses against several HIV-1 peptide variants. Polyfunctional CD4+ and CD8+ T cells, able to simultaneously proliferate and produce IFN-? and TNF-?, were also observed. This vaccine concept may cope with HIV-1 genetic diversity as well as provide increased population coverage, which are desirable features for an efficacious strategy against HIV-1/AIDS.

Almeida, Rafael Ribeiro; Rosa, Daniela Santoro; Ribeiro, Susan Pereira; Santana, Vinicius Canato; Kallas, Esper Georges; Sidney, John; Sette, Alessandro; Kalil, Jorge; Cunha-Neto, Edecio



Redox-mediated Mechanisms Regulate DNA Binding Activity of the G-group of Basic Region Leucine Zipper (bZIP) Transcription Factors in Arabidopsis*  

PubMed Central

Plant genes that contain the G-box in their promoters are responsive to a variety of environmental stimuli. Bioinformatics analysis of transcriptome data revealed that the G-box element is significantly enriched in promoters of high light-responsive genes. From nuclear extracts of high light-treated Arabidopsis plants, we identified the AtbZIP16 transcription factor as a component binding to the G-box-containing promoter fragment of light-harvesting chlorophyll a/b-binding protein2.4 (LHCB2.4). AtbZIP16 belongs to the G-group of Arabidopsis basic region leucine zipper (bZIP) type transcription factors. Although AtbZIP16 and its close homologues AtbZIP68 and AtGBF1 bind the G-box, they do not bind the mutated half-sites of the G-box palindrome. In addition, AtbZIP16 interacts with AtbZIP68 and AtGBF1 in the yeast two-hybrid system. A conserved Cys residue was shown to be necessary for redox regulation and enhancement of DNA binding activity in all three proteins. Furthermore, transgenic Arabidopsis lines overexpressing the wild type version of bZIP16 and T-DNA insertion mutants for bZIP68 and GBF1 demonstrated impaired regulation of LHCB2.4 expression. Finally, overexpression lines for the mutated Cys variant of bZIP16 provided support for the biological significance of Cys330 in redox regulation of gene expression. Thus, our results suggest that environmentally induced changes in the redox state regulate the activity of members of the G-group of bZIP transcription factors.

Shaikhali, Jehad; Noren, Louise; de Dios Barajas-Lopez, Juan; Srivastava, Vaibhav; Konig, Janine; Sauer, Uwe H.; Wingsle, Gunnar; Dietz, Karl-Josef; Strand, ?sa



Sequence polymorphisms of mtDNA HV1, HV2 and HV3 regions in eight population groups living in Taiwan  

Microsoft Academic Search

Analysis of human mitochondrial DNA (mtDNA) polymorphisms in the D-loop region has become a useful tool in forensic casework and matrilineal origin research. In this study, the mtDNA D-loop region including hypervariable region 1 (HV1), hypervariable region 2 (HV2), segment between HV1 and HV2 (7S DNA spanned region), and extended hypervariable region 3 (HV3ex) was sequenced in 539 unrelated individuals

Hsiao-Lin Hwa; Tsang-Ming Ko; Yen-Ching Chen; Chun-Yen Lin; Yu-Hsuan Huang; Li-Hui Tseng; Yi-Ning Su; James Chun-I Lee



DNA Sequencing Research Group (DSRG): Evaluation of RNA Amplification Kits at Subnanogram Input Amounts of Total RNA for RNA-Seq  

PubMed Central

Multiple recent publications on RNA-Seq have demonstrated the power of next generation sequencing technologies in whole transcriptome analysis. The vendor specific protocols used for RNA library construction typically require at least 100ng of total RNA. However, under certain conditions such as single cells, stem cells, difficult to isolate cell types, or fractionated cancer cells, only a small amount of material is available. In these cases, effective transcriptome profiling requires amplification of subnanogram amounts of RNA. Several RNA amplification kits are available for amplification prior to library construction and next generation sequencing but these kits have not been comprehensively field evaluated for accuracy and performance of RNA-Seq for picogram amounts of RNA. This study conducted by the DNA Sequencing Research Group (DSRG) focuses on the evaluation of amplification kits for RNA-Seq. Four commercial amplification kits were chosen: Ovation v2 (NuGEN Technologies), SMARTer (Clontech), Seqplex (Sigma Aldrich), and Super-AMP (Miltenyi Biotech). Starting material was 5ng, 500pg and 50pg of human total reference RNA (Clontech) spiked with Ambion ERCC control mix (Life Technologies) following the manufacturer's protocol. Each kit was tested at 3 different sites to assess reproducibility. Total RNA and ERCC RNA spike-in control mixes from the same lots were sent to 12 ABRF lab sites for amplification and cDNA generation. Ideally, this would have resulted in 36 different amplified samples, 3 from each input RNA. Libraries were constructed at one site from the amplified cDNAs using the TruSeq RNA library preparation kit on the Tecan Freedom EVO Liquid Handling Robot. As an unamplified control, ribosomal depletion and PolyA selection were performed separately using 5ng, 100ng and 1ug of total RNA prior to library construction. All libraries were pooled and sequenced using the Illumina HiSeq platform. An overview of the study and the results will be presented.

Nicolet, Charles; Paulson, Ariel; Shanker, Savita; Beckloff, N.; Bintzler, D.; Bivens, N. J.; Davis, R. R.; Donnelly, R. J.; Edenberg, H. J.; Gillaspy, A. F.; Grove, D.; Jafari, N.; Kerley-Hamilton, J. S.; Lashley, K.; Lyons, R. H.; Peak, A.; Perera, A.; Thimmapuram, J.; Wang, L.; Wright, C. L.; Alekseyev, Y.



Genetic variation in DNA-repair pathways and response to radiochemotherapy in esophageal adenocarcinoma: a retrospective cohort study of the Eastern Cooperative Oncology Group  

PubMed Central

Background Recent data in esophageal cancer suggests the variant allele of a single-nucleotide polymorphism (SNP) in XRCC1 may be associated with resistance to radiochemotherapy. However, this SNP has not been assessed in a histologically homogeneous clinical trial cohort that has been treated with a uniform approach. In addition, whether germline DNA may serve as a surrogate for tumor genotype at this locus is unknown in this disease. Our objective was to assess this SNP in relation to the pathologic complete response (pCR) rate in subjects with esophageal adenocarcinoma who received cisplatin-based preoperative radiochemotherapy in a multicenter clinical trial (Eastern Cooperative Oncology Group 1201). As a secondary aim, we investigated the rate of allelic imbalance between germline and tumor DNA. Methods Eighty-one eligible treatment-naïve subjects with newly diagnosed resectable esophageal adenocarcinoma received radiotherapy (45 Gy) concurrent with cisplatin-based chemotherapy, with planned subsequent surgical resection. The primary endpoint was pCR, defined as complete absence of tumor in the surgical specimen after radiochemotherapy. Using germline DNA from 60 subjects, we examined the base-excision repair SNP, XRCC1 Arg399Gln, and 4 other SNPs in nucleotide excision (XPD Lys751Gln and Asp312Asn, ERCC1 3' flank) and double-stranded break (XRCC2 5' flank) repair pathways, and correlated genotype with pCR rate. Paired tumor tissue was used to estimate the frequency of allelic imbalance at the XRCC1 SNP. Results The variant allele of the XRCC1 SNP (399Gln) was detected in 52% of subjects. Only 6% of subjects with the variant allele experienced a pCR, compared to 28% of subjects without the variant allele (odds ratio 5.37 for failing to achieve pCR, p = 0.062). Allelic imbalance at this locus was found in only 10% of informative subjects, suggesting that germline genotype may reflect tumor genotype at this locus. No significant association with pCR was noted for other SNPs. Conclusions Assessed for the first time in a prospective, interventional trial cohort of esophageal adenocarcinoma, XRCC1 399Gln was associated with resistance to radiochemotherapy. Further investigation of this genetic variation is warranted in larger cohorts. In addition, these data indicate that germline genotype may serve as a surrogate for tumor genotype at this locus.



A pteridine derivative with electron-withdrawing groups for binding and sensing of nucleobases in AP site-containing DNA duplexes.  


A pteridine derivative having electron-withdrawing CF(3) groups, 2-amino-6,7-bis(trifluoromethyl)-4-hydoroxypteridine (2CF(3)-pteridine), is presented as a candidate for multi-functional fluorescent ligand for single-nucleotide polymorphisms (SNPs) typing. In solutions buffered to pH 8.0 (I = 0.1 M, at 5 degrees C), 2CF(3)- pteridine can bind to guanine, cytosine and thymine opposite an abasic site in DNA duplexes (5'-TCTGC GTCCA GXG CAACGCACAC-3'/3'-AGACG CAGGT CNC GTTGCGTGTG-5', X = abasic site; Spacer-C3, N = G, C, A, T). For these three nucleobases, the binding of 2CF(3)-pteridine is explained by 1:1 complexation, and the binding affinities are comparable (K(11) / 10(5) M(-1): G: 3.0; C: 1.6; T: 3.3). Binding-induced fluorescence responses are effectively different between guanine and pyrimidines (C, T): the binding to pyrimidines is accompanied by a significant change in the shape of fluorescence spectra. These binding and sensing properties allow a detection of G/T or G/C mutation based on a single fluorescence ligand. PMID:18776280

Kanai, Eriko; Nishizawa, Seiichi; Teramae, Norio



Mucosal Immunization with High-Mobility Group Box 1 in Chitosan Enhances DNA Vaccine-Induced Protection against Coxsackievirus B3-Induced Myocarditis.  


Coxsackievirus B3 (CVB3), a small single-stranded RNA virus, belongs to the Picornaviridae family. Its infection is the most common cause of myocarditis, with no vaccine available. Gastrointestinal mucosa is the major entry port for CVB3; therefore, the induction of local immunity in mucosal tissues may help control initial viral infections and alleviate subsequent myocardial injury. Here we evaluated the ability of high-mobility group box 1 (HMGB1) encapsulated in chitosan particles to enhance the mucosal immune responses induced by the CVB3-specific mucosal DNA vaccine chitosan-pVP1. Mice were intranasally coimmunized with 4 doses of chitosan-pHMGB1 and chitosan-pVP1 plasmids, at 2-week intervals, and were challenged with CVB3 4 weeks after the last immunization. Compared with chitosan-pVP1 immunization alone, coimmunization with chitosan-pHMGB1 significantly (P < 0.05) enhanced CVB3-specific fecal secretory IgA levels and promoted mucosal T cell immune responses. In accordance, reduced severity of myocarditis was observed in coimmunized mice, as evidenced by significantly (P < 0.05) reduced viral loads, decreased myocardial injury, and increased survival rates. Flow cytometric analysis indicated that HMGB1 enhanced dendritic cell (DC) recruitment to mesenteric lymph nodes and promoted DC maturation, which might partly account for its mucosal adjuvant effect. This strategy may represent a promising approach to candidate vaccines against CVB3-induced myocarditis. PMID:24027262

Wang, Maowei; Yue, Yan; Dong, Chunsheng; Li, Xiaoyun; Xu, Wei; Xiong, Sidong



Efficient rejoining of radiation-induced DNA double-strand breaks in vertebrate cells deficient in genes of the RAD52 epistasis group  

Microsoft Academic Search

Rejoining of ionizing radiation (IR) induced DNA DSBs usually follows biphasic kinetics with a fast (t50: 5–30 min) component attributed to DNA-PK-dependent non-homologous endjoining (NHEJ) and a slow (t50: 1–20 h), as of yet uncharacterized, component. To examine whether homologous recombination (HR) contributes to DNA DSB rejoining, a systematic genetic study was undertaken using the hyper-recombinogenic DT40 chicken cell line

Huichen Wang; Zhao-Chong Zeng; Tu-Anh Bui; Eiichiro Sonoda; Minoru Takata; Shunichi Takeda; George Iliakis



DNA sequencing and gene expression of the emm gene cluster in an M50 group A streptococcus strain virulent for mice.  


The strain B514, an M serotype 50 strain, is capable of causing a natural upper respiratory infection leading to death in mice, as reported by Hook et al. in 1960 (E. W. Hook, R. R. Wagner, and R. C. Lancefield, Am. J. Hyg. 72:111-119, 1960). Thus, this strain was of interest for use in developing an animal model for group A streptococcal colonization and disease. The emm gene cluster for this strain was examined by PCR mapping and found to contain three emm family genes and cluster pattern 5. PCR-generated fragments corresponding to the SF4 (mrp50), SF2 (emmL50), and SF3 (enn50) genes were cloned and the entire gene cluster was sequenced. The gene cluster has greater than 97% DNA identity to previously sequenced regions of the gene cluster of the M2 strain T2/44/RB4 if two small divergent regions that encode the mature amino terminus of the SF-2 and SF-3 gene products are not included. If expressed, the genes encode proteins which bind human immunoglobulin G (Mrp50 and EmmL50) or immunoglobulin A (Enn50). However, in isolates taken directly after passage in mice, the surface proteins arising from these genes were barely detectable. The transcription of each gene in the B514 strain was investigated by Northern (RNA) hybridization, and mRNA transcripts were detected and quantitated relative to those of the recA gene, a housekeeping gene. Transcription of all three emm family genes was found to be over 30-fold attenuated relative to transcription of the same genes in strain T2/44/RB4. This suggests that the positive regulator, Mga, either is not expressed in this strain or has a different requirement for activation; it also suggests that the capsule may be sufficient to inhibit phagocytosis under these circumstances. PMID:8675326

Yung, D L; Hollingshead, S K



Phosphorus-nitrogen compounds: Part 28. Syntheses, structural characterizations, antimicrobial and cytotoxic activities, and DNA interactions of new phosphazenes bearing vanillinato and pendant ferrocenyl groups  

NASA Astrophysics Data System (ADS)

The gradually Cl replacement reactions of spirocyclic mono (1 and 2) and bisferrocenyl cyclotriphosphazenes (3-5) with the potassium salt of 4-hydroxy-3-methoxybenzaldehyde (potassium vanillinate) gave mono (1a-5a), geminal (gem-1b-5b), non-geminal (cis-1b, cis-5b and trans-2b-5b), tri (1c-5c) and tetra-substituted phosphazenes (1d-5d). Some phosphazenes have stereogenic P-center(s). The chirality of 4c was verified using chiral HPLC column. Electrochemical behaviors were influenced only by the number of ferrocene groups, but not the length of the amine chains and the substituent(s). The structures of the new phosphazenes were determined by FTIR, MS, 1H, 13C and 31P NMR, HSQC and HMBC spectral data. The solid-state structures of cis-1b and 4d were examined by single crystal X-ray diffraction techniques. The twelve phosphazene derivatives were screened for antimicrobial activity and the compounds 5a, cis-1b and 2c exhibited the highest antibacterial activity against G(+) and G(-) bacteria. In addition, it was found that overall gem-1b inhibited the growth of Mycobacterium tuberculosis. The compounds 1d, 2d and 4d were tested in HeLa cancer cell lines. Among these compounds, 2d had cytotoxic effect on HeLa cell in the first 48 h. Moreover, interactions between compounds 2a, gem-1b, gem-2b, cis-1b, 2c, 3c, 4c, 5c, 1d, 2d and 4d, and pBR322 plasmid DNA were investigated.

Tümer, Yasemin; Asmafiliz, Nuran; K?l?ç, Zeynel; Hökelek, Tuncer; Yasemin Koç, L.; Aç?k, Leyla; Yola, Mehmet Lütfi; Solak, Ali Osman; Öner, Ya?mur; Dündar, Devrim; Yavuz, Makbule



Incorporation of reporter molecule-labeled nucleotides by DNA polymerases. I. Chemical synthesis of various reporter group-labeled 2'-deoxyribonucleoside-5'-triphosphates  

Microsoft Academic Search

Fluorescent-labeled DNA is generated through enzy- matic incorporation of fluorophore-linked 2¢-deoxy- ribonucleoside-5¢-triphosphates (dNTPs) by DNA polymerases. We describe the synthesis of a variety of dye-labeled dNTPs. Amino-linker-modified 5¢-tri- phosphates of all four naturally occurring nucleo- bases were used as precursors. Commercially available dyes were coupled to the amino function of the side chain. In addition, we attached novel fluorophore derivatives.

Gerald Giller; Taurai Tasara; Bernhard Angerer; Klaus Muhlegger; Mario Amacker; Holger Winter



Performance characteristics and utilization of rapid antigen test, DNA probe, and culture for detection of group a streptococci in an acute care clinic.  


Group A streptococcus (GAS) antigen testing has become a routine point-of-care (POC) test in acute care settings. Concern about performance parameters (PP) of these tests as well as inappropriate antibiotic use has resulted in various recommendations regarding diagnosis of GAS. There were two objectives in this study. The first was to evaluate the rapid GAS antigen test presently in use (Thermo BioStar, Boulder, Colo.) and the GAS Direct probe test (Gen-Probe, San Diego, Calif.) compared to culture. The second was to define the optimal use of these technologies in a large acute care pediatric clinic. A total of 520 consecutive pediatric patients presenting with symptoms of pharyngitis at any of three Lahey Clinic acute care facilities were evaluated. Pharyngeal specimens were collected using a double-swab collection device (Copan, Corona, Calif.). One swab was used for the antigen test, the second was used for the probe test, and the pledget was placed in the collection device for culture on 5% sheep blood agar, incubated for 48 h anaerobically, and subsequently placed in Todd-Hewitt broth. After discrepant analysis, sensitivity, specificity, and positive and negative predictive values were as follows: 94.8, 100, 100, and 96.9% for the probe test and 86.1, 97.1, 93.7, and 93.4% for the antigen test, respectively. Sensitivity using an enhanced culture technique was 99.4% (163 of 164). False-positive (FP) antigen results were often seen from patients previously diagnosed and/or treated for GAS. No FP results were seen with the probe test. Colony counts for the false-negative (FN) antigen tests were higher than those for the FN probe tests. Compared to culture and DNA probe, the rapid antigen test (RAT) offered a result at the time of the patient's visit, with acceptable PP when prevalence of disease is high. Follow-up testing with the RAT of GAS patients who previously tested as positive should be avoided due to increased FP results. The probe test was comparable to culture in performance. Results indicate the probe test can be used as the primary test or as a backup to negative antigen tests. The probe test offers the advantage over culture of same-day reporting of a final result but, in contrast to a POC test, necessitates follow-up communication to the patient. Preliminary data show the specificity of the probe test to be greater than that of the RAT for patients previously diagnosed with GAS. PMID:12409399

Chapin, Kimberle C; Blake, Patricia; Wilson, Claire D



Unique grouping of the Far East Asian begomovirus complex based on sequence analyses of the DNA-A genome and associated DNAbeta satellite molecules isolated from tomato, honeysuckle and Eupatorium plants in Japan.  


Nucleotide (nt) sequencing has contributed to the identification of virus species and has also proved diagnostically useful in the control of tomato-infecting begomoviruses disease. We determined the complete nt sequences of the DNA-A genome and its cognate DNAbeta satellite molecules in isolates of Tobacco leaf curl Japan virus, Honeysuckle yellow vein mosaic virus, Eupatorium yellow vein virus in Japan. Pairwise comparison analyses based on the nt sequences of DNA-A from the genetic group of these viruses tentatively named as TbLCJV, HYVMV and EpYVV (TbJV/HYV/EpV) revealed that this group had a significance threshold of 84 % identity. Phylogenetic relationship analyses of the nt sequences of DNA-A and DNAbeta revealed that their isolates were separated into a discrete Far East Asian clade, distinct from all other begomoviruses. This clade was divided into two distinct clusters comprising the subgroups TbJV/HYV and EpV. Furthermore, recombination analysis revealed that members of the TbJV/HYV/EpV group had the genetic variation indicative of many recombination events. Our study demonstrates that this group forms a unique species complex, but that members have discrete lineages depending on their natural perennial host plants. PMID:18175045

Ueda, S; Onuki, M; Hanada, K; Takanami, Y



T Cell Activation Markers and African Mitochondrial DNA Haplogroups among Non-Hispanic Black Participants in AIDS Clinical Trials Group Study 384  

PubMed Central

Introduction Mitochondrial function influences T cell dynamics and is affected by mitochondrial DNA (mtDNA) variation. We previously reported an association between African mtDNA haplogroup L2 and less robust CD4 cell recovery on antiretroviral therapy (ART) in non-Hispanic black ACTG 384 subjects. We explored whether additional T cell parameters in this cohort differed by mtDNA haplogroup. Methods ACTG 384 randomized ART-naïve subjects to two different nucleoside regimens with efavirenz, nelfinavir, or both. CD4 and CD8 memory and activation markers were available at baseline and week 48 on most subjects. mtDNA sequencing was performed on whole blood DNA, and haplogroups were determined. We studied non-Hispanic black subjects with HIV RNA <400 copies/mL at week 48. Analyses included Wilcoxon ranksum test and linear regression. Results Data from 104 subjects were included. Major African mtDNA haplogroups included L1 (N?=?25), L2 (N?=?31), and L3 (N?=?32). Baseline age, HIV RNA, and CD4 cells did not differ between L2 and non-L2 haplogroups. Compared to non-L2 haplogroups, L2 subjects had lower baseline activated CD4 cells (median 12% vs. 17%; p?=?0.03) and tended toward lower activated CD8 cells (41% vs. 47%; p?=?0.06). At 48 weeks of ART, L2 subjects had smaller decreases in activated CD4 cells (?4% vs. ?11%; p?=?0.01), and smaller CD4 cell increases (+95 vs. +178; p?=?0.002). In models adjusting for baseline age, CD4 cells, HIV RNA, and naïve-to-memory CD4 cell ratio, haplogroup L2 was associated with lower baseline (p?=?0.04) and 48-week change in (p?=?0.01) activated CD4 cells. Conclusions Among ART-naïve non-Hispanic blacks, mtDNA haplogroup L2 was associated with baseline and 48-week change in T cell activation, and poorer CD4 cell recovery. These data suggest mtDNA variation may influence CD4 T cell dynamics by modulating T cell activation. Further study is needed to replicate these associations and identify mechanisms.

Hulgan, Todd; Robbins, Gregory K.; Kalams, Spyros A.; Samuels, David C.; Grady, Benjamin; Shafer, Robert; Murdock, Deborah G.; Selph, Doug; Haas, David W.; Pollard, Richard B.; De Gruttola, Victor; Snyder, Sally; Nevin, Thomas; Pettinelli, Carla; Dube, Michael; Fischl, Margaret; Delaphna, Robert; Gideon, Linda; D’Aquila, Richard; Vella, Stefano; Merigan, Thomas; Hirsch, Martin



I-PfoP3I: A Novel Nicking HNH Homing Endonuclease Encoded in the Group I Intron of the DNA Polymerase Gene in Phormidium foveolarum Phage Pf-WMP3  

PubMed Central

Homing endonucleases encoded in a group I self-splicing intron in a protein-coding gene in cyanophage genomes have not been reported, apart from some free-standing homing edonucleases. In this study, a nicking DNA endonuclease, I-PfoP3I, encoded in a group IA2 intron in the DNA polymerase gene of a T7-like cyanophage Pf-WMP3, which infects the freshwater cyanobacterium Phormidium foveolarum is described. The Pf-WMP3 intron splices efficiently in vivo and self-splices in vitro simultaneously during transcription. I-PfoP3I belongs to the HNH family with an unconventional C-terminal HNH motif. I-PfoP3I nicks the intron-minus Pf-WMP3 DNA polymerase gene more efficiently than the Pf-WMP4 DNA polymerase gene that lacks any intervening sequence in vitro, indicating the variable capacity of I-PfoP3I. I-PfoP3I cleaves 4 nt upstream of the intron insertion site on the coding strand of EXON 1 on both intron-minus Pf-WMP3 and Pf-WMP4 DNA polymerase genes. Using an in vitro cleavage assay and scanning deletion mutants of the intronless target site, the minimal recognition site was determined to be a 14 bp region downstream of the cut site. I-PfoP3I requires Mg2+, Ca2+ or Mn2+ for nicking activity. Phylogenetic analysis suggests that the intron and homing endonuclease gene elements might be inserted in Pf-WMP3 genome individually after differentiation from Pf-WMP4. To our knowledge, this is the first report of the presence of a group I self-splicing intron encoding a functional homing endonuclease in a protein-coding gene in a cyanophage genome.

Kong, Shuanglei; Liu, Xinyao; Fu, Liwen; Yu, Xiangchun; An, Chengcai



Multiplex PCR assay and phylogenetic analysis of sequences derived from D2 domain of 28S rDNA distinguished members of the Anopheles culicifacies complex into two groups, A/D and B/C/E.  


A multiplex PCR assay was developed using the sequences of the D2 region of 28S ribosomal DNA (rDNA) to discriminate the five members of the Anopheles culicifacies complex provisionally designated as species A, B, C, D and E. Two minus strand primers derived from sequence differences in the D2 variable region and a universal plus strand primer derived from the conserved 28S (rDNA) has delimited five members into species A and D (group 1) and species B, C and E (group 2) in a PCR diagnostic assay. The complete 28S rDNA-D2 region sequence of A. culicifacies sibling species is reported for the first time. Inter-specific sequence divergence was greater than the intra-specific divergence. The phylogenetic relationships inferred from maximum likelihood, maximum parsimony and the neighbor joining analysis confirmed the presence of two unambiguous monophyly clades one consisting of species A and D and the other of species B, C and E and that the A. culicifacies sibling species diverged relatively recently in evolutionary terms despite their considerable differences in bionomics. PMID:19138765

Raghavendra, K; Cornel, Anthony J; Reddy, B P Niranjan; Collins, Frank H; Nanda, Nutan; Chandra, Dinesh; Verma, Vaishali; Dash, Aditya Prasad; Subbarao, Sarala K



Methylation of histone H3 on lysine 79 associates with a group of replication origins and helps limit DNA replication once per cell cycle.  


Mammalian DNA replication starts at distinct chromosomal sites in a tissue-specific pattern coordinated with transcription, but previous studies have not yet identified a chromatin modification that correlates with the initiation of DNA replication at particular genomic locations. Here we report that a distinct fraction of replication initiation sites in the human genome are associated with a high frequency of dimethylation of histone H3 lysine K79 (H3K79Me2). H3K79Me2-containing chromatin exhibited the highest genome-wide enrichment for replication initiation events observed for any chromatin modification examined thus far (23.39% of H3K79Me2 peaks were detected in regions adjacent to replication initiation events). The association of H3K79Me2 with replication initiation sites was independent and not synergistic with other chromatin modifications. H3K79 dimethylation exhibited wider distribution on chromatin during S-phase, but only regions with H3K79 methylation in G1 and G2 were enriched in replication initiation events. H3K79 was dimethylated in a region containing a functional replicator (a DNA sequence capable of initiating DNA replication), but the methylation was not evident in a mutant replicator that could not initiate replication. Depletion of DOT1L, the sole enzyme responsible for H3K79 methylation, triggered limited genomic over-replication although most cells could continue to proliferate and replicate DNA in the absence of methylated H3K79. Thus, prevention of H3K79 methylation might affect regulatory processes that modulate the order and timing of DNA replication. These data are consistent with the hypothesis that dimethylated H3K79 associates with some replication origins and marks replicated chromatin during S-phase to prevent re-replication and preserve genomic stability. PMID:23754963

Fu, Haiqing; Maunakea, Alika K; Martin, Melvenia M; Huang, Liang; Zhang, Ya; Ryan, Michael; Kim, RyangGuk; Lin, Chii Meil; Zhao, Keji; Aladjem, Mirit I



Methylation of Histone H3 on Lysine 79 Associates with a Group of Replication Origins and Helps Limit DNA Replication Once per Cell Cycle  

PubMed Central

Mammalian DNA replication starts at distinct chromosomal sites in a tissue-specific pattern coordinated with transcription, but previous studies have not yet identified a chromatin modification that correlates with the initiation of DNA replication at particular genomic locations. Here we report that a distinct fraction of replication initiation sites in the human genome are associated with a high frequency of dimethylation of histone H3 lysine K79 (H3K79Me2). H3K79Me2-containing chromatin exhibited the highest genome-wide enrichment for replication initiation events observed for any chromatin modification examined thus far (23.39% of H3K79Me2 peaks were detected in regions adjacent to replication initiation events). The association of H3K79Me2 with replication initiation sites was independent and not synergistic with other chromatin modifications. H3K79 dimethylation exhibited wider distribution on chromatin during S-phase, but only regions with H3K79 methylation in G1 and G2 were enriched in replication initiation events. H3K79 was dimethylated in a region containing a functional replicator (a DNA sequence capable of initiating DNA replication), but the methylation was not evident in a mutant replicator that could not initiate replication. Depletion of DOT1L, the sole enzyme responsible for H3K79 methylation, triggered limited genomic over-replication although most cells could continue to proliferate and replicate DNA in the absence of methylated H3K79. Thus, prevention of H3K79 methylation might affect regulatory processes that modulate the order and timing of DNA replication. These data are consistent with the hypothesis that dimethylated H3K79 associates with some replication origins and marks replicated chromatin during S-phase to prevent re-replication and preserve genomic stability.

Fu, Haiqing; Maunakea, Alika K.; Martin, Melvenia M.; Huang, Liang; Zhang, Ya; Ryan, Michael; Kim, RyangGuk; Lin, Chii Meil; Zhao, Keji; Aladjem, Mirit I.



Germ-Line Variants in Methyl-Group Metabolism Genes and Susceptibility to DNA Methylation in Normal Tissues and Human Primary Tumors1  

Microsoft Academic Search

Aberrant DNA methylation is recognized as being a common feature of human neoplasia. CpG island hypermethylation and global genomic hy- pomethylation occur simultaneously in the cancer cell. However, very little is known about the interindividual inherited susceptibility to these epigenetic processes. To address this matter, we have genotyped in 233 cancer patients (with colorectal, breast, or lung tumors), four germ-line

Maria F. Paz; Sonia Avila; Mario F. Fraga; Marina Pollan; Gabriel Capella; Miquel Angel Peinado; Montserrat Sanchez-Cespedes; James G. Herman; Manel Esteller


DNA profiling analysis of 100 consecutive de novo acute myeloid leukemia cases reveals patterns of genomic instability that affect all cytogenetic risk groups  

Microsoft Academic Search

We have carried out a high-resolution whole genome DNA profiling analysis on 100 bone marrow samples from a consecutive series of de novo acute myeloid leukemia (AML) cases. After discarding copy number changes that are known to be genetic polymorphisms, we found that genomic aberrations (GA) in the form of gains or losses of genetic material were present in 74%

J Suela; S Álvarez; F Cifuentes; C Largo; B I Ferreira; D Blesa; M Ardanaz; R García; J A Marquez; M D Odero; M J Calasanz; J C Cigudosa



The effects of linear assembly of two carbazole groups on acid-base and DNA-binding properties of a ruthenium(II) complex  

NASA Astrophysics Data System (ADS)

A novel Ru(II) complex of [Ru(bpy)2(Hbcpip)](ClO4)2 {where bpy = 2,2-bipyridine, Hbcpip = 2-(4-(9H-3,9'-bicarbazol-9-yl)phenyl)-1H-imidazo[4,5-f][1,10]phenanthroline} is synthesized and characterized. Calf-thymus DNA-binding properties of the complex were studied by UV-vis absorption and luminescence titrations, steady-state emission quenching by [Fe(CN)6]4-, DNA competitive binding with ethidium bromide, thermal denaturation and DNA viscosity measurements. The results indicate that the complex partially intercalated into the DNA with a binding constant of (5.5 ± 1.4) × 105 M-1 in buffered 50 mM NaCl. The acid-base properties of the complex were also studied by UV-visible and luminescence spectrophotometric pH titrations, and ground- and excited-state acidity ionization constant values were derived.

Chen, Xi; Xue, Long-Xin; Ju, Chun-Chuan; Wang, Ke-Zhi



A biosensing of Toxoplasma gondii DNA with CdTe/Fe3O4 dual functional quantum dot as reporter group  

NASA Astrophysics Data System (ADS)

Toxoplasma gondii is an intestinal coccidium that parasitizes members of the cat family as definitive hosts and has a wide range of intermediate hosts. Infection is common in many warm-blooded animals, including humans, the early detection of Toxoplasma gondii was concerned in recent years. In the current research, we presented a fast, specific, and sensitive sensing probe to detect Toxoplasma gondii DNA based on mechanism of fluorescence energy transfer (FRET), and a magnetic-fluorescent CdTe/Fe3O4 core-shell quantum dots (mQDs) was utilized as energy donor, and a commercial quencher (BHQ-2) was used as energy acceptor, respectively. The CdTe/Fe3O4 mQDs were prepared by layer-by-layer (LBL) process at ambient temperature. The sensing probe was fabricated through labeling a stem-loop Toxoplasma gondii DNA oligonucleotide with mQDs at the 5' end and BHQ-2 at 3' end, respectively, and the resulting sensing probe can be simply isolated and purified from the reactant with a common magnet. Properties of mQDs and sensing probe were determined by transmission electron microscopy (TEM) and fluorescence spectrum (FS). The TEM data demonstrated that the size of mQDs was ~20nm. the FS data indicated fluorescence intensity (FI) was doubled after the complete complimentary target Toxoplasma gondii DNA was introduced comparing with the FI before addition of target Toxoplasma gondii DNA. Moreover, only weak FI change was observed when the target DNA with one-mismatch base pair was added, this result revealed the sensing probe has high sensitivity and specificity. The current sensing probe will has great potential applications in the life science and related research.

Liang, Chu; Xu, Shichao; Yang, Juan; Zhang, Jimei; Dai, Zhao; Sun, Bo; Sun, Shuqing; Feng, Tielin; Zi, Yan; Liu, Jingwei; Luo, Hao



DNA as nanoscale building blocks.  


The use of DNA as programmable building blocks to achieve highly-definable nanostructures, termed as DNA nanotechnology, has offered great opportunities to control matter at a very small scale. Fast growing researches along this direction has led to the emergence of several significant branches of DNA nanotechnology. This review intends to summarize the recent developments in this area. Several topics will be discussed with a focus on the works from the authors' group, including (1) DNA self-assembly and DNA-directed self-assembly, (2) DNA nanomachines, (3) DNA-based electronics, (4) DNA assisted nanofabrications, and (5) DNA computations. PMID:16430130

Deng, Zhaoxiang; Lee, Seung-Hyun; Mao, Chengde



Investigation of the A1555G mutation in mitochondrial DNA (MT-RNR1) in groups of Brazilian individuals with nonsyndromic deafness and normal-hearing  

PubMed Central

BACKGROUND: Mutations of mitochondrial DNA were described into two genes: The mitochondrially encoded 12S RNA (MT-RNR1) and the mitochondrially encoded tRNA serineucn (MT-TS1). The A1555G mutation in MT-RNR1 gene is a frequent cause of deafness in different countries. AIM: The aim of this work was to investigate the frequency of the A1555G mutation in the MT-RNR1 gene in the mitochondrial DNA in Brazilians individuals with nonsyndromic deafness, and listeners. MATERIALS AND METHODS: DNA samples were submitted to polymerase chain reaction and to posterior digestion with the Hae III enzyme. RESULTS: Seventy eight (78) DNA samples of deaf individuals were analyzed; 75 showed normality in the region investigated, two samples (2.5%) showed the T1291C substitution, which is not related to the cause of deafness, and one sample (1.3%) showed the A1555G mutation. Among the 70 non-impaired individuals no A1555G mutation or T1291C substitution was found. CONCLUSION: We can affirm that A1555G mutation is not prevalent, or it must be very rare in normal-hearing subjects in the State of Paraná, the south region of Brazil. The A1555G mutation frequency (1.3%) found in individual with nonsyndromic deafness is similar to those found in other populations, with nonsyndromic deafness. Consequently, it should be examined in deafness diagnosis. The investigation of the A1555G mutation can contribute towards the determination of the nonsyndromic deafness etiology, hence, contributing to the correct genetic counseling process.

Salomao, Karina Bezerra; Ayo, Christiane Maria; Della-Rosa, Valter Augusto



Report of the European DNA profiling group (EDNAP): an investigation of the complex STR loci D21S11 and HUMFIBRA (FGA)  

Microsoft Academic Search

This paper describes a collaborative exercise which was intended to demonstrate whether uniformity of DNA profiling results could be achieved between European laboratories using two complex short tandem repeat (STR) loci. The loci D21S11 and HUMFIBRA (FGA) were chosen because they are commonly used by different European laboratories. D21S11 has approximately 14 common alleles (f>0.001), whereas HUMFIBRA has 19 common

Peter Gill; E d'Aloja; J Andersen; B Dupuy; M Jangblad; V Johnsson; A. D Kloosterman; A Kratzer; M. V Lareu; M Meldegaard; C Phillips; H Pfitzinger; S Rand; M Sabatier; R Scheithauer; H Schmitter; P Schneider; M. C Vide



Human methionine synthase: cDNA cloning and identification of mutations in patients of the cblG complementation group of folate\\/cobalamin disorders  

Microsoft Academic Search

Methionine synthase catalyzes the remethylation of homocysteine to methionine in a methylcobalamin-depend- ent reaction. We used specific regions of homology within the methionine synthase sequences of several lower organisms to clone a human methionine synthase cDNA by a combination of RT-PCR and inverse PCR. The enzyme is 1265 amino acids in length and contains the seven residue structure-based sequence fingerprint

D. Leclerc; E. Campeau; P. Goyette; C. E. Adjalla; B. Christensen; M. Ross; P. Eydoux; D. S. Rosenblatt; R. Rozen; R. A. Gravel



Plasma Epstein-Barr virus DNA predicts outcome in advanced Hodgkin lymphoma: correlative analysis from a large North American cooperative group trial.  


Epstein-Barr virus (EBV) is associated with Hodgkin lymphoma (HL) and can be detected by in situ hybridization (ISH) of viral nucleic acid (EBER) in tumor cells. We sought to determine whether plasma EBV-DNA could serve as a surrogate for EBER-ISH and to explore its prognostic utility in HL. Specimens from the Cancer Cooperative Intergroup Trial E2496 were used to compare pretreatment plasma EBV-DNA quantification with EBV tumor status by EBER-ISH. A cutoff of >60 viral copies/100 µL plasma yielded 96% concordance with EBER-ISH. Pretreatment and month 6 plasma specimens were designated EBV(-) or EBV(+) by this cutoff. Patients with pretreatment EBV(+) plasma (n = 54) had inferior failure-free survival (FFS) compared with those with pretreatment EBV(-) plasma (n = 274), log-rank P = .009. By contrast, no difference in FFS was observed when patients were stratified by EBER-ISH. Pretreatment plasma EBV positivity was an independent predictor of treatment failure on multivariate analyses. At month 6, plasma EBV(+) patients (n = 7) had inferior FFS compared with plasma EBV(-) patients (n = 125), log-rank P = .007. These results confirm that plasma EBV-DNA is highly concordant with EBER-ISH in HL and suggest that it may have prognostic utility both at baseline and after therapy. This trial was registered at as #NCT00003389. PMID:23386127

Kanakry, Jennifer A; Li, Hailun; Gellert, Lan L; Lemas, M Victor; Hsieh, Wen-son; Hong, Fangxin; Tan, King L; Gascoyne, Randy D; Gordon, Leo I; Fisher, Richard I; Bartlett, Nancy L; Stiff, Patrick; Cheson, Bruce D; Advani, Ranjana; Miller, Thomas P; Kahl, Brad S; Horning, Sandra J; Ambinder, Richard F



The investigation of DNA repair polymorphisms with histopathological characteristics and hormone receptors in a group of Brazilian women with breast cancer.  


The association of tumor differentiation and estrogen receptor expression with the prognosis of breast cancer has been well established. Nevertheless, little is yet reported about the association of morphological characteristics of the tumor, estrogen receptor status and polymorphisms in low penetrance genes. The aim of the present study was to investigate a possible association between DNA repair gene polymorphisms (XRCC1, XPD, XRCC3, and RAD51) with histological type, grade and hormone receptor expression in a series of breast cancers. A cross-sectional study was carried out to evaluate 94 women with breast carcinoma, who had already been selected and included in a study on the association of DNA repair gene polymorphisms. For immunohistochemistry, formalin-fixed, paraffin-embedded tissue samples from breast tumors were consecutively retrieved from the histopathology files of our institution. DNA obtained from blood samples of the same patients was investigated for the presence of the following polymorphisms: Arg-399Gln located in the XRCC1 gene; 135C/G located in the RAD51 gene; Lys751Gln located in the XPD gene and Thr241Met located in the XRCC3 gene. Polymorphisms were considered to be independent variables and hormone receptor expression and the morphological characteristics of the tumors comprised the dependent variables. No statistically significant association was found between gene polymorphisms and hormone receptor status. The association between XRCC1-Arg399Gln polymorphism and ductal carcinoma was statistically significant (P = 0.02). The association of the XPD-Lys751Gln polymorphism with histological grade was also tatistically significant (p = 0.05). In conclusion, the XRCC1 genotype was found to be associated with ductal carcinoma histotypes and XPD genotype with low histological grade, which is the most frequent pattern of sporadic breast carcinomas. PMID:18752184

Dufloth, R M; Arruda, A; Heinrich, J K R; Schmitt, F; Zeferino, L C



Effect of an alkyl amino group on the binding of 1,8-naphthyridines to AP site-containing DNA duplexes.  


A 1,8-naphthyridine derivative having a positively charged side-chain, N-(3-aminopropyl)-5,6,7-trimethyl-1,8-naphthyridine-2-amine (APATMND), is synthesized, and its binding to AP site-containing DNA duplexes (5'- GCA GCT CCC GXG GTC TCC TCG-3'/ 5'-CGA GGA GAC CNC GGG AGC TGC-3', X = AP site; dSpacer, N = C, T) is examined in solutions buffered to pH 7.0 (I = 0.11 M, at 20 degrees C). Fluorescence titration experiments reveal that, as compared to a parent ligand, 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND), capable of selectively binding C over T opposite an AP site in the duplex (K(d)/nM: C: 56, T: 100), APATMND shows a stronger binding affinity for T, while an affinity for C is reduced (K(d)/nM: C: 135, T: 37). An examination of salt dependence of binding constants reveals that a polyelectrolyte contribution (Delta G(pe)) is indeed increased for C- and T-bindings of APATMND, but a loss of non-polyelectrolyte contribution (Delta G(t)) is significant when binding to C. These binding properties of APATMND are discussed with a view towards further development of DNA-binding ligands suitable for gene detection. PMID:18776281

Ichihashi, Toshiki; Sato, Yusuke; Seino, Takehiro; Nishizawa, Seiichi; Teramae, Norio



Imaging of a single DNA molecule by AFM: study of DNA conformation change in HMG-DNA complex  

Microsoft Academic Search

Conformation change of DNA under binding a DNA binding protein was studied using an AFM. An originally designed AFM mounted on an inverse microscope was used for imaging DNA. High mobility group (HMG) protein and pUC118 DNA were used as DNA binding protein and DNA for investigation in this study. The pUC118 DNA and its mixture with HMG2BJ were imaged

Hiroshi Muramatsu; Jong-Min Kim; Toshio Otani; Katsunori Homma; Mitsuteru Yoshida; Shin-ichi Tate; Masato Saito; Eiichi Tamiya



DNA codes  

SciTech Connect

We have begun to characterize a variety of codes, motivated by potential implementation as (quaternary) DNA n-sequences, with letters denoted A, C The first codes we studied are the most reminiscent of conventional group codes. For these codes, Hamming similarity was generalized so that the score for matched letters takes more than one value, depending upon which letters are matched [2]. These codes consist of n-sequences satisfying an upper bound on the similarities, summed over the letter positions, of distinct codewords. We chose similarity 2 for matches of letters A and T and 3 for matches of the letters C and G, providing a rough approximation to double-strand bond energies in DNA. An inherent novelty of DNA codes is 'reverse complementation'. The latter may be defined, as follows, not only for alphabets of size four, but, more generally, for any even-size alphabet. All that is required is a matching of the letters of the alphabet: a partition into pairs. Then, the reverse complement of a codeword is obtained by reversing the order of its letters and replacing each letter by its match. For DNA, the matching is AT/CG because these are the Watson-Crick bonding pairs. Reversal arises because two DNA sequences form a double strand with opposite relative orientations. Thus, as will be described in detail, because in vitro decoding involves the formation of double-stranded DNA from two codewords, it is reasonable to assume - for universal applicability - that the reverse complement of any codeword is also a codeword. In particular, self-reverse complementary codewords are expressly forbidden in reverse-complement codes. Thus, an appropriate distance between all pairs of codewords must, when large, effectively prohibit binding between the respective codewords: to form a double strand. Only reverse-complement pairs of codewords should be able to bind. For most applications, a DNA code is to be bi-partitioned, such that the reverse-complementary pairs are separated across the two blocks. For the foregoing reasons, these two blocks of codewords suffice as the hooks and loops of a digital Velcro. We began our investigations of such codes by constructing quaternary BCH reverse-complement codes, using cyclic codes and conventional Hamming distance [4]. We also obtained upper and lower bounds on the rate of reverse-complement codes with a metric function based on the foregoing similarities [3]. For most applications involving DNA, however, the reverse-complementary analogue of codes based on the insertion-deletion distance is more advantageous. This distance equals the codeword length minus the longest length of a common (not necessarily contiguous) subsequence. (The 'aligned' codes described above may be used under special experimental conditions), The advantage arises because, under the assumption that DNA is very flexible, the sharing of sufficiently long subsequences between codewords would be tantamount to the ability of one of their reverse complements to form a double strand with the other codeword. Thus far, using the random coding method, we have derived an asymptotic lower bound on the rate of reverse-complement insertion-deletion codes, as a function of the insertion-deletion distance fraction and of the alphabet size [1]. For the quaternary DNA alphabet of primary importance, this lower bound yields an asymptotically positive rate if the insertion-deletion-distance fraction does not exceed the threshold {approx} 0.19. Extensions of the Varsamov-Tenengol'ts construction of insertion-deletion codes [5] for reverse-complement insertion-deletion codes will be described. Experiments have been performed involving some of our DNA codes.

Torney, D. C. (David C.)



Plasma Concentrations of High-Mobility Group Box Protein 1, Soluble Receptor for Advanced Glycation End-Products and Circulating DNA in Patients with Acute Pancreatitis  

Microsoft Academic Search

Aims: High-mobility group box protein 1 (HMGB1), a late-acting proinflammatory cytokine, is secreted actively by inflammatory cells, and released passively from necrotic cells. From the aspect that both inflammation and necrosis are involved in the pathogenesis in acute pancreatitis, the aim of the study was a joint investigation of the plasma concentrations of HMGB1, its soluble receptor for advanced glycation

Á. K. Kocsis; A. Szabolcs; P. Hofner; T. Takács; G. Farkas; K. Boda; Y. Mándi



Ten polymorphic DNA loci, including five in the rat MHC ( RT1 ) region, form a single linkage group on rat chromosome 20  

Microsoft Academic Search

We have described ten markers for polymorphic loci on rat chromosome 20, including five in the rat MHC (RT1) region. These markers formed a single linkage group spanning a recombination distance of 0.40. The markers identified five expressed gene loci - RT1.N1 (thymus leukemia antigen 1), Tnfa (tumor necrosis factor α), Hspa1 (heat shock protein 70), Ggt1 (γ glutamyl-transferase 1),

Elaine F. Remmers; Ying Du; Hongbin Zha; Ellen A. Goldmuntz; Ronald L. Wilder



Using DNA-barcoding for sorting out protist species complexes: a case study of the Nebela tincta-collaris-bohemica group (Amoebozoa; Arcellinida, Hyalospheniidae).  


Species identification by means of morphology is often problematic in protists. Nebela tincta-collaris-bohemica (Arcellinida) is a species complex of small to medium-sized (ca.100 ?m) testate amoebae common in peat bogs and forest soils. The taxonomic validity of characters used to define species within this group is debated and causes confusion in studies of biogeography, and applications in palaeoecology. We examined the relationship between morphological and genetic diversity within this species complex by combined analyses of light microscopy imaging and Cytochrome Oxidase Subunit 1(COI) sequences obtained from the same individual amoeba cells. Our goals were (1) to clarify the taxonomy and the phylogenetic relationships within this group, and (2) to evaluate if individual genotypes corresponded to specific morphotypes and the extent of phenotypic plasticity. We show here that small variations in test morphology that have been often overlooked by traditional taxonomy correspond to distinct haplotypes. We therefore revise the taxonomy of the group. We redefine Nebela tincta (Leidy) Kosakyan et Lara and N. collaris (Ehrenberg 1848) Kosakyan et Gomaa, change N. tincta var. rotunda Penard to N. rotunda (Penard 1890), describe three new species: N. guttata n. sp. Kosakyan et Lara, N. pechorensis n. sp. Kosakyan et Mitchell, and N. aliciae n. sp. Mitchell et Lara. PMID:23092639

Kosakyan, Anush; Gomaa, Fatma; Mitchell, Edward A D; Heger, Thierry J; Lara, Enrique



Bipolar localization of the group II intron Ll.LtrB is maintained in Escherichia coli deficient in nucleoid condensation, chromosome partitioning and DNA replication.  


Group II introns are mobile genetic elements that invade their cognate intron-minus alleles via an RNA intermediate, in a process known as retrohoming. They can also retrotranspose to ectopic sites at low frequency. In Escherichia coli, retrotransposition of the lactococcal group II intron, Ll.LtrB, occurs preferentially within the Ori and Ter macrodomains of the E. coli chromosome. These macrodomains migrate towards the poles of the cell, where the intron-encoded protein, LtrA, localizes. Here we investigate whether alteration of nucleoid condensation, chromosome partitioning and replication affect retrotransposition frequencies, as well as bipolar localization of the Ll.LtrB intron integration and LtrA distribution in E. coli. We thus examined these properties in the absence of the nucleoid-associated proteins H-NS, StpA and MukB, in variants of partitioning functions including the centromere-like sequence migS and the actin homologue MreB, as well as in the replication mutants DeltaoriC, seqA, tus and topoIV (ts). Although there were some dramatic fluctuations in retrotransposition levels in these hosts, bipolar localization of integration events was maintained. LtrA was consistently found in nucleoid-free regions, with its localization to the cellular poles being largely preserved in these hosts. Together, these results suggest that bipolar localization of group II intron retrotransposition results from the residence of the intron-encoded protein at the poles of the cell. PMID:17005014

Beauregard, Arthur; Chalamcharla, Venkata R; Piazza, Carol Lyn; Belfort, Marlene; Coros, Colin J



Cleaving DNA with DNA  

NASA Astrophysics Data System (ADS)

A DNA structure is described that can cleave single-stranded DNA oligonucleotides in the presence of ionic copper. This ``deoxyribozyme'' can self-cleave or can operate as a bimolecular complex that simultaneously makes use of duplex and triplex interactions to bind and cleave separate DNA substrates. Bimolecular deoxyribozyme-mediated strand scission proceeds with a kobs of 0.2 min-1, whereas the corresponding uncatalyzed reaction could not be detected. The duplex and triplex recognition domains can be altered, making possible the targeted cleavage of single-stranded DNAs with different nucleotide sequences. Several small synthetic DNAs were made to function as simple ``restriction enzymes'' for the site-specific cleavage of single-stranded DNA.

Carmi, Nir; Balkhi, Shameelah R.; Breaker, Ronald R.



DNA: Animations  

NSDL National Science Digital Library

The Howard Hughes Medical Institute makes available twenty-five short, narrated animations about DNA at this link. The animations are viewable as video clips and topics include, but are not limited to DNA structure, DNA replication, transcription and translation, mutations in DNA, polymerase chain reaction, DNA sequencing, and shotgun sequencing.

Institute, Howard H.



Immobilization of DNA in polyacrylamide gel for the manufacture of DNA and DNA-oligonucleotide microchips.  

SciTech Connect

Activated DNA was immobilized in aldehyde-containing polyacrylamide gel for use in manufacturing the MAGIChip (microarrays of gel-immobilized compounds on a chip). First, abasic sites were generated in DNA by partial acidic depurination. Amino groups were then introduced into the abasic sites by reaction with ethylenediamine and reduction of the aldimine bonds formed. It was found that DNA could be fragmented at the site of amino group incorporation or preserved mostly unfragmented. In similar reactions, both amino-DNA and amino-oligonucleotides were attached through their amines to polyacrylamide gel derivatized with aldehyde groups. Single- and double-stranded DNA of 40 to 972 nucleotides or base pairs were immobilized on the gel pads to manufacture a DNA microchip. The microchip was hybridized with fluorescently labeled DNA-specific oligonucleotide probes. This procedure for immobilization of amino compounds was used to manufacture MAGIChips containing both DNA and oligonucleotides.

Proudnikov, D.; Timofeev, E.; Mirzabekov, A.; Center for Mechanistic Biology and Biotechnology; Engelhardt Inst. of Molecular Biology



Noninvasive determination of fetal rh blood group, D antigen status by cell-free DNA analysis in maternal plasma: experience in a Brazilian population.  


We evaluated the diagnostic accuracy of Rh blood group, D antigen (RHD) fetal genotyping, using real-time polymerase chain reaction in maternal blood samples, in a racially mixed population. We performed a prospective study conducted between January 2006 and December 2007, analyzing fetal RHD genotype in the plasma of 102 D- pregnant women by real-time polymerase chain reaction, targeting exons 7 and 10 of the RHD gene. Genotype results were compared with cord blood phenotype obtained after delivery or before the first intrauterine transfusion when necessary. Most of the participants (75.5%) were under 28 weeks of pregnancy, and 87.5% had at least one relative of black ancestry. By combining amplification of two exons, the accuracy of genotyping was 98%, sensitivity was 100%, and specificity was 92%. The positive likelihood ratio was 12.5, and the negative likelihood ratio was 0. The two false-positive cases were confirmed to be pseudogene RHD by real-time polymerase chain reaction. There were no differences between the patients with positive or negative Coombs test ( P?=?0.479). Determination of fetal RHD status in maternal peripheral blood was highly sensitive in this racially mixed population and was not influenced by the presence of antierythrocyte antibodies. PMID:20408112

Chinen, Paulo Alexandre; Nardozza, Luciano Marcondes Machado; Martinhago, Ciro Dresch; Camano, Luiz; Daher, Silvia; Pares, David Baptista da Silva; Minett, Thais; Araujo Júnior, Edward; Moron, Antonio Fernandes



DNA Transformation  

NSDL National Science Digital Library

Stanley Cohen and Herbert Boyer's historic experiment used techniques to cut and paste DNA to create the first custom-made organism containing recombined or 'recombinant' DNA. Cohen and Boyer inserted the recombinant DNA molecule they created into E. coli bacteria by means of a plasmid, thereby inducing the uptake and expression of a foreign DNA sequence known as 'transformation.' This animation from Cold Spring Harbor Laboratory's Dolan DNA Learning Center presents DNA transformation through a series of illustrations of the processes involved.



DNA ligases.  


The DNA ligase enzyme family catalyzes the formation of a phosphodiester bond between juxtaposed 5'-phosphate and 3'-hydroxyl termini in duplex DNA. This activity can seal nicks in duplex DNA or join double-stranded DNA fragments having either blunt or cohesive ends. DNA ligases are central enzymes in molecular biology, nucleic acid research, and in next-generation sequencing applications. Reaction conditions and applications for T4 DNA ligase, E. coli DNA ligase, and thermostable DNA ligases are described in this unit. These enzymes differ in their cofactor requirements, substrate specificity, and thermal stability. PMID:21472697

Lohman, Gregory J S; Tabor, Stanley; Nichols, Nicole M



Solution confirmation of the (-)-trans-anti-5-Methylchrysene-dG adduct oppposite dC in a DNA duplex: DNA bending associated with wedging of the Methyl group of 5-Methylchrysene to the 3{prime}-side of the modification site  

SciTech Connect

This paper reports on NMR-molecular mechanics structural studies of the (-)-trans-anti-[MC]dG adduct positioned opposite dC in the sequence context of the d(Cl-C2-A3-T4-C5-[MC]G6-C7-T8-A9-C10-C11){sm_bullet}d(G12-G13-T14-A15-G16-C17-G 18-A19-T20-G21-G22) duplex [designated (-)-trans-anti-[MC]dG{sm_bullet}dC 11-mer duplex]. This adduct is derived from the trans addition at C{sup 4} of (-)-anti-1(S),2(R)-dihydroxy-3(R),4(S)-epoxy-1,2,3,4-tetrahydro-5-methylchrysene [(-)-anti-5-MeCDE] to the N{sup 2} position of dG6 in this duplex sequence. The 5-methyl group is located adjacent to the MC(C{sup 4}) binding site, with these groups juxtaposed in a sterically crowded bay region in the adduct duplex. The 5-methylchrysenyl and the nucleic acid exchangeable and nonexchangeable protons were assigned following analysis of two-dimensional NMR data sets in H{sub 2}O and D{sub 2}O buffer solution. The solution structure of the trans-anti-[MC]dG{sm_bullet}dC 11-mer duplex has been determined by incorporating DNA-DNA and carcinogen-DNA proton-proton distances defined by lower and upper bounds deduced from NOESY data sets as restraints in molecular mechanics computations in torsion angle space. The results establish that the [MC]dG6{sm_bullet}dC17 base pair and flanking dC5{sm_bullet}dG18 and dC7{sm_bullet}dG16 base pairs retain Watson-Crick alignments upon adduct formation. 61 refs., 9 figs., 2 tabs.

Cosman, M.; Patel, D.J. [Memorial Sloan-Kettering Cancer Center, New York, NY (United States)] [and others



Immobilization of DNA in Polyacrylamide Gel for the Manufacture of DNA and DNA–Oligonucleotide Microchips  

Microsoft Academic Search

Activated DNA was immobilized in aldehyde-containing polyacrylamide gel for use in manufacturing the MAGIChip (microarrays of gel-immobilized compounds on a chip). First, abasic sites were generated in DNA by partial acidic depurination. Amino groups were then introduced into the abasic sites by reaction with ethylenediamine and reduction of the aldimine bonds formed. It was found that DNA could be fragmented

Dmitri Proudnikov; Edward Timofeev; Andrei Mirzabekov



Extracting DNA  

NSDL National Science Digital Library

This lesson for students in grades 9-12 introduces DNA, genes, chromosomes, the chemicals that make up DNA. After the basic information, students will do an experiment in which they will separate out DNA from peas. Knowing that DNA can be separated will give them a base of understanding for future lessons in biology, evolution, biotechnology, and health technology.

Science Netlinks;



DNA condensation  

Microsoft Academic Search

Recent progress in our understanding of DNA condensation includes the observation of the collapse of single DNA molecules, greater insights into the intermolecular forces driving condensation, the recognition of helix-structure perturbation in condensed DNA, and the increasing recognition of the likely biological consequences of condensation. DNA condensed with cationic liposomes is an efficient agent for the transfection of eukaryotic cells,

Victor A Bloomfield



A novel group of families of short interspersed repetitive elements (SINEs) in Xenopus: evidence of a specific target site for DNA-mediated transposition of inverted-repeat SINEs.  


We have isolated from Xenopus borealis members of a family of short interspersed repetitive elements (SINEs) that we have termed Xbr. Xbr elements are also present in other Xenopus genomes and are typically framed by 46 bp terminal inverted repeats (TIRs). These TIRs and those of two previously described families of inverted-repeat SINEs from X. laevis begin with the sequence TTAAAGGRR. Knowledge of this consensus, termed the T2 motif, allowed us to define four previously uncharacterized families of inverted-repeat SINEs from Xenopus database sequences. We estimate that the group of seven SINE families that possess the T2 motif accounts for about 10% of all X. laevis SINEs. Novel evidence for the transposition of inverted-repeat SINEs is provided: (1) by examples of the presence/absence of T2 elements at corresponding locations in either duplicated genes or pseudotetraploid gene homeologues; and (2) by the existence of contiguous elements from different T2 families that are joined precisely by their TIRs. These examples provide novel evidence for a DNA-mediated mechanism of T2 element transposition. They also show that the tetranucleotide, TTAA, which flanks integrated elements on both sides and is present once at unoccupied sites, is the obligate target site for T2 insertion. The use of a specific sequence as a target site for SINE insertion is unexpected, although such specificity is exhibited by a limited number of larger transposable elements that encode their own transposase. The clear evidence for DNA-mediated transposition provided by T2 elements demonstrates that the evolution and maintenance of SINE families in vertebrate genomes results from two distinctive mechanisms. PMID:7752242

Unsal, K; Morgan, G T



DNA vaccines  

Microsoft Academic Search

DNA vaccines use eukaryotic expression vectors to produce immunizing proteins in the vaccinated host. Popular methods of delivery are intramuscular and intradermal saline injections of DNA and gene gun bombardment of skin with DNA-coated gold beads. The method of DNA inoculation (gene gun versus intramuscular injection) and the form of the DNA-expressed antigen (cell-associated versus secreted) determine whether T-cell help

Harriet L. Robinson; Celia Aurora Tiglao Torres



DNA-DNA hybridization study of Bradyrhizobium strains.  


DNA-DNA hybridizations were performed between Bradyrhizobium strains, isolated mainly from Faidherbia albida and Aeschynomene species, as well as Bradyrhizobium reference strains. Results indicated that the genus Bradyrhizobium consists of at least 11 genospecies, I to XI. The genospecies formed four subgeneric groups that were more closely related to each other (>40% DNA hybridization) than to other genospecies (<40% DNA hybridization): (i) genospecies I (Bradyrhizobium japonicum), III (Bradyrhizobium liaoningense), IV and V; (ii) genospecies VI and VIII; (iii) genospecies VII and IX; and (iv) genospecies II (Bradyrhizobium elkanii), X and XI. Photosynthetic Aeschynomene isolates were found to belong to at least two distinct genospecies in one subgeneric group. DNA-DNA hybridization data are compared with data from amplified fragment length polymorphism analysis and 165-23S rDNA spacer sequence analysis. PMID:11491327

Willems, A; Doignon-Bourcier, F; Goris, J; Coopman, R; de Lajudie, P; De Vos, P; Gillis, M



Food Groups  


Choose a Food Group MyPlate illustrates the five food groups that are the building blocks for a healthy diet using a ... half your grains whole. >> See Grains Group Protein Foods Go lean with protein. >> See Protein Foods Group ...


Imaging of a single DNA molecule by AFM: study of DNA conformation change in HMG-DNA complex  

NASA Astrophysics Data System (ADS)

Conformation change of DNA under binding a DNA binding protein was studied using an AFM. An originally designed AFM mounted on an inverse microscope was used for imaging DNA. High mobility group (HMG) protein and pUC118 DNA were used as DNA binding protein and DNA for investigation in this study. The pUC118 DNA and its mixture with HMG2BJ were imaged by the AFM. In the AFM image of pUC118, DNA strands showed open structure with a few helix sites. The height of the helix part is 1.5 times higher than the ordinary DNA strand. Centrally AFM images of the mixture showed HMG-like particles on DNA strands. The height of the particle is 2-3 times higher than the DNA strands which showed the particles were not aggregating parts but HMG. The HMG bound on a crossing part of DNA which make a loop.

Muramatsu, Hiroshi; Kim, Jong-Min; Otani, Toshio; Homma, Katsunori; Yoshida, Mitsuteru; Tate, Shin-ichi; Saito, Masato; Tamiya, Eiichi



Nanoparticle bridge DNA biosensor  

NASA Astrophysics Data System (ADS)

A new DNA sensing method is demonstrated in which DNA hybridization events lead to the formation of nanoparticle satellites that bridge two electrodes and are detected electrically. The hybridization events are exclusively carried out only on specific locations, the surfaces of C-ssDNA modified 50 nm GNPs. The uniqueness of this work is that only a small number of T-ccDNA molecules (<10) is required to form the nanoparticle satellites, allowing ultra-sensitive DNA sensing. The principle of this new DNA sensing technique has been demonstrated using target DNA and three-base-pair-mismatched DNA in 20nM concentrations. Three single-stranded DNA (ssDNA) system is used in our experiment which includes Capture-ssDNA (C-ssDNA), Target-ssDNA (T-ssDNA) and Probe-ssDNA (P-ssDNA). Both C-ssDNA and P-ssDNA are modified by a thiol group and can hybridize with different portions of T-ssDNA. T-ssDNA requires no modification in three ssDNA system, which is beneficial in many applications. C-ssDNA modified 50nm gold nanoparticle (C-50au) and P-ssDNA modified 30nm gold nanoparticle (P-30au) are prepared through the reaction of thiol-gold chemical bonding between thiolated ssDNA and gold nanoparticle (GNP) (C-ssDNA with 50nm GNP, P-ssDNA with 30nm GNP). We controllably place the C-50au only on the SiO2 band surface (˜ 90nm width) between two gold electrodes (source and drain electrodes) by forming positively- and negatively-charged self-assembled monolayers (SAMs) on SiO2 and gold surface, respectively. DNA modified GNP is negatively charged due to ionization of phosphate group on DNA back bone. C-50au therefore is negatively charged and can only be attracted toward SiO2 area (repelled by negatively charged gold electrode surface). The amine group of positively-charged SAMs on SiO2 surface is then passivated by converting to non-polar methyl functional group after C-50au placement. P-30au is first hybridized with T-ssDNA in the solution phase (T-P- 30au formed) and is introduced into DNA detection device in which C-50au are immobilized on ˜90nm width SiO2 band (between two gold electrodes). The passivation step ensures every TP-30au are attached only to C-50au through hybridization (T-P-30au will not be attracted toward SiO2 surface or gold electrodes). GNP bridges are formed across the electrodes and provide an electrical path between two gold electrodes. We ensure that every T-P-30au only hybridizes on the surface of C-50au by (1) accurately controlling C-50au placement between two gold electrodes, (2) passivating positively-charged SAMs on SiO2 surface after C-50au immobilization. When T-P-30au hybridize with C-50au on ˜90nm wide SiO 2 surface, GNP bridges form and provide an electrical path between two gold electrodes even with only a few hybridization events. Experimental results show that even a few GNP bridges formed on SiO2 band can provide a significant conductance change from an open circuit to a conductive circuit (current = 0.5 uA at voltage = 0.1 V with four GNP bridge). We also used 3-base-pair-mismatched ssDNA (3mm-ssDNA) as a control experiment, which always resulted in an open circuit (no GNP bridge formed). Our detection device is compatible with current CMOS fabrication technology and can be manufactured on a wafer scale. The direct electrical output of this DNA detection technique provides a promising basis for high-throughput screening (can be fabricated on a wafer scale) with no expensive equipment required.

Huang, Hong-Wen


Molecular and cellular analysis of the DNA repair defect in a patient in Xeroderma pigmentosum complementation group D who has the clinical features of Xeroderma pigmentosum and Cockayne syndrome  

SciTech Connect

Xeroderma pigmentosum (XP) and Cockayne syndrome (CS) are quite distinct genetic disorders that are associated with defects in excision repair of UV-induced DNA damage. A few patients have been described previously with the clinical features of both disorders. In this paper we describe an individual in this category who has unusual cellular responses to UV light. We show that his cultured fibroblasts and lymphocytes are extremely sensitive to irradiation with UV-C, despite a level of nucleotide excision repair that is 30%-40% that of normal cells. The deficiency is assigned to the XP-D complementation group, and we have identified two causative mutations in the XPD gene: a gly{yields}arg change at amino acid 675 in the allele inherited from the patient`s mother and a -1 frameshift at amino acid 669 in the allele inherited from his father. These mutations are in the C-terminal 20% of the 760-amino-acid XPD protein, in a region where we have recently identified several mutations in patients with trichothiodystrophy. 44 refs., 5 figs., 2 tabs.

Broughton, B.C.; Thompson, A.F.; Harcourt, S.A.; Cole, J.; Arlett, C.F.; Lehmann, A.R. [Univ. of Sussex, Brighton (United Kingdom); Vermeulen, W.; Hoeijmakers, J.H.J. [Erasmus Univ., Rotterdam (United Kingdom); Botta, E.; Stefanini, M. [Istituto di Genetica, Pavia (Italy)] [and others



Use of DNA arrays to identify a mutation in the negative regulator, csrR, responsible for the high virulence of a naturally occurring type M3 group A streptococcus clinical isolate.  


We previously reported that type M3 group A streptococcus (GAS) showed a wide range of 50% lethal dose values in mice. Analysis using DNA arrays indicated that the most virulent strain, M3-f, expressed significantly higher levels of the products of several virulence genes than did the other M3 isolates. Sequencing of the csrS, csrR, luxS, and rgg genes in the isolates showed that the M-3f csrR gene contained a specific point mutation. Disruption of wild-type (wt) csrR in an M3 strain increased its virulence and the expression of hyaluronic acid, whereas complementation with wt but not type M3-f csrR attenuated these changes. Expression experiments showed that type M3-f CsrR counteracted the effects of wt CsrR. Although wt CsrR bound to the hasA promoter region, type M3-f CsrR did not. Thus, the high virulence of the type M3-f strain is associated with the decreased binding of type M3-f CsrR to its target sequences. PMID:16703511

Miyoshi-Akiyama, Tohru; Ikebe, Tadayoshi; Watanabe, Haruo; Uchiyama, Takehiko; Kirikae, Teruo; Kawamura, Yoshiaki



DNA Banking  

SciTech Connect

The author is involved in the ethical, legal, and social issues of banking of DNA and data from DNA analysis. In his attempt to determine the extent of DNA banking in the U.S., the author surveyed some commercial companies performing DNA banking services. This article summarizes the results of that survey, with special emphasis on the procedures the companies use to protect the privacy of individuals. 4 refs.

Reilly, P.R. (Eunice Kennedy Shriver Center for Mental Retardation, Waltham, MA (United States))



DNA Arrays  

NSDL National Science Digital Library

This animation from Cold Spring Harbor Laboratory's Dolan DNA Learning Center presents DNA arrays. The animation contains information on Pat Brown's discovery and the purpose of DNA arrays to study gene expression as well as its role in the development of pharmacogenomic treatment for diseases such as cancer.



Stretching DNA  

NSDL National Science Digital Library

Explore stretching just a single strand of DNA using optical tweezers or fluid flow. Experiment with the forces involved and measure the relationship between the stretched DNA length and the force required to keep it stretched. Is DNA more like a rope or like a spring?

Simulations, Phet I.; Perkins, Kathy; Malley, Chris; Perkins, Tom; Dubson, Mike; Adams, Wendy



DNA glycosylases  

Microsoft Academic Search

Various DNA glycosylases exist, which initiate the first step in base-excision repair. A summary of the kinetic and physical characteristics of three classes of DNA glycosylase are presented here. The first class discussed, include glycosylases which recognize alkylated DNA. Various data from enzymes derived from both prokaryotic and eukaryatic sources is discussed. The second class deals with a glycosylase that

Salvatore J. Caradonna; Yung-chi Cheng



Reading DNA  

NSDL National Science Digital Library

In this activity, learners use edible models of the DNA molecule to transcribe an mRNA sequence, and then translate it into a protein. This activity requires learners to have already constructed edible DNA models from the activity "Have Your DNA and Eat It Too" (see related resource).

Malone, Molly; Mitchell, April; Stark, Louisa; Starr, Harmony



Electronic effect of different positions of the -NO2 group on the DNA-intercalator of chiral complexes [Ru(bpy)2L]2+ (L =o-npip, m-npip and p-npip).  


New chiral Ru(II) complexes with intercalators L (L =o-npip, m-npip and p-npip) containing -NO2 at different positions on the phenyl ring were synthesized and characterized by elemental analysis, 1H NMR, ESI-MS and CD spectra. The DNA binding properties of these complexes have been investigated with UV-Vis, emission spectra, CD spectra and viscosity measurements. A subtle but detectable difference was observed in the interaction of these isomers with CT-DNA. Absorption spectroscopy experiments indicated that each of these complexes can interact with the DNA. The DNA-binding of the Delta-isomer is stronger than that of Lambda-isomer. DNA-viscosity experiments provided evidence that both Delta- and Lambda-[Ru(bpy)2(o-npip)](PF6)2 bind to DNA with partial intercalation, and both Delta- and Lambda-[Ru(bpy)(2)(p-npip)](PF6)2 fully intercalate with DNA. However, Delta- and Lambda- [Ru(bpy)2(m-npip)](PF6)2 bind to DNA through different modes, i.e., the Delta isomer by intercalation and Lambda isomer by partial intercalation. Under irradiation with UV light, Ru(II) complexes showed different efficiency of cleaving DNA. The most interesting feature is that neither 1 (Delta-1 and Lambda-1) nor 3 (Delta-3 and Lambda-3) emit luminescence either alone in aqueous solution or in the presence of DNA, whereas both Delta-2 and Lambda-2 emit luminescence under the same conditions. In addition, theoretical calculations for these three isomer complexes have been carried out applying the density functional theory (DFT) method at the level of the B3LYP/LanL2DZ basis set, and the calculated results can reasonably explain the obtained experimental trends in the DNA-binding affinities or binding constants (Kb) and some spectral properties of the complexes. PMID:15909056

Shi, Shuo; Liu, Jie; Li, Jun; Zheng, Kang C; Tan, Cai P; Chen, Lan M; Ji, Liang N



DNA aptamers and DNA enzymes  

Microsoft Academic Search

Investigators using combinatorial methods are revealing the surprising structural and functional abilities of DNA. A consequence of DNA's structure-forming potential is its ability to form highly specific receptors and ligands, and even its ability to catalyze chemical reactions. Unlike the classical images of double-stranded DNA, these DNA structures have many of the higher-ordered structural features that are found with ribozymes

Ronald R Breaker



Grouping Dinosaurs  

NSDL National Science Digital Library

In this classroom activity, young students are introduced to sets and subsets. The activity opens with background information for teachers about cladistics. After brainstorming different ways to group the class itself, students work in small groups to identify subsets of coins. The groups then complete a worksheet that challenges them to group dinosaurs into sets and subsets and share their results with the class.


Designer DNA Nanoarchitectures†  

PubMed Central

Naturally existing biological systems, from the simplest unicellular diatom to the most sophisticated organ such as human brain, are functional self-assembled architectures. Scientists have long been dreaming about building artificial nanostructures that can mimic such elegance in nature. Structural DNA nanotechnology, which uses DNA as blueprint and building material to organize matter with nanometer precision, represents an appealing solution to this challenge. Based on the knowledge of helical DNA structure and Watson-Crick base pairing rules, scientists have constructed a number of DNA nanoarchitectures with a large variety of geometries, topologies and periodicities with considerably high yields. Modified by functional groups, those DNA nanostructures can serve as scaffolds to control the positioning of other molecular species, which opens opportunities to study intermolecular synergies, such as protein-protein interactions, as well as to build artificial multi-component nano-machines. In this review, we summarize the principle of DNA self-assembly, describe the exciting progress of structural DNA nanotechnology in recent years and discuss the current frontier.

Lin, Chenxiang; Liu, Yan; Yan, Hao



The future of DNA-DNA hybridization studies  

Microsoft Academic Search

Summary This article draws on many vertebrate examples to assess the future of DNA-DNA hybridization studies. I first discuss whether applications of the method have reached the point of diminishing returns, or rather the start of a great leap forward, in our evolutionary understanding. Vertebrate groups whose relationships are especially likely to be illuminated include parrots, pigeons, bats, pinnipeds, mammalian

Jared M. Diamond



Group X  

SciTech Connect

This project is currently under contract for research through the Department of Homeland Security until 2011. The group I was responsible for studying has to remain confidential so as not to affect the current project. All dates, reference links and authors, and other distinguishing characteristics of the original group have been removed from this report. All references to the name of this group or the individual splinter groups has been changed to 'Group X'. I have been collecting texts from a variety of sources intended for the use of recruiting and radicalizing members for Group X splinter groups for the purpose of researching the motivation and intent of leaders of those groups and their influence over the likelihood of group radicalization. This work included visiting many Group X websites to find information on splinter group leaders and finding their statements to new and old members. This proved difficult because the splinter groups of Group X are united in beliefs, but differ in public opinion. They are eager to tear each other down, prove their superiority, and yet remain anonymous. After a few weeks of intense searching, a list of eight recruiting texts and eight radicalizing texts from a variety of Group X leaders were compiled.

Fields, Susannah



DNase I - DNA interaction alters DNA and protein conformations.  


Human DNase I is an endonuclease that catalyzes the hydrolysis of double-stranded DNA predominantly by a single-stranded nicking mechanism under physiological conditions in the presence of divalent Mg and Ca cations. It binds to the minor groove and the backbone phosphate group and has no contact with the major groove of the right-handed DNA duplex. The aim of this study was to examine the effects of DNase I - DNA complexation on DNA and protein conformations. We monitored the interaction of DNA with DNase I under physiological conditions in the absence of Mg2+, with a constant DNA concentration (12.5 mmol/L; phosphate) and various protein concentrations (10-250 micromol/L). We used Fourier transfrom infrared, UV-visible, and circular dichroism spectroscopic methods to determine the protein binding mode, binding constant, and effects of polynucleotide-enzyme interactions on both DNA and protein conformations. Structural analyses showed major DNase-PO2 binding and minor groove interaction, with an overall binding constant, K, of 5.7 x 10(5) +/- 0.78 x 10(5) (mol/L)-1. We found that the DNase I - DNA interaction altered protein secondary structure, with a major reduction in alpha helix and an increase in beta sheet and random structures, and that a partial B-to-A DNA conformational change occurred. No DNA digestion was observed upon protein-DNA complexation. PMID:18523485

N'soukpoé-Kossi, C N; Diamantoglou, S; Tajmir-Riahi, H A



A DNA-fuelled molecular machine made of DNA.  


Molecular recognition between complementary strands of DNA allows construction on a nanometre length scale. For example, DNA tags may be used to organize the assembly of colloidal particles, and DNA templates can direct the growth of semiconductor nanocrystals and metal wires. As a structural material in its own right, DNA can be used to make ordered static arrays of tiles, linked rings and polyhedra. The construction of active devices is also possible--for example, a nanomechanical switch, whose conformation is changed by inducing a transition in the chirality of the DNA double helix. Melting of chemically modified DNA has been induced by optical absorption, and conformational changes caused by the binding of oligonucleotides or other small groups have been shown to change the enzymatic activity of ribozymes. Here we report the construction of a DNA machine in which the DNA is used not only as a structural material, but also as 'fuel'. The machine, made from three strands of DNA, has the form of a pair of tweezers. It may be closed and opened by addition of auxiliary strands of 'fuel' DNA; each cycle produces a duplex DNA waste product. PMID:10949296

Yurke, B; Turberfield, A J; Mills, A P; Simmel, F C; Neumann, J L



Hot Groups.  

ERIC Educational Resources Information Center

|Collaborators sparked by creative ideas and obsessed by a common task may not realize they're part of a "hot group"--a term coined by business professors Harold J. Leavitt and Jean Lipman-Blumen. Spawned by group decision making and employee empowerment, hot groups can flourish in education settings. They're typically small, short lived, and goal…

Vail, Kathleen



Home Groups.  

ERIC Educational Resources Information Center

|All students enrolled in the entry level foundations course in the College of Education of Kutztown University (Pennsylvania) participate in home groups, a cooperative learning strategy. Each student is assigned to a five- or six-person home group on the first day of class. Although group placements are made on the basis of class lists, every…

Stahler, Theresa M.


Patterning nanocrystals using DNA  

SciTech Connect

One of the goals of nanotechnology is to enable programmed self-assembly of patterns made of various materials with nanometer-sized control. This dissertation describes the results of experiments templating arrangements of gold and semiconductor nanocrystals using 2'-deoxyribonucleic acid (DNA). Previously, simple DNA-templated linear arrangements of two and three nanocrystals structures have been made.[1] Here, we have sought to assemble larger and more complex nanostructures. Gold-DNA conjugates with 50 to 100 bases self-assembled into planned arrangements using strands of DNA containing complementary base sequences. We used two methods to increase the complexity of the arrangements: using branched synthetic doublers within the DNA covalent backbone to create discrete nanocrystal groupings, and incorporating the nanocrystals into a previously developed DNA lattice structure [2][3] that self-assembles from tiles made of DNA double-crossover molecules to create ordered nanoparticle arrays. In the first project, the introduction of a covalently-branched synthetic doubler reagent into the backbone of DNA strands created a branched DNA ''trimer.'' This DNA trimer templated various structures that contained groupings of three and four gold nanoparticles, giving promising, but inconclusive transmission electron microscopy (TEM) results. Due to the presence of a variety of possible structures in the reaction mixtures, and due to the difficulty of isolating the desired structures, the TEM and gel electrophoresis results for larger structures having four particles, and for structures containing both 5 and 10 nm gold nanoparticles were inconclusive. Better results may come from using optical detection methods, or from improved sample preparation. In the second project, we worked toward making two-dimensional ordered arrays of nanocrystals. We replicated and improved upon previous results for making DNA lattices, increasing the size of the lattices to a length greater than 20 {micro}m, and collecting atomic force microscopy (AFM) images up to 30 {micro}m. We found the lattices' requirement of divalent magnesium cations to stabilize Holliday junctions to be incompatible with the stability of charge-stabilized gold nanoparticles used for the experiments here, and gold particles added indiscriminately to the lattice surface through non-specific binding. Redesigning the lattices to avoid magnesium may improve results.

Williams, Shara Carol



DNA nanomachines  

Microsoft Academic Search

We are learning to build synthetic molecular machinery from DNA. This research is inspired by biological systems in which individual molecules act, singly and in concert, as specialized machines: our ambition is to create new technologies to perform tasks that are currently beyond our reach. DNA nanomachines are made by self-assembly, using techniques that rely on the sequence-specific interactions that

Jonathan Bath; Andrew J. Turberfield



DNA nanomachines.  


We are learning to build synthetic molecular machinery from DNA. This research is inspired by biological systems in which individual molecules act, singly and in concert, as specialized machines: our ambition is to create new technologies to perform tasks that are currently beyond our reach. DNA nanomachines are made by self-assembly, using techniques that rely on the sequence-specific interactions that bind complementary oligonucleotides together in a double helix. They can be activated by interactions with specific signalling molecules or by changes in their environment. Devices that change state in response to an external trigger might be used for molecular sensing, intelligent drug delivery or programmable chemical synthesis. Biological molecular motors that carry cargoes within cells have inspired the construction of rudimentary DNA walkers that run along self-assembled tracks. It has even proved possible to create DNA motors that move autonomously, obtaining energy by catalysing the reaction of DNA or RNA fuels. PMID:18654284

Bath, Jonathan; Turberfield, Andrew J



DNA nanomachines  

NASA Astrophysics Data System (ADS)

We are learning to build synthetic molecular machinery from DNA. This research is inspired by biological systems in which individual molecules act, singly and in concert, as specialized machines: our ambition is to create new technologies to perform tasks that are currently beyond our reach. DNA nanomachines are made by self-assembly, using techniques that rely on the sequence-specific interactions that bind complementary oligonucleotides together in a double helix. They can be activated by interactions with specific signalling molecules or by changes in their environment. Devices that change state in response to an external trigger might be used for molecular sensing, intelligent drug delivery or programmable chemical synthesis. Biological molecular motors that carry cargoes within cells have inspired the construction of rudimentary DNA walkers that run along self-assembled tracks. It has even proved possible to create DNA motors that move autonomously, obtaining energy by catalysing the reaction of DNA or RNA fuels.

Bath, Jonathan; Turberfield, Andrew J.



Lie Groups  

Microsoft Academic Search

\\u000a This chapter discusses problems on Lie groups, Lie algebras and homogeneous spaces. After considering some specific examples\\u000a of Lie groups and Lie algebras and some questions on them, we consider homomorphisms, Lie subgroups and Lie subalgebras, integration\\u000a on Lie groups, the exponential map exp and its differential map exp*, the adjoint representation Ad and its differential map ad, and Lie

P. M. Gadea; J. Muñoz Masqué


Describing Groups  

Microsoft Academic Search

Two ways of describing a group are considered.\\u000a1. A group is finite-automaton presentable\\u000aif its elements can be represented by strings over a finite alphabet,\\u000ain such a way that the set of representing strings and\\u000athe group operation can be recognized by finite automata.\\u000a2. An infinite f.g. group is quasi-finitely axiomatizable\\u000aif there is a description consisting

André Nies



[DNA computing].  


Biocomputers can be an alternative for traditional "silicon-based" computers, which continuous development may be limited due to further miniaturization (imposed by the Heisenberg Uncertainty Principle) and increasing the amount of information between the central processing unit and the main memory (von Neuman bottleneck). The idea of DNA computing came true for the first time in 1994, when Adleman solved the Hamiltonian Path Problem using short DNA oligomers and DNA ligase. In the early 2000s a series of biocomputer models was presented with a seminal work of Shapiro and his colleguas who presented molecular 2 state finite automaton, in which the restriction enzyme, FokI, constituted hardware and short DNA oligomers were software as well as input/output signals. DNA molecules provided also energy for this machine. DNA computing can be exploited in many applications, from study on the gene expression pattern to diagnosis and therapy of cancer. The idea of DNA computing is still in progress in research both in vitro and in vivo and at least promising results of these research allow to have a hope for a breakthrough in the computer science. PMID:21735816

B?asiak, Janusz; Krasi?ski, Tadeusz; Pop?awski, Tomasz; Sakowski, Sebastian



DNA nanodevices.  


The molecular recognition properties of DNA molecules combined with the distinct mechanical properties of single and double strands of DNA can be utilized for the construction of nanodevices, which can perform ever more tasks with possible applications ranging from nanoconstruction to intelligent drug delivery. With the help of DNA it is possible to construct machinelike devices that are capable of rotational motion, pulling and stretching, or even unidirectional motion. It is possible to devise autonomous nanodevices, to grab and release molecules, and also to perform simple information-processing tasks. PMID:17193445

Simmel, Friedrich C; Dittmer, Wendy U



Novel applications of DNA materials  

NASA Astrophysics Data System (ADS)

This paper describes preparations of innovative photonic devices based on high purity DNA molecules which are obtained from Salmon roe. DNA molecules have characteristic features of double helical chain structures where aromatic compounds can intercalate into the stacked layers so that various optically active aromatic dyes indicate strong enhancement effects of photonic activities. Thus, various DNA photonic devices have been developed in the world in terms of optical switches, electro-luminescence (EL), lasers and so on. However, these DNA photonic devices adsorb moisture in the air because of hydrophilic character of DNA molecules, leading to decrease photonic activities. Nevertheless, it was found by my group that a novel hybridization method of the dye-intercalated DNA molecules by means of so-called so-gel process increased stabilities and durability of DNA photonic devices under environmental changes. Also, hybridization of dye-intercalated DNA devices with synthetic polymers including fluorinated poly(methylmethacrylate ) or polycarbonates was successfully carried out by solution blending method, followed by casting the solution to obtain these films which showed stability and durability increases of these DNA photonic devices. DNA-lipid complexes showed a very strong fluorescence amplification by chelating with rare earth metals such as Europium or Telbiumu compounds. This paper also describes the chelate effects of rare earth metal compounds for light amplifications.

Ogata, Naoya; Yamaoka, Kanji; Yoshida, Junichi



Point Groups  

NSDL National Science Digital Library

This exercise involves identifying symmetry in crystals and using that information to assign crystals to crystal systems and point groups. Students examine cardboard models and wooden blocks and fill their symmetry elements into a table. Then they figure out what what crystal system and point group each sample belongs to and fill in another table.

Perkins, Dexter


Group Theatre.  

ERIC Educational Resources Information Center

|The group interpretation approach to theatre production is defined as a method that will lead to production of plays that will appeal to "all the layers of the conscious and unconscious mind." In practice, it means that the group will develop and use resources of the theatre that orthodox companies too often ignore. The first two chapters of this…

Clark, Brian


Are isolated anti-HBc blood donors in high risk group? The detection of HBV DNA in isolated anti-HBc cases with nucleic acid amplification test (NAT) based on transcription-mediated amplification (TMA) and HBV discrimination  

Microsoft Academic Search

AimHepatitis B virus (HBV) can be transmitted by blood transfusions even so using serological tests having high sensitivity and specificity. We aimed to detect HBV DNA in isolated Anti-HBc donors and show if they have transfusion risk or not.

Hüsnü Altunay; Erdogan Kosan; Ilhan Birinci; Armagan Aksoy; Kaan Kirali; Suat Saribas; Mustafa Aslan; Pelin Yuksel; Esra Alan; Osman Sadi Yenen; Bekir Kocazeybek



Dancing DNA.  

ERIC Educational Resources Information Center

|An imaging technique that uses fluorescent dyes and allows scientists to track DNA as it moves through gels or in solution is described. The importance, opportunities, and implications of this technique are discussed. (KR)|

Pennisi, Elizabeth



DNA Dynamics.  

ERIC Educational Resources Information Center

|Explains a method to enable students to understand DNA and protein synthesis using model-building and role-playing. Acquaints students with the triplet code and transcription. Includes copies of the charts used in this technique. (DDR)|

Warren, Michael D.



DNA Dynamics.  

ERIC Educational Resources Information Center

Explains a method to enable students to understand DNA and protein synthesis using model-building and role-playing. Acquaints students with the triplet code and transcription. Includes copies of the charts used in this technique. (DDR)

Warren, Michael D.



DNA Extraction  

NSDL National Science Digital Library

Teachers' Domain presents this interactive, adapted from the University of Nebraska's Plant and Soil Science eLibrary, with reading material and animations to help students learn the basics of DNA extraction. The lesson is divided into and introduction and the four processes involved: cell lysis, dismantling the cell membrane, removing unwanted cell parts, and precipitating the DNA. On the site, visitors will also find a supplemental background essay, discussion questions, and standards alignment from Teachers' Domain.



DNA Vaccines  

Microsoft Academic Search

This chapter describes the R&D activities which have been carried in the last 9 years at the CEBQ, with the specific objective\\u000a of tackling some of the new scientific and technological challenges associated with the development of DNA vaccines. Following\\u000a a brief introduction on the DNA vaccine topic, the research under way is described and some significant results are highlighted.

Duarte Miguel F. Prazeres; Gabriel Amaro Monteiro


DNA as scaffolding for nanophotonic structures  

NASA Astrophysics Data System (ADS)

Deoxyribonucleic acid (DNA) chains can be engineered for diverse nanophotonics applications by the insertion of molecular groups in different spatial configurations. DNA chains can be assembled into wire-like structures, origami structures, photonic crystal-like assemblies, liquid-crystal phases, and thin films. These structures can be made to serve as scaffolds for the organization of various organic molecules and nanoparticles. The properties of nanostructures can be modified by the use of DNA and DNA modified by the surfactants.

Matczyszyn, Katarzyna; Olesiak-Banska, Joanna



Comparative functional genomics of mammalian DNA methyltransferases  

Microsoft Academic Search

DNA methylation involves biochemical modification of DNA by addition of methyl groups onto CpG dinucleotides, and this epigenetic mechanism regulates gene expression in disease and development. Mammalian DNA methyltransferases, DNMT (DNMT1, DNMT3A and DNMT3B), together with the accessory protein DNMT3L establish specific DNA methylation patterns in the genome during gametogenesis, embryogenesis and somatic tissue development. The present study addresses the

Nelida Rodriguez-Osorio; Hongfeng Wang; Jennifer Rupinski; Susan M. Bridges; Erdogan Memili



New Noncleavable Analogs of 8-Oxoguanine-DNA Glycosylase Substrates  

Microsoft Academic Search

8-Oxoguanine-DNA glycosylases play a key role in repairing oxidatively damaged DNA. Excision repair enzymes Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg protein) and human 8-oxoguanine-DNA glycosylase (hOGG1) catalyze excision of 7,8-dihydro-8-oxoguanine (oxoG) from DNA and subsequent cleavage of the sugar–phosphate backbone. Contacts between DNA phosphate groups and amino acid residues of the active centers of the enzymes are of importance for specific

M. V. Taranenko; E. M. Volkov; M. K. Saparbaev; S. A. Kuznetsova



Research Groups

This group provides key consultations across NCI, developing and using statistical analysis of biological data, computer and mathematical models, and conducting research in biostatistical and epidemiological methodologies and mathematical modeling of processes.


Plane Groups  

NSDL National Science Digital Library

This is a lengthy PDF document (60 pages+) about plane groups and symmetry. It includes colorful images of each of the 17 plane groups, in several different forms. Additionally, there are some summarizing graphics that show unit cells, lattices, symmetry elements, etc. There is lots here to choose from -- I doubt that anyone will want to use all of the images. Studying plane groups is a good way to introduce crystal systems, point groups, lattices, symmetry operators, etc. All is in 2-D, but it is easy to tell students that the principles are the same in 3-D. For those who like to make changes, the PDF document was created from individual EPS files. This means that the files can be opened in Adobe Illustrator, Corel Draw, etc., and modified to fit your own needs.

Perkins, Dexter


Important Role of Class I Heat Shock Genes hrcA and dnaK in the Heat Shock Response and the Response to pH and NaCl Stress of Group I Clostridium botulinum Strain ATCC 3502?  

PubMed Central

Class I heat shock genes (HSGs) code for molecular chaperones which play a major role in the bacterial response to sudden increases of environmental temperature by assisting protein folding. Quantitative reverse transcriptase real-time PCR gene expression analysis of the food-borne pathogen Clostridium botulinum grown at 37°C showed that the class I HSGs grpE, dnaK, dnaJ, groEL, and groES and their repressor, hrcA, were expressed at constant levels in the exponential and transitional growth phases, whereas strong downregulation of all six genes was observed during stationary phase. After heat shock from 37 to 45°C, all HSGs were transiently upregulated. A mutant with insertionally inactivated hrcA expressed higher levels of class I HSGs during exponential growth than the wild type, followed by upregulation of only groES and groES after heat shock. Inactivation of hrcA or of dnaK encoding a major chaperone resulted in lower maximum growth temperatures than for the wild type and reduced growth rates under optimal conditions compared to the wild type. The dnaK mutant showed growth inhibition under all tested temperature, pH, and NaCl stress conditions. In contrast, the growth of an hrcA mutant was unaffected by mild temperature or acid stress compared to the wild-type strain, indicating that induced class I HSGs support growth under moderately nonoptimal conditions. We show that the expression of class I HSGs plays a major role for survival and growth of C. botulinum under the stressful environmental conditions that may be encountered during food processing or growth in food products, in the mammalian intestine, or in wounds.

Selby, Katja; Lindstrom, Miia; Somervuo, Panu; Heap, John T.; Minton, Nigel P.; Korkeala, Hannu



Group dynamics.  


Group dynamics play a significant role within any organization, culture, or unit. The important thing to remember with any of these structures is that they are made up of people--people with different ideas, motivations, background, and sometimes different agendas. Most groups, formal or informal, look for a leader in an effort to maintain cohesiveness of the unit. At times, that cultural bond must be developed; once developed, it must be nurtured. There are also times that one of the group no longer finds the culture comfortable and begins to act out behaviorally. It is these times that become trying for the leader as she or he attempts to remain objective when that which was once in the building phase of group cohesiveness starts to fall apart. At all times, the manager must continue to view the employee creating the disturbance as an integral part of the group. It is at this time that it is beneficial to perceive the employee exhibiting problem behaviors as a special employee, as one who needs the benefit of your experience and skills, as one who is still part of the group. It is also during this time that the manager should focus upon her or his own views in the area of power, communication, and the corporate culture of the unit that one has established before attempting to understand another's point of view. Once we understand our own motivation and accept ourselves, it is then that we may move on to offer assistance to another. Once we understand our insecurities recognizing staff dysfunction as a symptom of system dysfunction will not be so threatening to the concept of the manager that we perceive ourselves to be. It takes a secure person to admit that she or he favors staff before deciding to do something to change things. The important thing to know is that it can be done. The favored staff can find a new way of relating to others, the special employee can find new modes of behavior (and even find self-esteem in the process), the group can find new ways of interacting, and the corporate culture can boast of a leader with new views at the helm. In marriage, it takes only two; in a group, it takes a lot more. The dynamics of many people interacting may present difficulties at times; however, the birth of the bond of that group is well worth the effort. Ask any manager. PMID:2081114

Scandiffio, A L



DNA vaccines  

NASA Astrophysics Data System (ADS)

Immunization by genes encoding immunogens, rather than with the immunogen itself, has opened up new possibilities for vaccine research and development and offers chances for new applications and indications for future vaccines. The underlying mechanisms of antigen processing, immune presentation and regulation of immune responses raise high expectations for new and more effective prophylactic or therapeutic vaccines, particularly for vaccines against chronic or persistent infectious diseases and tumors. Our current knowledge and experience of DNA vaccination is summarized and critically reviewed with particular attention to basic immunological mechanisms, the construction of plasmids, screening for protective immunogens to be encoded by these plasmids, modes of application, pharmacokinetics, safety and immunotoxicological aspects. DNA vaccines have the potential to accelerate the research phase of new vaccines and to improve the chances of success, since finding new immunogens with the desired properties is at least technically less demanding than for conventional vaccines. However, on the way to innovative vaccine products, several hurdles have to be overcome. The efficacy of DNA vaccines in humans appears to be much less than indicated by early studies in mice. Open questions remain concerning the persistence and distribution of inoculated plasmid DNA in vivo, its potential to express antigens inappropriately, or the potentially deleterious ability to insert genes into the host cell's genome. Furthermore, the possibility of inducing immunotolerance or autoimmune diseases also needs to be investigated more thoroughly, in order to arrive at a well-founded consensus, which justifies the widespread application of DNA vaccines in a healthy population.

Gregersen, Jens-Peter



[DNA vaccines].  


Immunization with plasmid DNA is a new trend in vaccine development that could enhance the safety and efficacy of currently used vaccines. Simultaneously, it will enable preparation of new vaccines that could not be developed by existing procedures. The main methods of plasmid-DNA application are intramuscular injection and intradermal delivery into skin by a gene gun. As a protein antigen is produced inside host cells, both humoral and cell-mediated immunity are significantly activated. The dominant role is played by dendritic cells presenting an antigen. The type and intensity of immune reaction induced can be influenced by various ways. Modification of gene coding for immunization antigen, combination with genes for immunostimulatory factors, and utilization of adjuvant effect of stimulatory CpG motifs are the major methods of improvement of immunization with plasmid DNA. Immune reactions against viral, bacterial, and parasitic infectious agents were successfully stimulated in many experimental systems. Other experiments are under way utilizing DNA vaccines for treatment of malignant tumors, autoimmune diseases, and allergy. The fast progress in DNA-vaccine development resulted in continually increasing number of clinical trials. PMID:12428419

Smahel, M



Identifying spiders through DNA barcodes  

Microsoft Academic Search

With almost 40 000 species, the spiders provide important model systems for studies of sociality, mating systems, and sexual dimorphism. However, work on this group is regularly constrained by difficulties in species identi- fication. DNA-based identification systems represent a promising approach to resolve this taxonomic impediment, but their efficacy has only been tested in a few groups. In this study,

Rowan D. H. Barrett; Paul D. N. Hebert



DNA nanostructure immobilization to lithographic DNA arrays  

Microsoft Academic Search

Although DNA is well known for its genetic role in biology, DNA has also been sought-after as a material for the self-assembly of biological and electronic devices. Examples of DNA nanostructure construction include DNA tiled self-assembly and DNA Origami, where by controlling the sequence and concentration of DNA molecules, the rational design of geometric DNA nanostructures is possible. The assembly

Omar D. Negrete



Cantor Groups  

ERIC Educational Resources Information Center

|The Cantor subset of the unit interval [0, 1) is "large" in cardinality and also "large" algebraically, that is, the smallest subgroup of [0, 1) generated by the Cantor set (using addition mod 1 as the group operation) is the whole of [0, 1). In this paper, we show how to construct Cantor-like sets which are "large" in cardinality but "small"…

Mathes, Ben; Dow, Chris; Livshits, Leo



Neandertal DNA  

NSDL National Science Digital Library

The view of some scientists that modern humans did not descend from the Neandertals gained support when scientists from Munich, Germany analyzed DNA from a Neandertal. A news article from Archeology Online News discusses the recent research and provides links to additional news clips. This site covers one of the top ten scientific breakthroughs of 1997, compiled in the December 19, 1997 issue of Science. The top scientific breakthrough of 1997 was the cloning of a sheep, resulting in a lamb named Dolly. The nine runners up were: the Pathfinder mission to Mars, synchrotrons, biological clock genes, gamma ray bursts, Neandertal DNA, nanotubes, Europa's ocean, whole genome sequencing, and neurons.



DNA origami nanopores for controlling DNA translocation.  


We combine DNA origami structures with glass nanocapillaries to reversibly form hybrid DNA origami nanopores. Trapping of the DNA origami onto the nanocapillary is proven by imaging fluorescently labeled DNA origami structures and simultaneous ionic current measurements of the trapping events. We then show two applications highlighting the versatility of these DNA origami nanopores. First, by tuning the pore size we can control the folding of dsDNA molecules ("physical control"). Second, we show that the specific introduction of binding sites in the DNA origami nanopore allows selective detection of ssDNA as a function of the DNA sequence ("chemical control"). PMID:23734828

Hernández-Ainsa, Silvia; Bell, Nicholas A W; Thacker, Vivek V; Göpfrich, Kerstin; Misiunas, Karolis; Fuentes-Perez, Maria Eugenia; Moreno-Herrero, Fernando; Keyser, Ulrich F



The 1998-1999 collaborative exercises and proficiency testing program on DNA typing of the Spanish and Portuguese Working Group of the International Society for Forensic Genetics (GEP-ISFG)  

Microsoft Academic Search

A total of 28 laboratories (labs) submitted results for the 1998 collaborative exercise and the proficiency testing program of the Spanish and Portuguese Working Group of the International Society for Forensic Genetics (GEP-ISFG) group. This number increased to 46 labs in 1999. Six bloodstains were submitted, each one with 200 ml soaked in cotton except the sample no. 6 submitted

Josefina Gomez; Angel Carracedo


Taxonomy of the Lacto bacillus acidophilus Group  

Microsoft Academic Search

A total of 89 strains designated Lactobtrcillus acidophilus were examined for physiological properties, type of lactic acid produced, cell wall sugar pattern, guanine plus cytosine content of deoxyribonucleic acid (DNA), and DNA homol- ogy values compared with selected reference strains. Immunological reactions among a group of the strains were determined by gel diffusion tests, using antiserum to purified lactic acid




Melanesian mtDNA Complexity  

Microsoft Academic Search

Melanesian populations are known for their diversity, but it has been hard to grasp the pattern of the variation or its underlying dynamic. Using 1,223 mitochondrial DNA (mtDNA) sequences from hypervariable regions 1 and 2 (HVR1 and HVR2) from 32 populations, we found the among-group variation is structured by island, island size, and also by language affiliation. The more isolated

Jonathan S. Friedlaender; Françoise R. Friedlaender; Jason A. Hodgson; Matthew Stoltz; George Koki; Gisele Horvat; Sergey Zhadanov; Theodore G. Schurr; D. Andrew Merriwether; Henry Harpending



Origami DNA  

NSDL National Science Digital Library

In this activity, learners create an origami model of DNA, demonstrating its double helix structure. Two templates are available as PDFs: a standard template with the base pairs already colored or a blank template where the learners have to color the four bases A, C, T and G and mark them in the correct location on the template.

Bateman, Alex; Deshpande, Preeti



DNA Investigations.  

ERIC Educational Resources Information Center

|Presents a simulation activity that allow students to work through the exercise of DNA profiling and to grapple with some analytical and ethical questions involving a couple arranging with a surrogate mother to have a baby. Can be used to teach the principles of restriction enzyme digestion, gel electrophoresis, and probe hybridization. (MDH)|

Mayo, Ellen S.; Bertino, Anthony J.



Biophysical characterization of DNA binding from single molecule force measurements  

PubMed Central

Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.

Chaurasiya, Kathy R.; Paramanathan, Thayaparan; McCauley, Micah J.; Williams, Mark C.



Fabrication of patterned DNA surfaces.  

PubMed Central

Two photolithographic methods are described for the formation of patterned single or multiple DNA species on SiO2 substrates. In the first approach, substrates are treated with a photochemically labile organosilane monolayer film. Irradiation of these surfaces with patterned deep UV (193 nm) light results in patterned chemically reactive groups which are then reacted with heterobifunctional crosslinking molecules. Covalent attachment of modified synthetic DNA oligomers to the crosslinker results in stable DNA patterns. Alternatively, a photoresist is spin-coated over a silane film which had been previously modified with the heterobifunctional crosslinker. Upon patterned irradiation and subsequent development, the underlying crosslinker-modified layer is revealed, and is then reacted with a chemically modified DNA. Feature dimensions to 1 micron are observed when a single fluorescent DNA is attached to the surface. By performing sequential exposures, we have successfully immobilized two distinguishable DNA oligomers on a single surface. Synthetic DNA immobilized in this manner retains the ability to hybridize to its complementary strand, suggesting that these approaches may find utility in the development of miniaturized DNA-based biosensors.

Chrisey, L A; O'Ferrall, C E; Spargo, B J; Dulcey, C S; Calvert, J M



Methylation of DNA  

PubMed Central

The methylated bases of DNA are formed by the transfer of the methyl group from S-adenosylmethionine to a polynucleotide acceptor. This transfer is catalyzed by highly specific enzymes which recognize a limited number of available sites in the DNA. The mechanism for the recognition is presently unknown. In some instances, there is evidence that other cellular components, such as lipopolysaccharides, can influence the methylation reaction. Certain bacteriophages induce new methylases upon infection of their hosts. Phage T3 is unique in establishing an environment in which methylation of neither the phage nor the host nucleic acid can occur. By superinfecting T3-infected cells with other phages, the latter can be obtained with methyl-deficient DNA. Although a great deal is known about the enzymology of the methylation reaction, and there appears to be a strong correlation between the in vitro and in vivo reactions, studies in which DNA is either supermethylated or totally unmethylated have not yielded any insight as to what the possible function of the methylated bases may be.

Gold, Marvin; Gefter, Malcolm; Hausmann, Rudolph; Hurwitz, Jerard



Label-free and selective photoelectrochemical detection of chemical DNA methylation damage using DNA repair enzymes.  


Exogenous chemicals may produce DNA methylation that is potentially toxic to living systems. Methylated DNA bases are difficult to detect with biosensors because the methyl group is small and chemically inert. In this report, a label-free photoelectrochemical sensor was developed for the selective detection of chemically methylated bases in DNA films. The sensor employed two DNA repair enzymes, human alkyladenine DNA glycosylase and human apurinic/apyrimidinic endonuclease, to convert DNA methylation sites in DNA films on indium tin oxide electrodes into strand breaks. A DNA intercalator, Ru(bpy)2(dppz)(2+) (bpy=2,2'-bipyridine, dppz = dipyrido[3,2-a:2',3'-c]phenazine) was then used as the photoelectrochemical signal indicator to detect the DNA strand breaks. Its photocurrent signal was found to correlate inversely with the amount of 3-methyladenines (metAde) produced with a methylating agent, methylmethane sulfonate (MMS). The sensor detected the methylated bases produced with as low as 1 mM MMS, at which concentration the amount of metAde on the sensor surface was estimated to be 0.5 pg, or 1 metAde in 1.6 × 10(5) normal bases. Other DNA base modification products, such as 5-methylcytosine and DNA adducts with ethyl and styrene groups did not attenuate the photocurrent, demonstrating good selectivity of the sensor. This strategy can be utilized to develop sensors for the detection of other modified DNA bases with specific DNA repair enzymes. PMID:23777269

Wu, Yiping; Zhang, Bintian; Guo, Liang-Hong



DNA ploidy status and DNA content instability within single tumors in renal cell carcinoma.  


In order to investigate the relationship between genetic instability and DNA aneuploidy of malignant cells in human solid tumors, we studied the variations of DNA index within a single tumor. Multiple sampling (mean of 6.4 samples per tumor) was performed in 24 renal cell carcinomas (RCC). Based on the variations in DNA indices within a single tumor, RCC were divided into three groups: 1) tumors with stable DNA indices (variation within the range of the measurement error), including all DNA diploid tumors (n = 8), all hyperdiploid tumors (n = 3), a hypodiploid tumor (n = 1), and only 2 of 11 tetraploid and hypotetraploid tumors; 2) tumors with moderate variations in DNA indices, which were all close to tetraploidy (n = 5); and 3) tumors with large variations of DNA indices. In this last group, subclones present within a tumor varied widely in their DNA indices from the tetraploid to the triploid region, reflecting the DNA content instability within the tumor cell population. These results suggest that DNA aneuploidy can arise by two different mechanisms: 1) loss or gain of chromosomes leading to hypodiploid or hyperdiploid tumors with no apparent increase in DNA content instability, and 2) doubling of the chromosome set followed by random loss of chromosomes as suggested by the DNA indices ranging from tetraploid to triploid region found in three tumors. Differences in DNA indices within one tumor characterize subclones which may arise by chromosome loss or gain. PMID:8354129

Bringuier, P P; Bouvier, R; Berger, N; Piaton, E; Revillard, J P; Perrin, P; Devonec, M



Mechanism of DNA flexibility enhancement by HMGB proteins  

Microsoft Academic Search

The mechanism by which sequence non-specific DNA-binding proteins enhance DNA flexibility is studied by examining complexes of double- stranded DNA with the high mobility group type B proteins HMGB2 (Box A) and HMGB1 (Box A+B) using atomic force microscopy. DNA end-to-end distances and local DNA bend angle distributions are analyzed for protein complexes deposited on a mica surface. For HMGB2

Jingyun Zhang; Micah J. McCauley; L. James Maher III; Mark C. Williams; N. E. Israeloff



Molecular Models of DNA  

NSDL National Science Digital Library

The featured molecules this month come from the paper by David T. Crouse on the X-ray determination of the structure of DNA. Given that most students are aware of the double helix, it seems appropriate to back up a little and examine the components that give rise to this structure. Accordingly, the molecule collection includes: Purine and pyrimidine, structural precursors of the four bases found in DNA: cytosine (C), thymine (T), adenine (A), and guanine (G) The four corresponding deoxyribonucleosides The four deoxyribonucleotides (the nucleoside monophosphates) A two-base-pair fragment showing the AT and GC hydrogen-bonded complements Several small 24-base-pair DNA fragments polyAT, polyGC, and a random array of bases. The DNA fragments provide a good opportunity to have students explore features of the Jmol and Chime menus. Using the Jmol menu as an example (right-click on the structure to bring up the menu) students can use the measuring tools to get an idea of the length of a complete turn in the DNA, the relative widths of the major and minor grooves, and the diameter of the helix. They can use the coloring schemes to detect the various base pair combinations, and learn to read the code for the random sequence. In Chime they can use the Shapely coloring scheme for this same purpose. Exploring other aspects of the menu will allow students to present the molecules in the various forms, including ribbon and cartoon views. In RNA, thymine is replaced by uracil, and the sugar moiety has an axial hydroxyl group on the carbon atom adjacent to the base binding site (the 2? carbon). The structures of uracil and of uridine monophosphate are included in the molecule collection. Students can use the Web to download and examine more complex DNAs using a site such as the Nucleic Acid Database at Rutgers University.


Moving DNA around: DNA transposition and retroviral integration  

PubMed Central

Mobile DNA elements are found in all kingdoms of life, and they employ numerous mechanisms to move within and between genomes. Here we review recent structural advances in understanding two very different families of DNA transposases and retroviral integrases: the DDE and Y1 groups. Even within the DDE family which shares a conserved catalytic domain, there is great diversity in the architecture of the synaptic complexes formed by the intact enzymes with their cognate element end DNAs. However, recurring themes arise from comparing these complexes, such as stabilization by an intertwined network of protein-DNA and protein-protein contacts, and catalysis in trans, where each active subunit catalyzes the chemical steps on one DNA segment but also binds specific sequences on the other.

Montano, Sherwin P.; Rice, Phoebe A.



Growth of Salmonella bacteriophage P22 in Escherichia coli dna(Ts) mutants.  

PubMed Central

Salmonella bacteriophage P22 grows in two deoxyribonucleic acid initiation mutants of Escherichia coli under nonpermissive conditions, dnaA and dnaC. Functional products of genes dnaE, dnaZ, lig, dnaK, and dnaG are indispensable for deoxyribonucleic acid replication of P22. In 11 E. coli dnaB mutants belonging to all phenotypic groups, phage were produced at 42 degrees C.

Schanda-Mulfinger, U E; Schmieger, H



DNA sequencing using fluorescence background electroblotting membrane  


A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through said smino groups contained on the surface thereof. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to said target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membrances may be reprobed numerous times.

Caldwell, Karin D. (Salt Lake City, UT); Chu, Tun-Jen (Salt Lake City, UT); Pitt, William G. (Orem, UT)



DNA sequencing using fluorescence background electroblotting membrane  


A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through amino groups contained on the surface. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to the target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membranes may be reprobed numerous times. No Drawings

Caldwell, K.D.; Chu, T.J.; Pitt, W.G.



Automata representation for Abelian groups  

NASA Astrophysics Data System (ADS)

A finite automaton is one of the classic models of recognition devices, which is used to determine the type of language a string belongs to. A string is said to be recognized by a finite automaton if the automaton "reads" the string from the left to the right starting from the initial state and finishing at a final state. Another type of automata which is a counterpart of sticker systems, namely Watson-Crick automata, is finite automata which can scan the double-stranded tapes of DNA strings using the complimentary relation. The properties of groups have been extended for the recognition of finite automata over groups. In this paper, two variants of automata, modified deterministic finite automata and modified deterministic Watson-Crick automata are used in the study of Abelian groups. Moreover, the relation between finite automata diagram over Abelian groups and the Cayley table is introduced. In addition, some properties of Abelian groups are presented in terms of automata.

Fong, Wan Heng; Gan, Yee Siang; Sarmin, Nor Haniza; Turaev, Sherzod



The centipede genus Eupolybothrus Verhoeff, 1907 (Chilopoda: Lithobiomorpha: Lithobiidae) in North Africa, a cybertaxonomic revision, with a key to all species in the genus and the first use of DNA barcoding for the group  

PubMed Central

Abstract The centipede genus Eupolybothrus Verhoeff, 1907 in North Africa is revised. A new cavernicolous species, Eupolybothrus kahfi Stoev & Akkari, sp. n., is described from a cave in Jebel Zaghouan, northeast Tunisia. Morphologically, it is most closely related to Eupolybothrus nudicornis (Gervais, 1837) from North Africa and Southwest Europe but can be readily distinguished by the long antennae and leg-pair 15, a conical dorso-median protuberance emerging from the posterior part of prefemur 15, and the shape of the male first genital sternite. Molecular sequence data from the cytochrome c oxidase I gene (mtDNA–5’ COI-barcoding fragment) exhibit 19.19% divergence between Eupolybothrus kahfi and Eupolybothrus nudicornis, an interspecific value comparable to those observed among four other species of Eupolybothrus which, combined with a low intraspecific divergence (0.3–1.14%), supports the morphological diagnosis of Eupolybothrus kahfi as a separate species. This is the first troglomorphic myriapod to be found in Tunisia, and the second troglomorph lithobiomorph centipede known from North Africa. Eupolybothrus nudicornis is redescribed based on abundant material from Tunisia and its post-embryonic development, distribution and habitat preferences recorded. Eupolybothrus cloudsley-thompsoni Turk, 1955, a nominal species based on Tunisian type material, is placed in synonymy with Eupolybothrus nudicornis. To comply with the latest technological developments in publishing of biological information, the paper implements new approaches in cybertaxonomy, such as fine granularity XML tagging validated against the NLM DTD TaxPub for PubMedCentral and dissemination in XML to various aggregators (GBIF, EOL, Wikipedia), vizualisation of all taxa mentioned in the text via the dynamically created Pensoft Taxon Profile (PTP) page, data publishing, georeferencing of all localities via Google Earth, and ZooBank, GenBank and MorphBank registration of datasets. An interactive key to all valid species of Eupolybothrus is made with DELTA software.

Stoev, Pavel; Akkari, Nesrine; Zapparoli, Marzio; Porco, David; Enghoff, Henrik; Edgecombe, Gregory D.; Georgiev, Teodor; Penev, Lyubomir



Permanent or reversible conjugation of 2?-O- or 5?-O-aminooxymethylated nucleosides with functional groups as a convenient and efficient approach to the modification of RNA and DNA sequences  

PubMed Central

2?-O-Aminooxymethyl ribonucleosides are prepared from their 3?,5?-disilylated 2?-O-phthalimidooxymethyl derivatives by treatment with NH4F in MeOH. The reaction of these novel ribonucleosides with 1-pyrenecarboxaldehyde results in the efficient formation of stable and yet reversible ribonucleoside 2?-conjugates in yields of 69–82%. Indeed, exposure of these conjugates to 0.5?M tetra-n-butylammonium fluoride (TBAF) in THF results in the cleavage of their iminoether functions to give the native ribonucleosides along with the innocuous nitrile side product. Conversely, the reaction of 5-cholesten-3-one or dansyl chloride with 2?-O-aminooxymethyl uridine provides permanent uridine 2?-conjugates, which are left essentially intact upon treatment with TBAF. Alternatively, 5?-O-aminooxymethyl thymidine is prepared by hydrazinolysis of its 3?-O-levulinyl-5?-O-phthalimidooxymethyl precursor. Pyrenylation of 5?-O-aminooxymethyl thymidine and the sensitivity of the 5?-conjugate to TBAF further exemplify the usefulness of this nucleoside for modifying DNA sequences either permanently or reversibly. Although the versatility and uniqueness of 2?-O-aminooxymethyl ribonucleosides in the preparation of modified RNA sequences is demonstrated by the single or double incorporation of a reversible pyrenylated uridine 2?-conjugate into an RNA sequence, the conjugation of 2?-O-aminooxymethyl ribonucleosides with aldehydes, including those generated from their acetals, provides reversible 2?-O-protected ribonucleosides for potential applications in the solid-phase synthesis of native RNA sequences. The synthesis of a chimeric polyuridylic acid is presented as an exemplary model.

Cieslak, Jacek; Grajkowski, Andrzej; Ausin, Cristina; Gapeev, Alexei; Beaucage, Serge L.



Forensic DNA typing in China  

Microsoft Academic Search

In the field of forensic genetics, essential developmental impulses come from the advances of the molecular biology and human genome projects. This paper overviews existing technologies for forensic genetics in China and gives a perspective of forensic DNA analysis. In China, work has been done in the development of blood group serology of the conventional markers. Forensic scientists in China

Y. P. Hou



Understanding spontaneous sharp bending of DNA  

NASA Astrophysics Data System (ADS)

Gene expression often requires the interplay of two distant genetic regions and thus sharp bending of DNA is essential for gene functioning. Contrary to the conventional thinking that the bending of DNA strand below its persistent length was essentially facilitated by DNA binding proteins, Widom's group recently demonstrated, using cyclization assay, that such kind of sharp bending can be spontaneously formed (Mol. Cell, 2004, 355). Two models were referred in the original work to explain this ``enhanced'' flexibility of short DNA strand, namely, the melted single- and double-bubble models. To elucidate the detailed mechanism behind the DNA sharp bending, DNA molecules containing single- and double-melted bubbles was synthesized by introducing non Watson-Crick base pairs to the DNA backbone. Time resolved fluorescence energy transfer was used as the major tool to evaluate the bending stiffness of afore mentioned short DNA strand. The effect of bubble size, number and position on the DNA stiffness was independently evaluated. The energetic penalty of forming the locally melted structure was determined using other individual experiments. These results not only clarify the physical origin of the previously observed cyclizability of short DNA strand but also help to interpret the cyclization data of DNA molecules of wider size ranges.

Yuan, Chongli; Rhoades, Elizabeth; Archer, Lynden



Prognostic Significance of DNA and Histone Methylation

Nutritional Science Research Group Recently Funded Projects Prognostic Significance of DNA and Histone Methylation Principal Investigator: Piyathilake, Chandrika J Institution: University of Alabama at Birmingham   NCI/DCP Program Director: Ross, Sharon


HMGNs, DNA Repair and Cancer  

PubMed Central

DNA lesions threaten the integrity of the genome and are a major factor in cancer formation and progression. Eukaryotic DNA is organized in nucleosome-based higher order structures, which form the chromatin fiber. In recent years, considerable knowledge has been gained on the importance of chromatin dynamics for the cellular response to DNA damage and for the ability to repair DNA lesions. High Mobility Group N 1 (HMGN1) protein is an emerging factor that is important for chromatin alterations in response to DNA damage originated from both ultra violet light (UV) and ionizing irradiation (IR). HMGN1 is a member in the HMGN family of chromatin architectural proteins. HMGNs bind directly to nucleosomes and modulate the structure of the chromatin fiber in a highly dynamic manner. This review focuses mainly on the roles of HMGN1 in the cellular response pathways to different types of DNA lesions and in transcriptional regulation of cancer-related genes. In addition, emerging roles for HMGN5 in cancer progression and for HMGN2 as a potential tool in cancer therapy will be discussed.

Gerlitz, Gabi



HMGNs, DNA repair and cancer.  


DNA lesions threaten the integrity of the genome and are a major factor in cancer formation and progression. Eukaryotic DNA is organized in nucleosome-based higher order structures, which form the chromatin fiber. In recent years, considerable knowledge has been gained on the importance of chromatin dynamics for the cellular response to DNA damage and for the ability to repair DNA lesions. High Mobility Group N1 (HMGN1) protein is an emerging factor that is important for chromatin alterations in response to DNA damage originated from both ultra violet light (UV) and ionizing irradiation (IR). HMGN1 is a member in the HMGN family of chromatin architectural proteins. HMGNs bind directly to nucleosomes and modulate the structure of the chromatin fiber in a highly dynamic manner. This review focuses mainly on the roles of HMGN1 in the cellular response pathways to different types of DNA lesions and in transcriptional regulation of cancer-related genes. In addition, emerging roles for HMGN5 in cancer progression and for HMGN2 as a potential tool in cancer therapy will be discussed. PMID:20004154

Gerlitz, Gabi



Mitochondrial DNA replacement versus nuclear DNA persistence  

NASA Astrophysics Data System (ADS)

In this paper we consider two populations whose generations are not overlapping and whose size is large. The number of males and females in both populations is constant. Any generation is replaced by a new one and any individual has two parents concerning nuclear DNA and a single one (the mother) concerning mtDNA. Moreover, at any generation some individuals migrate from the first population to the second. In a finite random time T, the mtDNA of the second population is completely replaced by the mtDNA of the first. In the same time, the nuclear DNA is not completely replaced and a fraction F of the ancient nuclear DNA persists. We compute both T and F. Since this study shows that complete replacement of mtDNA in a population is compatible with the persistence of a large fraction of nuclear DNA, it may have some relevance for the 'out of Africa'/multiregional debate in palaeoanthropology.

Serva, Maurizio



DNA systematics. Volume II  

Microsoft Academic Search

This book discusses the following topics: PLANTS: PLANT DNA: Contents and Systematics. Repeated DNA Sequences and Polyploidy in Cereal Crops. Homology of Nonrepeated DNA Sequences in Phylogeny of Fungal Species. Chloropast DNA and Phylogenetic Relationships. rDNA: Evolution Over a Billion Years. 23S rRNA-derived Small Ribosomal RNAs: Their Structure and Evolution with Reference to Plant Phylogeny. Molecular Analysis of Plant DNA




DNA Banking of Primary Immunodeficiency Disorders in Iran  

Microsoft Academic Search

Primary immunodeficiency disorders are a heterogeneous group of genetic disorders, with different modes of inheritance, consisting of more than 100 different types. We constructed the DNA banking of primary immunodeficiency disorders for the first time in Iran. The DNA of 31 immunodeficient patients and their families (total of 92 samples) were collected, as the first step for construction of DNA

Anna Isaian; Mostafa Moin; Zahra Pourpak; Nima Rezaei; Asghar Aghamohammadi; Masoud Movahedi; Mohammad Gharagozlou; Javad Ghaffari; Fariborz Zandieh; Mahboubeh Mansouri; Abolhassan Farhoudi


[Dna comets as markers of cells death].  


Unstimulated human peripheral blood lymphocytes gradually underwent death during incubation in vitro. According to morphological criteria, the type of death was identified as apoptosis. After immobilization in agarose, lysis, and electrophoresis, these lymphocytes formed DNA comets, which differed in DNA content, tail length, tail moment, and the fraction of DNA migrating in the comet tail. We classified the comets in 3 groups in accordance with the values of these parameters. There was a good correlation between the fraction of apoptotic cells (morphological data) and the fraction of "apoptotic" DNA comets. The results showed that DNA comets may be adequate markers of cell death (including apoptosis). The use of DNA comets as markers of spontaneous death made it possible to reveal an increased level of apoptosis in vitro lymphocytes from patients with systemic lupus erythematosus. PMID:10418679

Tronov, V A; Nikol'skaia, T A; Konopliannikov, M A


DNA-negative temperature-sensitive mutants of herpes simplex virus type 1: patterns of viral DNA synthesis after temperature shift-up.  

PubMed Central

Temperature-sensitive mutants of herpes simplex virus type 1 belonging to four DNA- complementation groups exhibited two distinct patterns of viral DNA synthesis after shift-up to the nonpermissive temperature. In cultures infected with mutants belonging to complementation groups A, C, and D, little or no viral DNA was synthesized after shift-up. In cultures infected with a mutant in complementation group B, nearly normal amounts of viral DNA were synthesized after shift-up.

Schaffer, P A; Bone, D R; Courtney, R J



Dual fluorescent labeling method to visualize plasmid DNA degradation.  


The efficiency of nonviral vectors for gene delivery may be enhanced by understanding the key barriers that limit the translocation of the therapeutic DNA into the nucleus. One such barrier is the instability of DNA in the cytoplasm. In this work, we have developed a method to dual-label plasmid DNA to be utilized as a tool to elucidate DNA instability during its trafficking in the intracellular microenvironment. Plasmid DNA containing rhodamine and maleimide groups linked using peptide nucleic acid (PNA) linkers was utilized for conjugation. Covalent conjugation of the maleimide group with a second fluorophore, fluorescein, did not alter the electrophoretic mobility or the structural integrity of the DNA, as confirmed by gel electrophoresis. The intact DNA was visualized as a single color (yellow) due to the close proximity of the green and red fluorophores. DNA degradation was simulated using restriction endonucleases (BamH1 and PflMI) to cut the DNA at two or more sites resulting in color separation. Confocal time-lapse imaging was utilized to follow DNA stability upon incubation of Lipofectamine2000/dual-labeled DNA complexes in CHO-K1 cells. Yellow fluorescent voxels were seen in the cell cytoplasm indicating the presence of intact DNA. Red and green fluorescent voxels were also seen in a few cells, suggesting separation of the fluorophores and probable DNA degradation. The methodology developed in this report provides a new tracking tool for investigators to explore DNA degradation at the molecular level inside single cell. PMID:19086903

Srinivasan, Charudharshini; Siddiqui, Shafiuddin; Silbart, Lawrence K; Papadimitrakopoulos, Fotios; Burgess, Diane J



DNA point mutation detection based on DNA ligase reaction and nano-Au amplification: A piezoelectric approach  

Microsoft Academic Search

A novel piezoelectric method for DNA point mutation detection based on DNA ligase reaction and nano-Au-amplified DNA probes is proposed. A capture probe was designed with the potential point mutation site located at the 3? end and a thiol group at the 5? end to be immobilized on the gold electrode surface of quartz crystal microbalance (QCM). Successive hybridization with

Lanlan Pang; Jishan Li; Jianhui Jiang; Guoli Shen; Ruqin Yu



DNA adsorption characteristics of hollow spherule allophane nano-particles.  


To understand the propensity of natural allophane to adsorb the DNA molecules, the adsorption characteristics were assessed against natural allophane (AK70), using single-stranded DNA (ss-DNA) and adenosine 5'-monophosphate (5'-AMP) as a reference molecule. The adsorption capacity of ss-DNA on AK70 exhibited one order of magnitude lower value as compared with that of 5'-AMP. The adsorption capacity of ss-DNA decreased with increasing pH due to the interaction generated between phosphate groups of ss-DNA and functional Al-OH groups on the wall perforations through deprotonating, associated with higher energy barrier for the adsorption of ss-DNA. The adsorption morphologies consisting of the individual ss-DNA with mono-layer coverage of the clustered allophane particle were observed successfully through transmission electron microscopy analysis. PMID:24094227

Matsuura, Yoko; Iyoda, Fumitoshi; Arakawa, Shuichi; John, Baiju; Okamoto, Masami; Hayashi, Hidetomo



Mitochondrial DNA diversity in the Polish Roma.  


Mitochondrial DNA variability in the Polish Roma population has been studied by means of hypervariable segment I and II (HVS I and II) sequencing and restriction fragment-length polymorphism analysis of the mtDNA coding region. The mtDNA haplotypes detected in the Polish Roma fall into the common Eurasian mitochondrial haplogroups (H, U3, K, J1, X, I, W, and M*). The results of complete mtDNA sequencing clearly indicate that the Romani M*-lineage belongs to the Indian-specific haplogroup M5, which is characterized by three transitions in the coding region, at sites 12477, 3921 and 709. Molecular variance analysis inferred from mtDNA data reveals that genetic distances between the Roma groups are considerably larger than those between the surrounding European populations. Also, there are significant differences between the Bulgarian Roma (Balkan and Vlax groups) and West European Roma (Polish, Lithuanian and Spanish groups). Comparative analysis of mtDNA haplotypes in the Roma populations shows that different haplotypes appear to demonstrate impressive founder effects: M5 and H (16261-16304) in all Romani groups; U3, I and J1 in some Romani groups. Interestingly, haplogroup K (with HVS I motif 16224-16234-16311) found in the Polish Roma sample seems to be specific for Ashkenazi Jewish populations. PMID:16626330

Malyarchuk, B A; Grzybowski, T; Derenko, M V; Czarny, J; Mi?cicka-Sliwka, D



Site-directed DNA crosslinking of large multisubunit protein-DNA complexes.  


Several methods have been developed to site-specifically incorporate photoreactive nucleotide analogs into DNA for the purpose of identifying the proteins and their domains that are in contact with particular regions of DNA. The synthesis of several deoxynucleotide analogs that have a photoreactive group tethered to the nucleotide base and the incorporation of these analogs into DNA are described. In a second approach, oligonucleotide with a photoreactive group attached to the phosphate backbone is chemically synthesized. The photoreactive oligonucleotide is then enzymatically incorporated into DNA by annealing it to a complementary DNA template and extending with DNA polymerase. Both approaches have been effectively used to map protein-DNA interactions in large multisubunit complexes such as the eukaryotic transcription or ATP-dependent chromatin remodeling complexes. Not only do these techniques map the binding sites of the various subunits in these complexes, but when coupled with peptide mapping also determine the protein domain that is in close proximity to the different DNA sites. The strength of these techniques is the ability to scan a large number of potential sites by making combinations of different DNA probes and is facilitated by using an immobilized DNA template for synthesis. PMID:19378181

Persinger, Jim; Bartholomew, Blaine



Complex Reflection Groups, Braid Groups, Hecke Algebras  

Microsoft Academic Search

Presentations "à la Coxeter" are given for all (irreducible) finite complex reflection groups. They provide presentations for the corresponding generalized braid groups (for all but six cases), which allow us to generalize some of the known properties of finite Coxeter groups and their associated braid groups, such as the computation of the center of the braid group and the construction

Michel Broué; Gunter Malle; Raphaël Rouquier



Group Composition, Creative Synergy, and Group Performance.  

ERIC Educational Resources Information Center

A study of 94 intact autonomous work groups performing multi-part tasks revealed that group creative performance increased exponentially with the number of highly creative group members composing the group. However, this occurred only when Team Creativity-Relevant Processes within the group were relatively high. (Contains references.) (Author/CR)

Taggar, Simon



Detection and quantitation of single nucleotide polymorphisms, DNA sequence variations, DNA mutations, DNA damage and DNA mismatches  

Microsoft Academic Search

DNA mutation binding proteins alone and as chimeric proteins with nucleases are used with solid supports to detect DNA sequence variations, DNA mutations and single nucleotide polymorphisms. The solid supports may be flow cytometry beads, DNA chips, glass slides or DNA dips sticks. DNA molecules are coupled to solid supports to form DNA-support complexes. Labeled DNA is used with unlabeled

McCutchen-Maloney; Sandra L



Ancient DNA from ice age insects: proceed with caution  

NASA Astrophysics Data System (ADS)

The paucity of ancient DNA (aDNA) studies in insects can be traced to the dismissal of the 1990s reports of DNA isolation from amber-entombed insects. In retrospect, amber was an obvious place to start, but it has since been demonstrated that DNA preservation is not necessarily correlated with physical preservation. The discipline of aDNA is rapidly progressing as issues regarding contamination with modern sequences and detection of DNA damage are addressed. Two major concerns in ancient DNA studies are the co-purification of DNA polymerase inhibitors and the presence of DNA lesions. Preliminary data demonstrate DNA extraction is possible from beetle remains isolated from packrat middens. Although specimens from permafrost sediments and ancient rodent middens are potential sources of aDNA, collection and curation procedures require modification to minimize contamination and optimize DNA yield. Since aDNA isolation in insects requires the complete destruction of fossil material, another consideration is the taxonomic groups that are adequately represented to justify the sacrifice of geological specimens. Although most recommended aDNA authentication procedures are easily followed, some are impossible for insect samples due to their small size, making the establishment of authentication procedures of aDNA from small samples a final consideration.

Reiss, Rebecca A.



Quantitative DNA fiber mapping  


The present invention relates generally to the DNA mapping and sequencing technologies. In particular, the present invention provides enhanced methods and compositions for the physical mapping and positional cloning of genomic DNA. The present invention also provides a useful analytical technique to directly map cloned DNA sequences onto individual stretched DNA molecules.

Gray, Joe W. (San Francisco, CA); Weier, Heinz-Ulrich G. (Oakland, CA)



DNA Secret Sharing  

Microsoft Academic Search

The aim of the paper is to obtain a DNA secret sharing scheme for general access structure that plays an important role in cryptography. Our scheme involves two very simple DNA computing techniques known as mixing and DNA sequencing. The simplicity of these two techniques and the compact nature of DNA make the system easy to implement. Moreover the scheme

Avishek Adhikari



DNA Demethylation by TDG  

PubMed Central

Summary DNA methylation has long been considered a very stable DNA modification in mammals that could only be removed by replication in the absence of re-methylation, i.e. by mere dilution of this epigenetic mark (so-called passive DNA demethylation). However, in recent years, a significant number of studies have revealed the existence of active processes of DNA demethylation in mammals, with important roles in development and transcriptional regulation, allowing the molecular mechanisms of active DNA demethylation to be unraveled. Here we review the recent literature highlighting the prominent role played in active DNA demethylation by base excision repair and especially by Thymine DNA Glycosylase.

Dalton, Shannon R.; Bellacosa, Alfonso



Poxvirus DNA replication.  


Poxviruses are large, enveloped viruses that replicate in the cytoplasm and encode proteins for DNA replication and gene expression. Hairpin ends link the two strands of the linear, double-stranded DNA genome. Viral proteins involved in DNA synthesis include a 117-kDa polymerase, a helicase-primase, a uracil DNA glycosylase, a processivity factor, a single-stranded DNA-binding protein, a protein kinase, and a DNA ligase. A viral FEN1 family protein participates in double-strand break repair. The DNA is replicated as long concatemers that are resolved by a viral Holliday junction endonuclease. PMID:23838441

Moss, Bernard



Cross-linking of DNA through HMGA1 suggests a DNA scaffold  

PubMed Central

Binding of proteins to DNA is usually considered 1D with one protein bound to one DNA molecule. In principle, proteins with multiple DNA binding domains could also bind to and thereby cross-link different DNA molecules. We have investigated this possibility using high-mobility group A1 (HMGA1) proteins, which are architectural elements of chromatin and are involved in the regulation of multiple DNA-dependent processes. Using direct stochastic optical reconstruction microscopy (dSTORM), we could show that overexpression of HMGA1a-eGFP in Cos-7 cells leads to chromatin aggregation. To investigate if HMGA1a is directly responsible for this chromatin compaction we developed a DNA cross-linking assay. We were able to show for the first time that HMGA1a can cross-link DNA directly. Detailed analysis using point mutated proteins revealed a novel DNA cross-linking domain. Electron microscopy indicates that HMGA1 proteins are able to create DNA loops and supercoils in linearized DNA confirming the cross-linking ability of HMGA1a. This capacity has profound implications for the spatial organization of DNA in the cell nucleus and suggests cross-linking activities for additional nuclear proteins.

Vogel, Benjamin; Loschberger, Anna; Sauer, Markus; Hock, Robert



Active DNA Demethylation Mediated by DNA Glycosylases  

PubMed Central

Active DNA demethylation is involved in many vital developmental and physiological processes of plants and animals. Recent genetic and biochemical studies in Arabidopsis have demonstrated that a subfamily of DNA glycosylases function to promote DNA demethylation through a base excision-repair pathway. These specialized bifunctional DNA glycosylases remove the 5-methylcytosine base and then cleave the DNA backbone at the abasic site, resulting in a gap that is then filled with an unmethylated cytosine nucleotide by as yet unknown DNA polymerase and ligase enzymes. Evidence suggests that active DNA demethylation in mammalian cells is also mediated at least in part by a base excision repair pathway where the AID/Apobec family of deaminases convert 5-methylcytosine to thymine followed by G/T mismatch repair by the DNA glycosylase MBD4 or TDG. This review also discusses other possible mechanisms of active DNA demethylation, how genome DNA methylation status might be sensed to regulate the expression of demethylase genes, and the targeting of demethylases by small RNAs.

Zhu, Jian-Kang



Functions of DNA Polymerase  

Microsoft Academic Search

Eukaryotes contain multiple DNA polymerases which ensure the accurate and efficient repli- cation of the genome as well as protection and repair from endogenous and environmental DNA damaging agents. In most eukaryotes, the main replicative enzymes are DNA poly- merases a, d ,a nde (reviewed in Garcia-Diaz andBebenek, 2007).Inyeast,DNA polymerase a (DNA pol a) initiates synthesis on the lagging strand.

Nancy A. Eckardt



DNA Transformation, Continued  

NSDL National Science Digital Library

DNA transformation is a naturally occurring but rare event in which DNA can be transferred into bacteria. In 1970, Morton Mandel and Akiko Higa discovered a way to make E. coli more 'competent' for transforming foreign DNA. Their calcium chloride method is widely used today to obtain high-efficiency transforming cells. This animation from Cold Spring Harbor Laboratory's Dolan DNA Learning Center presents the second part of explaining DNA transformation through a series of illustrations of the processes involved.



Amplified DNA Biosensors  

Microsoft Academic Search

\\u000a Amplified detection of DNA is a central research topic in modern bioanalytical science. Electronic or optical transduction\\u000a of DNA recognition events provides readout signals for DNA biosensors. Amplification of the DNA analysis is accomplished by\\u000a the coupling of nucleic acid-functionalized enzymes or nucleic acid-functionalized nanoparticles (NP) as labels for the DNA\\u000a duplex formation. This chapter discusses the amplified amperometric analysis

Itamar Willner; Bella Shlyahovsky; Bilha Willner; Maya Zayats



Application of nested PCR and mass spectrometry for DNA-based virus detection: HBV-DNA detected in the majority of isolated anti-HBc positive sera  

Microsoft Academic Search

DNA preparations from three different groups of serum samples were examined for HBV-DNA via a nested polymerase chain reaction assay (lower detection limit: 10 viral genomes in 100 ?l serum): Group I consisted of 11 uninfected control sera, group II consisted of sera obtained from 11 HBV infected patients and group III consisted of 21 isolated anti-HBc positive samples. The

Christian Jurinke; Bernhard Zöllner; Heinz-Hubert Feucht; Dirk van den Boom; Anette Jacob; Susanne Polywka; Rainer Laufs; Hubert Köster



Fluorescence Studies of DNA, DNA Binding Drugs and Dna-Drug Interactions.  

NASA Astrophysics Data System (ADS)

The complex fluorescence behaviors of 9-amino -6-chloro-2-methoxyacridine (ACMA) and quinacrine are studied using time-resolved fluorescence spectroscopy. The fluorescence emission properties of ACMA under various experimental conditions are examined in detail. After eliminating most of the possible explanations, it is shown that the nonexponential fluorescence decay of ACMA is due to an excited state cis and trans isomerization of the methoxy group. In the case of quinacrine, excited state proton transfer as well as the cis to trans isomerization of the methoxy group combined with motions of the side chain at the 9-position may contribute to the complex fluorescence emission in this molecule. Using quinacrine and ACMA as fluorescence probes, anisotropic internal motions of natural DNA and various synthetic polynucleotides are studied through time-resolved fluorescence polarization anisotropy (FPA) of the intercalated dye/DNA complex. The observation that the value of the DNA torsion constant is independent of the choice of intercalating dye justifies using fluorescence measurements to probe DNA motion on the nanosecond timescale, although an absolute value of the DNA torsional rigidity might be difficult to determine because this parameter is model dependent and the exact dye binding site geometries are uncertain. The torsional rigidity of DNA is sequence dependent. Assuming that the quinacrine binding site geometry is the same in various polynucleotides, the torsional rigidities of the compounds studied decrease in the order: poly(rI) cdotpoly(rC) > poly(dI) cdotpoly(dC) ~ CT DNA > poly(dA-dT)cdot poly(dA-dT) ~ poly(dA) cdotpoly(dT). The (A-form) ribonucleotide poly(rI)cdotpoly(rC) is more rigid than the corresponding (B-form) deoxyribonucleotide poly(dI) cdotpoly(dC). The binding of intercalators ethidium bromide and acridine orange on the Z-form poly(dG-m^5 dC)cdotpoly(dG-m^5 dC) is characterized using fluorescence titration measurements, CD measurements and energy transfer experiments. It is found that below the critical drug concentrations both drugs can bind to Z-form DNA by intercalation, but with lower binding constant compared to that on B-form DNA. The binding of these molecules introduces significant structural distortion of the Z-form DNA near the binding site, and the local structure at the binding site is likely to resemble the right handed B-form DNA. The binding of nonintercalators on Z-form DNA is also studied indirectly through energy transfer experiments. The mode of binding of nonintercalators on B- and Z-form DNA is similar, and there are no dye induced structural transformations within the Z-form DNA.

Fan, Pei


Correlated motions in DNA  

SciTech Connect

The furanose ring of nucleic acids plays a key role in detrmining the conformations of nucleic acids because it shares a common bond C3'-C4'(psi') with the sugar-phosphate backbone. This structural feature enables the transmission of conformational changes between the side-chain base and the backbone through conformational correlations between the base and sugar. Thermally-induced local fluctuations of P can be transmitted along the backbone through psi', particularly when the sugar is in the C2'-endo domain. The sugar pucker-dependent flexibility of DNA is further exemplified by studies that have shown that due to steric interactions, absence of the 2'-OH group in deoxyribose tends to increase the conformational flexibility about the internucleotide phosphodiester (,') especially when the sugar assumes the C2'-endo pucker.

Sundaralingam, M.; Westhof, E.



Study of the DNA damage checkpoint using Xenopus egg extracts.  


On a daily basis, cells are subjected to a variety of endogenous and environmental insults. To combat these insults, cells have evolved DNA damage checkpoint signaling as a surveillance mechanism to sense DNA damage and direct cellular responses to DNA damage. There are several groups of proteins called sensors, transducers and effectors involved in DNA damage checkpoint signaling (Figure 1). In this complex signaling pathway, ATR (ATM and Rad3-related) is one of the major kinases that can respond to DNA damage and replication stress. Activated ATR can phosphorylate its downstream substrates such as Chk1 (Checkpoint kinase 1). Consequently, phosphorylated and activated Chk1 leads to many downstream effects in the DNA damage checkpoint including cell cycle arrest, transcription activation, DNA damage repair, and apoptosis or senescence (Figure 1). When DNA is damaged, failing to activate the DNA damage checkpoint results in unrepaired damage and, subsequently, genomic instability. The study of the DNA damage checkpoint will elucidate how cells maintain genomic integrity and provide a better understanding of how human diseases, such as cancer, develop. Xenopus laevis egg extracts are emerging as a powerful cell-free extract model system in DNA damage checkpoint research. Low-speed extract (LSE) was initially described by the Masui group. The addition of demembranated sperm chromatin to LSE results in nuclei formation where DNA is replicated in a semiconservative fashion once per cell cycle. The ATR/Chk1-mediated checkpoint signaling pathway is triggered by DNA damage or replication stress. Two methods are currently used to induce the DNA damage checkpoint: DNA damaging approaches and DNA damage-mimicking structures. DNA damage can be induced by ultraviolet (UV) irradiation, ?-irradiation, methyl methanesulfonate (MMS), mitomycin C (MMC), 4-nitroquinoline-1-oxide (4-NQO), or aphidicolin. MMS is an alkylating agent that inhibits DNA replication and activates the ATR/Chk1-mediated DNA damage checkpoint. UV irradiation also triggers the ATR/Chk1-dependent DNA damage checkpoint. The DNA damage-mimicking structure AT70 is an annealed complex of two oligonucleotides poly-(dA)70 and poly-(dT)70. The AT70 system was developed in Bill Dunphy's laboratory and is widely used to induce ATR/Chk1 checkpoint signaling. Here, we describe protocols (1) to prepare cell-free egg extracts (LSE), (2) to treat Xenopus sperm chromatin with two different DNA damaging approaches (MMS and UV), (3) to prepare the DNA damage-mimicking structure AT70, and (4) to trigger the ATR/Chk1-mediated DNA damage checkpoint in LSE with damaged sperm chromatin or a DNA damage-mimicking structure. PMID:23149695

Willis, Jeremy; DeStephanis, Darla; Patel, Yogin; Gowda, Vrushab; Yan, Shan



DNA degradation with ozone.  


DNA was ozonized in solution and the reaction was followed with polarimetry and with iodimetry. Polarimetry was used to determine the molar ratio DNA/O(3) when the DNA optical activity vanishes completely. At a molar ratio DNA/O(3)=2.3 the supramolecular structure of DNA collapses completely. Instead, iodimetry shows that the ozonolysis proceeds until all the nucleobases have been destroyed, an event which occurs at a molar ratio DNA/O(3)=1.1. The ozonolysis of DNA was also followed spectrophotometrically. DNA is reactive with ozone also in the solid state, as fixed bed. Clear indication about its oxidation derives from the FT-IR spectra from polarimetric measurements and from thermal analysis performed by thermogravimetric analysis (TGA), differential thermogravimetric analysis (DTG) and from differential thermal analysis (DTA). Particular remarkable is the fact that RNA has been found much less reactive toward ozone in the solid state than DNA. PMID:16616954

Cataldo, Franco



Dietary DNA in blood and organs of Atlantic salmon ( Salmo salar L.)  

Microsoft Academic Search

The objective of this study was to investigate the uptake of dietary DNA into blood, kidney, and liver of salmon, and to determine the DNA fragment size if dietary DNA was detected. Salmon in groups of five fish were force-fed a feed containing a high copy number of three polymerase chain reaction (PCR) amplified DNA fragments. Tissue samples were dissected

Christer Røss Nielsen; Knut G. Berdal; Anne Marie Bakke-McKellep; Arne Holst-Jensen



Vinylsulfonamide and Acrylamide Modification of DNA for Cross-linking with Proteins.  


Bioorthogonal covalent cross-linking of DNA-binding proteins (p53) to DNA was achieved through novel DNA probes bearing a reactive vinylsulfonamide (VS) group. The VS-modified dCTP served as building block for polymerase synthesis of modified DNA, which was readily conjugated with cysteine-containing peptides and proteins by Michael addition. PMID:23939933

Dadová, Jitka; Orság, Petr; Pohl, Radek; Brázdová, Marie; Fojta, Miroslav; Hocek, Michal



Molecular Mechanisms of DNA Polymerase Clamp Loaders  

NASA Astrophysics Data System (ADS)

Clamp loaders are ATP-driven multiprotein machines that couple ATP hydrolysis to the opening and closing of a circular protein ring around DNA. This ring-shaped clamp slides along DNA, and interacts with numerous proteins involved in DNA replication, DNA repair and cell cycle control. Recently determined structures of clamp loader complexes from prokaryotic and eukaryotic DNA polymerases have revealed exciting new details of how these complex AAA+ machines perform this essential clamp loading function. This review serves as background to John Kuriyan's lecture at the 2010 Erice School, and is not meant as a comprehensive review of the contributions of the many scientists who have advanced this field. These lecture notes are derived from recent reviews and research papers from our groups.

Kelch, Brian; Makino, Debora; Simonetta, Kyle; O'Donnell, Mike; Kuriyan, John


DNA ligase-mediated translation of DNA into densely functionalized nucleic acid polymers.  


We developed a method to translate DNA sequences into densely functionalized nucleic acids by using T4 DNA ligase to mediate the DNA-templated polymerization of 5'-phosphorylated trinucleotides containing a wide variety of appended functional groups. This polymerization proceeds sequence specifically along a DNA template and can generate polymers of at least 50 building blocks (150 nucleotides) in length with remarkable efficiency. The resulting single-stranded highly modified nucleic acid is a suitable template for primer extension using deep vent (exo-) DNA polymerase, thereby enabling the regeneration of template DNA. We integrated these capabilities to perform iterated cycles of in vitro translation, selection, and template regeneration on libraries of modified nucleic acid polymers. PMID:23256841

Hili, Ryan; Niu, Jia; Liu, David R



DNA Ligase-Mediated Translation of DNA Into Densely Functionalized Nucleic Acid Polymers  

PubMed Central

We developed a method to translate DNA sequences into densely functionalized nucleic acids by using T4 DNA ligase to mediate the DNA-templated polymerization of 5?-phosphorylated trinucleotides containing a wide variety of appended functional groups. This polymerization proceeds sequence specifically along a DNA template and can generate polymers of at least 50 building blocks (150 nucleotides) in length with remarkable efficiency. The resulting single-stranded highly modified nucleic acid is a suitable template for primer extension using deep vent (exo-) DNA polymerase, thereby enabling the regeneration of template DNA. We integrated these capabilities to perform iterated cycles of in vitro translation, selection, and template regeneration on libraries of modified nucleic acid polymers.



Chemical method for introducing haptens on to DNA probes  

SciTech Connect

The authors developed a versatile chemical method of attaching hapten moieties onto DNA, for the construction of nonisotopic DNA probes. The DNA is reacted with N-bromosuccinimide at alkaline pH, resulting in bromination of a fraction of the thymine, guanine, and cytosine residues, with adenine modified to a lesser extent. The bromine is subsequently displaced by a primary amino group, attached to a linker arm. The other end of the linker arm has a detectable group preattached to it. They have labeled cloned hepatitis B viral (HBV) DNA with the hapten 2,4-dinitrophenyl (DNP) and used it in combination with a high affinity rabbit anti-DNP antibody, for the detection of hepatitis B DNA by slot blotting. This probe was sensitive enough to specifically detect 1 x 10/sup -17/ mol (1 x 10/sup 6/ copies) of HBV DNA in total DNA from human serum.

Keller, G.H.; Cumming, C.U.; Huang, D.P.; Manak, M.M.; Ting, R.



Ultraviolet light-denatured DNA/anti-ultraviolet light-denatured DNA immune-complex nephritis in rabbits  

SciTech Connect

Two groups of preimmunized rabbits were studied during a 3-month course of daily intravenous injections of uv DNA in amounts sufficient to neuralize circulating antibody. One group was given high-molecular-weight uv DNA, and the other group, US uv DNA. Rabbits receiving US uv DNA formed potentially more damaging immune complexes, since this group of animals developed greater rises in blood urea and greater falls in C3. Both groups of animals developed evidence of immune complex-mediated glomerular nephritis as evidenced by heavy granular deposits of IgG and C3 in the glomeruli. The results suggest that immune complexes formed with US uv DNA may be more nephrotoxic.

Sweny, P.



DNA bar-coding for phytoplasma identification.  


Phytoplasma identification has proved difficult due to their inability to be maintained in vitro. DNA barcoding is an identification method based on comparison of a short DNA sequence with known sequences from a database. A DNA barcoding tool has been developed for phytoplasma identification. While other sequence-based methods may be well adapted to identification of particular strains of phytoplasmas, often they cannot be used for the simultaneous identification of phytoplasmas from different groups. The phytoplasma DNA barcoding protocol in this chapter, based on the tuf and 16SrRNA genes, can be used to identify the following phytoplasma groups: 16SrI, 16SrII, 16SrIII, 16SrIV, 16SrV, 16SrVI, 16SrVII, 16SrIX, 16SrX, 16SrXI, 16SrXII, 16SrXV, 16SrXX, 16SrXXI. PMID:22987426

Makarova, Olga; Contaldo, Nicoletta; Paltrinieri, Samanta; Bertaccini, Assunta; Nyskjold, Henriette; Nicolaisen, Mogens



Small-Group Teaching  

NSDL National Science Digital Library

This text explores the organization, methodology, and effectiveness of small group instruction. The following topics are discussed in detail: 1) rationale and objectives for small group instruction; 2) group roles and interpersonal dynamics; 3) different types of groups and their instructional purpose; 4) group organization; 5) skills required in group interaction; and 6) group activities such as discussions, games, role playing, and simulations.

Sharan, Shlomo; Sharan, Yael



Genetic evidence for the involvement of DNA ligase IV in the DNA-PK-dependent pathway of non-homologous end joining in mammalian cells  

Microsoft Academic Search

Cells of vertebrates remove DNA double-strand breaks (DSBs) from their genome predominantly utilizing a fast, DNA-PKcs-dependent form of non- homologous end joining (D-NHEJ). Mutants with inactive DNA-PKcs remove the majority of DNA DSBs utilizing a slow, DNA-PKcs-independent pathway that does not utilize genes of the RAD52 epistasis group, is error-prone and can therefore be classified as af orm of NHEJ

Huichen Wang; Zhao-Chong Zeng; Ange R. Perrault; Xinbo Cheng; Wei Qin; George Iliakis



Persistence of cccDNA during the natural history of chronic hepatitis B and decline during adefovir dipivoxil therapy 1 1 In addition to the Adefovir Dipivoxil cccDNA Study Group investigators, the authors thank the study site personnel and patients who participated in this study; Huiling Yang, Manuel Tsiang, Anant Jain, Craig James, Rick Fallis, John Fry, and Michael Wulfsohn of Gilead Sciences for their support and advice during this study; Hans Will and Maura Dandri for critical review of this manuscript; and Brian Sutton and Jennifer Elder of Inveresk (Cary, North Carolina) for advice and independent validation of statistical analyses. P.M. represents the Adefovir Dipivoxil cccDNA Study Group, which also includes the following clinical investigators: Peter Buggisch (Universitätskrankenhaus Hamburg-Eppendorf, Germany); Ian Kronberg (Western Hospital, Melbourne, Australia); William Sievert (Monash University and Medical Centre, Melbourne, Australia); Stanislas Pol (Hôpital Necker, Pa  

Microsoft Academic Search

Background & Aims: Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) is a unique episomal replicative intermediate responsible for persistent infection of hepatocytes. Technical constraints have hampered the direct study of cccDNA maintenance and clearance mechanisms in patients. The aim of this study was to develop a sensitive and specific assay for quantifying cccDNA in biopsy samples from chronic

Scott Bowden; Stephen Locarnini; Karsten Wursthorn; Jorg Petersen; George Lau; Christian Trepo; Patrick Marcellin; Zachary Goodman; William E. Delaney; Shelly Xiong; Carol L. Brosgart; Craig S. Gibbs; Fabien Zoulim



Readily reusable electrochemical DNA hybridization biosensor based on the interaction of DNA with single-walled carbon nanotubes.  


Carboxylic group-functionalized single-walled carbon nanotubes (SWNTs) were assembled vertically on the glassy carbon electrode using ethylenediamine as linking agent to fabricate an aligned electrode (SWNTE). Single-stranded DNA (ssDNA) wrapped around the SWNTs to form ssDNA-wrapped SWNTE structures based on the interaction between ssDNA and SWNT. A sensitive differential pulse voltammetric (DPV) response was obtained at the ssDNA-wrapped SWNTE owing to the electrooxidation of guanine bases. Double-stranded DNA (dsDNA) was formed when ssDNA on the ssDNA-wrapped SWNTE was hybridized with complementary ssDNA (cDNA). The dsDNA was removed from the SWNTs by undergoing a process of preconditioning at -0.6 V. Consequentially, the DPV response of guanine bases decreased. The used SWNTE could be renewed easily via ultrasonically rinsing. On the basis of this mechanism, a label-free and readily reusable electrochemical DNA hybridization biosensor was designed by directly monitoring the current change of guanine bases. Under optimum conditions, the plot of the measurement signal of guanine bases versus the cDNA concentrations was a good straight line in the range of 40-110 nM with a detection limit of 20 nM (3s). The biosensor can be switched to detect different target DNAs easily. PMID:20337392

Zhang, Xuzhi; Jiao, Kui; Liu, Shufeng; Hu, Yuwei



HMGB Binding to DNA: Single and Double Box Motifs  

PubMed Central

High Mobility Group (HMG) proteins are nuclear proteins believed to significantly affect DNA interactions by altering nucleic acid flexibility. HMG group B proteins contain HMG box domains known to bind into the DNA minor groove without sequence specificity, slightly intercalating base pairs and inducing a strong bend in the DNA helix axis. A dual beam optical tweezers is used to extend double–stranded DNA (dsDNA) in the absence and presence of a single box derivative of human HMGB2 [HMGB2(box A)] and a double box derivative of rat HMGB1 [HMGB1(box A+B)]. The single box domain is observed to reduce the persistence length of the double helix, generating sharp DNA bends with an average bend angle of 99 ± 9°, and at very high concentrations also stabilizing dsDNA against denaturation. The double box protein contains two consecutive HMG box domains joined by a flexible tether. This protein also reduces the DNA persistence length, induces an average bending angle of 77 ± 7° and stabilizes dsDNA at significantly lower concentrations. These results suggest that the single and double box proteins increase DNA flexibility and stability, but both effects are achieved at much lower protein concentrations for the double box. In addition, at low concentrations the single box protein can alter DNA flexibility without stabilizing dsDNA, while stabilization at higher concentration is likely achieved through a cooperative binding mode.

McCauley, Micah J.; Zimmerman, Jeff; Maher, L. James; C.Williams, Mark



Nucleotide sequence of cassava latent virus DNA  

Microsoft Academic Search

Only two groups of plant viruses, the caulimoviruses1,2 and the geminiviruses3, are known to contain a genome of DNA. Unlike that of the caulimoviruses, the genome of the geminivinises is composed of single-stranded, covalently-closed circles of DNA. There is evidence that the geminiviruses, specifically bean golden mosaic virus4 and tomato golden mosaic virus5, have a genome composed of two similar-sized

John Stanley; Michael R. Gay



Amplified DNA Biosensors  

NASA Astrophysics Data System (ADS)

Amplified detection of DNA is a central research topic in modern bioanalytical science. Electronic or optical transduction of DNA recognition events provides readout signals for DNA biosensors. Amplification of the DNA analysis is accomplished by the coupling of nucleic acid-functionalized enzymes or nucleic acid-functionalized nanoparticles (NP) as labels for the DNA duplex formation. This chapter discusses the amplified amperometric analysis of DNA by redox enzymes, the amplified optical sensing of DNA by enzymes or DNAzymes, and the amplified voltammetric, optical, or microgravimetric analysis of DNA using metallic or semiconductor nanoparticles. Further approaches to amplify DNA detection involve the use of micro-carriers of redox compounds as labels for DNA complex formation on electrodes, or the use of micro-objects such as liposomes, that label the resulting DNA complexes on electrodes and alter the interfacial properties of the electrodes. Finally, DNA machines are used for the optical detection of DNA, and the systems are suggested as future analytical procedures that could substitute the polymerase chain reaction (PCR) process.

Willner, Itamar; Shlyahovsky, Bella; Willner, Bilha; Zayats, Maya


Identification of Phytophthora citrophthora with Cloned DNA Probes  

PubMed Central

Two different DNA fragments, one of 2.9 kilobases and the other of 5.1 kilobases, were cloned from Phytophthora citrophthora and showed no homology with DNA from plants and other related fungi. These DNA probes hybridized with DNA from 12 different P. citrophthora isolates obtained from a variety of hosts but did not hybridize with DNA from 6 P. citrophthora isolates obtained from cacao. Southern blot analysis revealed that the probes contained repetitive DNA, and restriction fragment length polymorphisms were identified among several P. citrophthora isolates. Of the isolates tested, two major groups were observed whose genetic similarity correlated with geographical distribution. One of the DNA probes was used to detect P. citrophthora growing from infected citrus roots incubated on semiselective medium. P. citrophthora was not detected by a hybridization assay of total DNA extracted directly from infected roots. Images

Goodwin, P. H.; Kirkpatrick, B. C.; Duniway, J. M.



DNA strands robed with ionic liquid moiety.  


An ionic liquid domain was successfully prepared outside double-stranded DNA by fixing 1-alkyl-3-methyl-imidazolium (C(n)MI) cations on the phosphate groups of DNA. First, four species of ionic liquid were made using phosphoric acid di-n-butyl ester and C(n)MI (n=2,4,8, and 12) as a low molecular weight model. They were obtained as liquid salts, and their ionic conductivity ranged up to 10(-5)Scm(-1) at 50 degrees C. Based on this model study, counter cations of the phosphate groups of DNA were exchanged for four kinds of imidazolium cations. The resulting ionic liquid-robed DNA (IL-robed DNA) was soluble in ordinary organic solvents such as methanol or ethanol. Ionic conductivity was low, because the ion density was insufficient to form a continuous ionic liquid domain around the DNA strands. When 11mol% 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIBF(4)), which is a typical ionic liquid, was mixed with the IL-robed DNA, an ionic conductivity of 5.4 x 10(-5) S cm(-1) at 30 degrees C was observed because a continuous ionic liquid domain was successfully formed. PMID:15860212

Nishimura, Naomi; Nomura, Yasuhiro; Nakamura, Nobuhumi; Ohno, Hiroyuki



Promiscuous DNA synthesis by human DNA polymerase ?  

PubMed Central

The biological role of human DNA polymerase ? (POLQ) is not yet clearly defined, but it has been proposed to participate in several cellular processes based on its translesion synthesis capabilities. POLQ is a low-fidelity polymerase capable of efficient bypass of blocking lesions such as abasic sites and thymine glycols as well as extension of mismatched primer termini. Here, we show that POLQ possesses a DNA polymerase activity that appears to be template independent and allows efficient extension of single-stranded DNA as well as duplex DNA with either protruding or multiply mismatched 3?-OH termini. We hypothesize that this DNA synthesis activity is related to the proposed role for POLQ in the repair or tolerance of double-strand breaks.

Hogg, Matthew; Sauer-Eriksson, A. Elisabeth; Johansson, Erik



Enzymatic Photoreactivation of DNA.  

National Technical Information Service (NTIS)

The distinguishing hallmarks of photoreactivation of DNA is the enzyme-mediated, light-dependent monomerization of pyrimidine dimers resulting in repair of the DNA and restoration of its biological integrity. Photoreactivation is differentiated from sensi...

B. M. Sutherland



Make a DNA Model  

NSDL National Science Digital Library

In this activity, learners make a 3-D model of DNA using paper and toothpicks. While constructing this model, learners will explore the composition and structure of DNA. The activity also gives suggestions for alternate materials and challenges to explore.

History, American M.



Modified DNA polymerases  

US Patent & Trademark Office Database

The present invention provides, among other things, modified DNA polymerases containing amino acid alterations based on mutations identified in directed evolution experiments designed to select enzymes that are better suited for applications in recombinant DNA technologies.

Bourn; William (Western Cape, ZA); Faurholm; Bjarne (Western Cape, ZA); Foskett; John (Western Cape, ZA)



On braid groups and homotopy groups  

Microsoft Academic Search

This article is an exposition of certain connections between the braid groups, classical homotopy groups of the 2-sphere, as well as Lie algebras attached to the descending central series of pure braid groups arising as Vassiliev invariants of pure braids. Natural related questions are posed at the end of this article.

F R Cohen; Jie Wu



Interagency mechanical operations group numerical systems group  

SciTech Connect

This report consists of the minutes of the May 20-21, 1971 meeting of the Interagency Mechanical Operations Group (IMOG) Numerical Systems Group. This group looks at issues related to numerical control in the machining industry. Items discussed related to the use of CAD and CAM, EIA standards, data links, and numerical control.




Facilitating Reminiscence Groups: Perceptions of Group Leaders  

ERIC Educational Resources Information Center

|This article presents the results of a two-year qualitative investigation in which group leaders provided their perceptions of the process of facilitating reminiscence groups with elderly persons in a residential care facility. Group Culture emerged as the dominant construct. Findings from this study can serve guide leaders who are interested in…

Christensen, Teresa M.; Hulse-Killacky, Diana; Salgado, Roy A.; Thornton, Mark D.; Miller, Jason L.



Structure of DNA-functionalized dendrimer nanoparticles  

NASA Astrophysics Data System (ADS)

Atomistic molecular dynamics simulations have been carried out to reveal the characteristic features of ethylenediamine (EDA) cored protonated poly amido amine (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) that are functionalized with single stranded DNAs (ssDNAs). The four ssDNA strands that are attached via alkythiolate [-S (CH2)6-] linker molecule to the free amine groups on the surface of the PAMAM dendrimers observed to undergo a rapid conformational change during the 25 ns long simulation period. From the RMSD values of ssDNAs, we find relative stability in the case of purine rich ssDNA strands than pyrimidine rich ssDNA strands. The degree of wrapping of ssDNA strands on the dendrimer molecule was found to be influenced by the charge ratio of DNA and the dendrimer. As G4 dendrimer contains relatively more positive charge than G3 dendrimer, we observe extensive wrapping of ssDNAs on the G4 dendrimer. The ssDNA strands along with the linkers are seen to penetrate the surface of the dendrimer molecule and approach closer to the center of the dendrimer indicating the soft sphere nature of the dendrimer molecule. The effective radius of DNA-functionalized dendrimer nanoparticle was found to be independent of base composition of ssDNAs and was observed to be around 19.5 {\\AA} and 22.4 {\\AA} when we used G3 and G4 PAMAM dendrimer as the core of the nanoparticle respectively. The observed effective radius of DNA-functionalized dendrimer molecule apparently indicates the significant shrinkage in the structure that has taken place in dendrimer, linker and DNA strands. As a whole our results describe the characteristic features of DNA-functionalized dendrimer nanoparticle and can be used as strong inputs to design effectively the DNA-dendrimer nanoparticle self-assembly for their active biological applications.

Satish Kumar, Mattaparthi Venkata; Maiti, Prabal K.


A microchannel electrophoresis DNA sequencing system  

SciTech Connect

Last year, the Joint Genome Institute was the third leading sequencing group in the world with over 20 million bases of human DNA finished. The goal of the human genome project is to sequence the 3 billion bases of human DNA sequence by 2003. In order to increase the DNA sequencing throughput of the Joint Genome Institute, we have developed a microchannel electrophoresis system. One critical new and unique element of this system is a process for production of 96 and 384 microchannels on bonded glass substrates up to 14 x 58 cm. In order to utilize these instruments for DNA production sequencing, we have been evaluating and implementing software to convert raw electropherograms into called DNA bases with an associated probability of error. Our original intent was to utilize the DNA base calling software known as Plan and Phred developed by the University of Washington. In our tests and evaluations of this software applied to microchannel data, we observed that the electropherograms are of a different statistical and underlying signal structure compared to slab gels. We have modified Plan and Phred to improve base calling performance for the microchannel data. In this paper, we will present 1) the microchannel DNA sequencing system and show the advantages compared to current slab gel and capillary systems. 2) The signal processing modules needed for DNA base calling including correction of multiple wavelength channels, signal averaging, non-uniform sampling, variable DNA mobility, and peak shape and spreading effects. 3) A comparison of the DNA base signatures in the raw data of microchannels vs. slab gels including some simple modeling results. This will be propagated through the base calling software to show the impact on DNA sequencing.

Balch, J W; Bass, M S; Brewer, L R; Copeland, A C; Davidson, J C; Fitch, J P; Kegelmeyer; Kimbrough, J R; L M; Madabhushi, R S; McCready, P M; Nelson, D O; Pastrone, R L; Richardson, P M; Swierkowski, S P; Tarte, L A; Vainer, M; Warth, T E



Group Learning in Workshops.  

ERIC Educational Resources Information Center

|To facilitate effective group learning, adult educators should understand group dynamics, group size and structure, process, expectations and ground rules, and learning styles. Cooperation, active learning, and creative problem solving are enhanced in group instruction. (SK)|

Will, Anne M.



Microparticles and DNA Vaccines  

Microsoft Academic Search

Developing deoxyribonucleic acid (DNA) vaccines potent enough to be clinically useful will likely require an understanding\\u000a of the mechanism of action both of naked DNA vaccines themselves, and of adjuvant formulations that may be combined with DNA.\\u000a Mechanisms of action attributed to naked DNA vaccines described thus far include transfection of keratinocytes (1), muscle cells (2), and dendritic cells (DCs)

Kimberly Denis-Mize; Manmohan Singh; Derek T. O’Hagan; Jeffrey B. Ulmer; John J. Donnelly


Early DNA Sequencing  

NSDL National Science Digital Library

Two sequencing techniques were developed independently in the 1970s. The method developed by Fred Sanger used chemically altered 'dideoxy' bases to terminate newly synthesized DNA fragments at specific bases (either A, C, T, or G). These fragments are then size-separated, and the DNA sequence can be read. This animation from Cold Spring Harbor Laboratory's Dolan DNA Learning Center presents early DNA sequencing through a series of illustrations of the processes involved.



Nanoparticle bridge DNA biosensor  

Microsoft Academic Search

A new DNA sensing method is demonstrated in which DNA hybridization events lead to the formation of nanoparticle satellites that bridge two electrodes and are detected electrically. The hybridization events are exclusively carried out only on specific locations, the surfaces of C-ssDNA modified 50 nm GNPs. The uniqueness of this work is that only a small number of T-ccDNA molecules

Hong-Wen Huang



Photoelectrochemical synthesis of DNA microarrays  

PubMed Central

Optical addressing of semiconductor electrodes represents a powerful technology that enables the independent and parallel control of a very large number of electrical phenomena at the solid-electrolyte interface. To date, it has been used in a wide range of applications including electrophoretic manipulation, biomolecule sensing, and stimulating networks of neurons. Here, we have adapted this approach for the parallel addressing of redox reactions, and report the construction of a DNA microarray synthesis platform based on semiconductor photoelectrochemistry (PEC). An amorphous silicon photoconductor is activated by an optical projection system to create virtual electrodes capable of electrochemically generating protons; these PEC-generated protons then cleave the acid-labile dimethoxytrityl protecting groups of DNA phosphoramidite synthesis reagents with the requisite spatial selectivity to generate DNA microarrays. Furthermore, a thin-film porous glass dramatically increases the amount of DNA synthesized per chip by over an order of magnitude versus uncoated glass. This platform demonstrates that PEC can be used toward combinatorial bio-polymer and small molecule synthesis.

Chow, Brian Y.; Emig, Christopher J.; Jacobson, Joseph M.



Fast Phylogenetic DNA Barcoding  

Microsoft Academic Search

We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from

Kasper Munch; Wouter Boomsma; Eske Willerslev; Rasmus Nielsen



DNA-based Cryptography  

Microsoft Academic Search

Abstract Recent research has considered DNA as a medium for ultra - scale computation and for ultra - compact information storage One potential key application is DNA - based, molecular cryptogra - phy systems We present some procedures for DNA - based cryptography based on one - time - pads that are in principle unbreakable Practical applications of cryptographic systems

Ashish Gehani; Thomas H. Labean; John H. Reif



DNA secret writing techniques  

Microsoft Academic Search

The paper presents the principles of bio molecular computation (BMC) and several algorithms for DNA (deoxyribonucleic acid) steganography and cryptography: One-Time-Pad (OTP), DNA XOR OTP and DNA chromosomes indexing. It represents a synthesis of our work in the field, sustained by former referred publications. Experimental results obtained using Matlab Bioinformatics Toolbox and conclusions are ending the work.




Hiding Data in DNA  

Microsoft Academic Search

Just like disk or RAM, DNA and RNA can store vast amounts of information, and just like data stored in digital media, DNA data can be easily copied or tampered with. However, unlike in the digital realm, there are no techniques for watermarking, annotating, or encrypting information in DNA and RNA. The ability to catalogue genes, place checksums, watermark, and

Boris Shimanovsky; Jessica Feng; Miodrag Potkonjak



Yeast DNA Extraction  

NSDL National Science Digital Library

This laboratory exercise is designed to show learners how DNA can easily be extracted from yeast using simple materials. Use this experiment to supplement any unit on genetics and to demonstrate how scientists study DNA. Adult supervision is recommended. This resource guide includes tips and suggestions for instructors as well as other DNA extraction experiments and a chart for learners to answer questions.

Hays, Lana



DNA barcoding for ecologists  

Microsoft Academic Search

DNA barcoding - taxon identification using a standar- dized DNA region - has received much attention recently, and is being further developed through an international initiative. We anticipate that DNA barcod- ing techniques will be increasingly used by ecologists. They will be able to not only identify a single species from a specimen or an organism's remains but also determine

Alice Valentini; Francois Pompanon; Pierre Taberlet



Replicating animal mitochondrial DNA  

PubMed Central

The field of mitochondrial DNA (mtDNA) replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s) used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark) has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading- and lagging-strand synthesis (resembling bacterial genome replication) and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS). The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase ?, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase). Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

McKinney, Emily A.; Oliveira, Marcos T.



Forensic DNA and bioinformatics  

Microsoft Academic Search

The field of forensic science is increasingly based on biomolecular data and many European countries are establishing forensic databases to store DNA profiles of crime scenes of known offenders and apply DNA testing. The field is boosted by statistical and technological advances such as DNA microarray sequencing, TFT biosensors, machine learning algorithms, in particular Bayesian networks, which provide an effective

Lucia Bianchi; Pietro Liò



Method of Targeting DNA.  

National Technical Information Service (NTIS)

The invention relates to a method of forming a three-stranded DNA molecule wherein each strand of the three-stranded DNA molecule is hybridized (that is, non-covalently bound) to at least one other strand of the three-stranded DNA molecule. The method com...

R. D. Camerini-Otero M. McIntosh C. S. Camerini-Otero L. J. Ferrin



Nanopores: Flossing with DNA  

NASA Astrophysics Data System (ADS)

Passing a DNA strand many times back-and-forth through a protein nanopore would enable the interaction between them to be studied more closely. This may now be possible, using a dumbbell-shaped DNA-polymer complex, which may lead to a more reliable analysis of DNA sequences using nanopores.

Kasianowicz, John J.



Synthesis and properties of DNA-PNA chimeric oligomers.  

PubMed Central

Adenine, thymine and cytosine PNA monomers have been prepared using 3-amino-1,2-propanediol as a starting material. The benzoyl group was used to protect the exocyclic amines of the heterocyclic bases of A and C PNA monomers and the backbone primary amine was protected with the monomethoxytrityl group. The thymine and cytosine PNA monomers were used in conjunction with standard DNA synthesis monomers to produce chimeric PNA DNA (PDC) oligomers. Ultraviolet melting studies confirmed that these oligomers form stable hybrids with complementary DNA strands and that mismatches in the DNA but more so in the PNA sections lead to duplex destabilisation.

Finn, P J; Gibson, N J; Fallon, R; Hamilton, A; Brown, T



Comparison of sequence analysis of 16S-23S rDNA spacer regions, AFLP analysis and DNA-DNA hybridizations in Bradyrhizobium  

Microsoft Academic Search

The sequences of the 16S-23S rDNA intergenic spacer region of 62 strains of Bradyrhizobium, including representatives of the three valid species, were determined. The majority of strains had a single rRNA operon type and all contained a tRNAAla and a tRNAIle gene. Analysis of the sequence data produced groupings in line with previously obtained AFLP data. DNA-DNA hybridizations were performed

Anne Willems; Renata Coopman; Monique Gillis



Evidence for two groups of banana bunchy top virus isolates  

Microsoft Academic Search

Banana bunchy top virus (BBTV) DNA component 1 from isolates from 10 different countries was cloned and sequenced and the sequences were aligned and com- pared. This analysis indicated two groups: the South Pacific group (isolates from Australia, Burundi, Egypt, Fiji, India, Tonga and Western Samoa) and the Asian group (isolates from the Philippines, Taiwan and Vietnam). The mean sequence

Mirko Karan; Robert M. Harding; James L. Dale



DNAzymes in DNA Nanomachines and DNA Analysis  

NASA Astrophysics Data System (ADS)

This chapter discusses our efforts in using DNAzymes in DNA nano-machines and DNA analysis systems. 10-23 DNAzymes can cleave specific phos-phodiester bonds in RNA. We use them to construct an autonomous DNA-RNA chimera nanomotor, which constantly extracts chemical energy from RNA substrates and transduces the energy into a mechanical motion: cycles of contraction and extension. The motor's motion can be reversibly turned on and off by a DNA analogue (brake) of the RNA substrate. Addition and removal of the brake stops and restarts, respectively, the motor's motion. Furthermore, when the RNA substrates are preorganized into a one-dimensional track, a DNAzyme can continuously move along the track so long as there are substrates available ahead. Based on a similar mechanism, a novel DNA detection system has been developed. A target DNA activates a DNAzyme to cleave RNA-containing molecular beacons (MB), which generates an enhanced fluorescence signal. A following work integrates two steps of signal amplifications: a rolling-circle amplification (RCA) to synthesize multiple copies of DNAzymes, and the DNAzymes catalyze a chemical reaction to generate a colorimetric signal. This method allows detection of DNA analytes whose concentration is as low as 1 pM.

He, Yu; Tian, Ye; Chen, Yi; Mao, Chengde


Electrochemical biosensors for DNA hybridization and DNA damage  

Microsoft Academic Search

Recent trends in the development of DNA biosensors for nucleotide sequence-specific DNA hybridization and for the detection of the DNA damage are briefly reviewed. Changes in the redox signals of base residues in DNA immobilized at the surface of carbon or mercury electrodes can be used as a sign of the damage of DNA bases. Some compounds interacting with DNA

Emil Pale?ek; Miroslav Fojta; Miroslav Tomschik; Joseph Wang



Small Molecules, Inhibitors of DNA-PK, Targeting DNA Repair, and Beyond.  


Many current chemotherapies function by damaging genomic DNA in rapidly dividing cells ultimately leading to cell death. This therapeutic approach differentially targets cancer cells that generally display rapid cell division compared to normal tissue cells. However, although these treatments are initially effective in arresting tumor growth and reducing tumor burden, resistance and disease progression eventually occur. A major mechanism underlying this resistance is increased levels of cellular DNA repair. Most cells have complex mechanisms in place to repair DNA damage that occurs due to environmental exposures or normal metabolic processes. These systems, initially overwhelmed when faced with chemotherapy induced DNA damage, become more efficient under constant selective pressure and as a result chemotherapies become less effective. Thus, inhibiting DNA repair pathways using target specific small molecule inhibitors may overcome cellular resistance to DNA damaging chemotherapies. Non-homologous end joining a major mechanism for the repair of double-strand breaks (DSB) in DNA is regulated in part by the serine/threonine kinase, DNA dependent protein kinase (DNA-PK). The DNA-PK holoenzyme acts as a scaffold protein tethering broken DNA ends and recruiting other repair molecules. It also has enzymatic activity that may be involved in DNA damage signaling. Because of its' central role in repair of DSBs, DNA-PK has been the focus of a number of small molecule studies. In these studies specific DNA-PK inhibitors have shown efficacy in synergizing chemotherapies in vitro. However, compounds currently known to specifically inhibit DNA-PK are limited by poor pharmacokinetics: these compounds have poor solubility and have high metabolic lability in vivo leading to short serum half-lives. Future improvement in DNA-PK inhibition will likely be achieved by designing new molecules based on the recently reported crystallographic structure of DNA-PK. Computer based drug design will not only assist in identifying novel functional moieties to replace the metabolically labile morpholino group but will also facilitate the design of molecules to target the DNA-PKcs/Ku80 interface or one of the autophosphorylation sites. PMID:23386830

Davidson, David; Amrein, Lilian; Panasci, Lawrence; Aloyz, Raquel



DNA nanoarchitectonics: assembled DNA at interfaces.  


DNA is a powerful biomaterial for creating rationally designed and functionally enhanced nanostructures. DNA nanoarchitectures positioned at substrate interfaces can offer unique advantages leading to improved surface properties relevant to biosensing, nanotechnology, materials science, and cell biology. This Perspective highlights the benefits and challenges of using assembled DNA as a nanoscale building block for interfacial layers and surveys their applications in three areas: homogeneous dense surface coatings, bottom-up nanopatterning, and 3D nanoparticle lattices. Possible future research developments are discussed at the end of the Perspective. PMID:23373872

Howorka, Stefan



Molecular Dynamics Simulations of DNA-Polycation Complex Formation  

PubMed Central

Abstract Complexes formed from DNA and polycations are of interest because of their potential use in gene therapy; however, there remains a lack of understanding of the structure and formation of DNA-polycation complexes at atomic scale. In this work, molecular dynamics simulations of the DNA duplex d(CGCGAATTCGCG) in the presence of polycation chains are carried out to shed light on the specific atomic interaction that result in complex formation. The structures of complexes formed from DNA with polyethylenimine, which is considered one of the most promising DNA vector candidates, and a second polycation, poly-L-lysine, are compared. After an initial separation of ?50 Å, the DNA and polycation come together and form a stable complex within 10 ns. The DNA does not undergo any major structural changes on complexation and remains in the B-form. In the formed complex, the charged amine groups of the polycation mainly interact with DNA phosphate groups, with polycation intrusion into the major and minor grooves dependent on the identity and charge state of the polycation. The ability of the polycation to effectively neutralize the charge of the DNA phosphate groups and the resulting influence on the DNA helix interaction are discussed.

Ziebarth, Jesse; Wang, Yongmei



DNA Mapping Made Simple  

NSDL National Science Digital Library

The universality of the genetic code has allowed DNA isolated from a specific organism to be transferred and incorporated in another organism, transforming bacterial, yeast, plant, and animal cells. This transformation ability is the essence of recombinant DNA technology. Recombinant DNA has been used to make medically useful proteins that would otherwise have been difficult to obtain in necessary amounts, or to engineer plants to be herbicide or insect resistant. The following activity, which focuses on mapping DNA using restriction enzymes, can help students gain a better understanding about DNA and its manipulation. The activity is designed for high school and college biology students.

Chagas, Isabel; Arraba�a, J�ao; Marques, Miguel



DNA Sequencing apparatus  


An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.

Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)



The GROOP effect: groups mimic group actions.  


Research on perception-action links has focused on an interpersonal level, demonstrating effects of observing individual actions on performance. The present study investigated perception-action matching at an inter-group level. Pairs of participants responded to hand movements that were performed by two individuals who used one hand each or they responded to hand movements performed by an individual who used both hands. Apart from the difference in the number of observed agents, the observed hand movements were identical. If co-actors form action plans that specify the actions to be performed jointly, then participants should have a stronger tendency to mimic group actions than individual actions. Confirming this prediction, the results showed larger mimicry effects when groups responded to group actions than when groups responded to otherwise identical individual actions. This suggests that representations of joint tasks modulate automatic perception-action links and facilitate mimicry at an inter-group level. PMID:21074148

Tsai, Jessica Chia-Chin; Sebanz, Natalie; Knoblich, Günther



DNA in Nanoscale Electronics  

NASA Astrophysics Data System (ADS)

DNA, the quintessential molecule of life, possesses a number of attractive properties for use in nanoscale circuits. Charge transport (CT) through DNA itself is of both fundamental and practical interest. Fundamentally, DNA has a unique configuration of ?-stacked bases in a well ordered, double helical structure. Given its unparalleled importance to life processes and its arrangement of conjugated subunits, DNA has been a compelling target of conductivity studies. In addition, further understanding of DNA CT will elucidate the biological implications of this process and advance its use in sensing technologies. We have investigated the fundamentals of DNA CT by measuring the electrochemistry of DNA monolayers under biologically-relevant conditions. We have uncovered both fundamental kinetic parameters to distinguish between competing models of operation as well as the practical implications of DNA CT for sensing. Furthermore, we are leveraging our studies of DNA conductivity for the manufacture of nanoscale circuits. We are investigating the electrical properties and self-assembly of DNA nanowires containing artificial base pair surrogates, which can be prepared through low cost and high throughput automated DNA synthesis. This unique and economically viable approach will establish a new paradigm for the scalable manufacture of nanoscale semiconductor devices.

Slinker, Jason



Electronic Transport in DNA  

PubMed Central

We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localization lengths (crudely speaking, the length over which electrons travel). Various types of disorder, including random potentials, are employed to account for different real environments. We have performed calculations on poly(dG)-poly(dC), telomeric-DNA, random-ATGC DNA, and ?-DNA. We find that random and ?-DNA have localization lengths allowing for electron motion among a few dozen basepairs only. A novel enhancement of localization lengths is observed at particular energies for an increasing binary backbone disorder. We comment on the possible biological relevance of sequence-dependent charge transfer in DNA.

Klotsa, Daphne; Romer, Rudolf A.; Turner, Matthew S.



`DNA snapback' peptides  

PubMed Central

Thermal denaturation studies show that 10-15% of the calf thymus DNA in the heat denatured (Tyr-Gly-Tyr-Gly-Tyr)-DNA complex renatures spontaneously after colling. The double-strandness of this DNA was verified by its resistance to single-strand Neurospora endonuclease and by its elution profile on hydroxypatite columns. The renatured DNA isolated by the latter technique was found to contain 56% GC compared to the 41% GC content of the whole thymus DNA. Alternating tryptophanyl-glycyl and histidyl-glycyl peptides also catalyze the same renaturation. A linear correlation was found between the thermal stabilization afforded to the DNA by the various peptides and their ability to “catalyze” DNA strand renaturation.

Novak, Robert L.; Dohnal, James



Retroviral DNA Integration  

PubMed Central

DNA integration is a unique enzymatic process shared by all retroviruses and retrotransposons. During integration, double-stranded linear viral DNA is inserted into the host genome in a process catalyzed by the virus-encoded integrase (IN). The mechanism involves a series of nucleophillic attacks, the first of which removes the terminal 2 bases from the 3? ends of the long terminal repeats and of the second which inserts the viral DNA into the host genome. IN specifically recognizes the DNA sequences at the termini of the viral DNA, juxtaposing both ends in an enzyme complex that inserts the viral DNA into a single site in a concerted manner. Small duplications of the host DNA, characteristic of the viral IN, are found at the sites of insertion. At least two host proteins, HMG-I(Y) and BAF, have been shown to increase the efficiency of the integration reaction.

Hindmarsh, Patrick; Leis, Jonathan



Optimized Group Rekey for Group Communication Systems  

Microsoft Academic Search

In this paper we describe an efficient algorithmfor the man- agement of group-keys. Our algorithm is based on a proto- col for secure IP-multicast and is used to manage group- keys in group-communicationsystems. Unlike prior work, based on centralized key-servers, our solution is completely distributed and fault-tolerant and its performance is com- parable to the centralized solution.

Ohad Rodeh; Kenneth P. Birman; Danny Dolev



Mitochondrial DNA inherited variants are associated with successful aging and longevity in humans  

Microsoft Academic Search

Mitochondrial DNA (mtDNA) is char- acterized by high variability, maternal inheritance, and absence of recombination. Studies of human populations have revealed ancestral associated poly- morphisms whose combination defines groups of mtDNA types (haplogroups) that are currently used to reconstruct human evolution lineages. We used such inherited mtDNA markers to compare mtDNA population pools between a sample of individuals selected for



Inherited Mendelian defects of nuclear–mitochondrial communication affecting the stability of mitochondrial DNA  

Microsoft Academic Search

The presence of mtDNA abnormalities inherited as Mendelian traits indicates the existence of mutations in nuclear genes affecting the integrity of the mitochondrial genome. Two groups of nucleus-driven abnormalities have been described: qualitative alterations of mtDNA, i.e. multiple large-scale deletions of mtDNA, and quantitative decrease of the mtDNA copy number, i.e. tissue-specific depletion of mtDNA. Autosomal dominant or recessive (adPEO),

Anna Limongelli; Valeria Tiranti



Studies of nanoscale structural ordering in planar DNA complexes with amphiphilic mono- and polycations  

Microsoft Academic Search

Formation of DNA complexes with Langmuir monolayers of cationic lipid octadecylamine (ODA) and new amphiphilic polycation poly-4-vinylpyridine with 16% cetylpyridinium groups (PVP-16) on the surface of native DNA aqueous solution with low ionic strength has been studied. AFM topographic images of DNA\\/ODA and DNA\\/PVP-16 complex Langmuir–Blodgett films deposited on the mica substrates were obtained. The complex structures and individual DNA

Maria N. Antipina; Radmir V. Gainutdinov; Anna A. Rachnyanskaya; Alla L. Tolstikhina; Tatiana V. Yurova; Gennady B. Khomutov



Low level occupational exposure to styrene: its effects on DNA damage and DNA repair.  


The present study aimed to evaluate the effects of styrene exposure at levels below the recommended standards of the Threshold Limit Value (TLV-TWA(8)) of 20 ppm (ACGIH, 2004) in reinforced-fiberglass plastics workers. Study subjects comprised 50 exposed workers and 40 control subjects. The exposed workers were stratified by styrene exposure levels, i.e. group I (<10 ppm, <42.20 mg/m(3)), group II (10-20 ppm, 42.20-84.40 mg/m(3)), and group III (>20 ppm, >84.40 mg/m(3)). The mean styrene exposure levels of exposed workers were significantly higher than those of the control workers. Biomarkers of exposure to styrene, including blood styrene and the urinary metabolites, mandelic acid (MA) and phenylglyoxylic acid (PGA), were significantly increased with increasing levels of styrene exposure, but were not detected in the control group. DNA damage, such as DNA strand breaks, 8-hydroxydeoxyguanosine (8-OHdG), and DNA repair capacity, were used as biomarkers of early biological effects. DNA strand breaks and 8-OHdG/10(5)dG levels in peripheral leukocytes of exposed groups were significantly higher compared to the control group (P<0.05). In addition, DNA repair capacity, determined by the cytogenetic challenge assay, was lower in all exposed groups when compared to the control group (P<0.05). The expression of CYP2E1, which is involved in styrene metabolism, in all styrene exposed groups, was higher than that of the control group at a statistically significant level (P<0.05). Levels of expression of the DNA repair genes hOGG1 and XRCC1 were significantly higher in all exposed groups than in the control group (P<0.05). In addition to styrene contamination in ambient air, a trace amount of benzene was also found but, the correlation between benzene exposure and DNA damage or DNA repair capacity was not statistically significant. The results obtained from this study indicate an increase in genotoxic effects and thus health risk from occupational styrene exposure, even at levels below the recommended TLV-TWA(8) of 20 ppm. PMID:21030303

Wongvijitsuk, Sirilak; Navasumrit, Panida; Vattanasit, Udomratana; Parnlob, Varabhorn; Ruchirawat, Mathuros



Magnetic subperiodic groups.  


The magnetic subperiodic groups, the 31 magnetic frieze-group types, the 394 magnetic rod-group types and the 528 magnetic layer-group types, are derived and given symbols based on the symbols for the nonmagnetic subperiodic groups in Volume E of International Tables for Crystallography. The symbols are constructed in analogy to the Opechowski-Guccione symbols for magnetic space groups. Tables are given that list one group from each type. Each group is specified not only by its symbol but also by explicitly listing the coset representatives of the coset decomposition of the group with respect to its translational subgroup. PMID:10927306




Can Groups Learn?  

ERIC Educational Resources Information Center

Evaluated the work of sixth grade students' creative problem-solving groups, proposing that providing students with specific guidelines about what makes an exemplary group product would improve the character of the discussion and quality of the group product. Student groups did learn as a result of their discussions and creation of group products.…

Cohen, Elizabeth G.; Lotan, Rachel A.; Abram, Percy L.; Scarloss, Beth A.; Schultz, Susan E.



Fiber optic SPR biosensing of DNA hybridization and DNA-protein interactions.  


In this paper we present a fiber optic surface plasmon resonance (SPR) sensor as a reusable, cost-effective and label free biosensor for measuring DNA hybridization and DNA-protein interactions. This is the first paper that combines the concept of a fiber-based SPR system with DNA aptamer bioreceptors. The fibers were sputtered with a 50nm gold layer which was then covered with a protein repulsive self-assembled monolayer of mixed polyethylene glycol (PEG). Streptavidin was attached to the PEG's carboxyl groups to serve as a versatile binding element for biotinylated ssDNA. The ssDNA coated SPR fibers were first evaluated as a nucleic acid biosensor through a DNA-DNA hybridization assay for a random 37-mer ssDNA. This single stranded DNA showed a 15 nucleotides overlap with the receptor ssDNA on the SPR fiber. A linear calibration curve was observed in 0.5-5 microM range. A negative control test did not reveal any significant non-specific binding, and the biosensor was easily regenerated. In a second assay the fiber optic SPR biosensor was functionalized with ssDNA aptamers against human immunoglobulin E. Limits of detection (2nM) and quantification (6nM) in the low nanomolar range were observed. The presented biosensor was not only useful for DNA and protein quantification purposes, but also to reveal the binding kinetics occurring at the sensor surface. The dissociation constant between aptamer and hIgE was equal to 30.9+/-2.9nM. The observed kinetics fully comply with most data from the literature and were also confirmed by own control measurements. PMID:19775884

Pollet, Jeroen; Delport, Filip; Janssen, Kris P F; Jans, Karolien; Maes, Guido; Pfeiffer, Helge; Wevers, Martine; Lammertyn, Jeroen



The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives  

Microsoft Academic Search

This paper presents an overview of the organisation and the results of the collaborative exercises (CE) of the European DNA Profiling (EDNAP) Group’s mitochondrial DNA population database project (EMPOP). The aim of the collaborative exercises was to determine whether uniformity of mtDNA sequencing results could be achieved among different laboratories. These were asked to sequence either the complete mtDNA control

Walther Parson; Anita Brandstätter; Antonio Alonso; Nathalie Brandt; Bernd Brinkmann; Angel Carracedo; Daniel Corach; Olivier Froment; Ivana Furac; Tomasz Grzybowski; Karin Hedberg; Christine Keyser-Tracqui; Tomasz Kupiec; Sabine Lutz-Bonengel; Bente Mevag; Rafal Ploski; Hermann Schmitter; Peter Schneider; Denise Syndercombe-Court; Eric Sørensen; Heather Thew; Gillian Tully; Richard Scheithauer



Fern spore extracts can damage DNA  

PubMed Central

The carcinogenicity of the vegetative tissues of bracken fern (Pteridium) has long been established. More recently, the carcinogenic effects of the spores of bracken have also been recognized. Both vegetative tissues and spores of bracken can induce adducts in DNA in animal tissues, but the possible genotoxic or carcinogenic effects of spores from fern species other than bracken are unknown. The single-cell gel electrophoresis (‘comet’) assay was used to investigate whether fern spores can cause DNA damage in vitro. Extracts of spores from six fern species were administered to cultured human premyeloid leukaemia (K562) cells. Spore extracts of five fern species: Anemia phyllitidis, Dicksonia antarctica, Pteridium aquilinum, Pteris vittata and Sadleria pallida, induced significantly more DNA strand breaks than those in the control groups. Only in one species, Osmunda regalis, was the effect no different from that in the control groups. Using extracts from A. phyllitidis and P. vittata, the extent of DNA damage was increased by increasing the original dose 10 times, whereas an experiment in which exposure times were varied suggested that the highest levels of strand breaks appear after 2 h exposure. Simultaneous incubation with human S9 liver enzyme mix ablated the damaging effect of the extracts. Our data show that fern spore extracts can cause DNA damage in human cells in vitro. Considering the strong correlation between DNA damage and carcinogenic events, the observations made in this report may well have some implications for human health. © 2000 Cancer Research Campaign

Siman, S E; Povey, A C; Ward, T H; Margison, G P; Sheffield, E



Group Time: Building Language at Group Time  

ERIC Educational Resources Information Center

|This article features energizing and surprising activities for children at group time. In the drawing activity, children are asked to give instructions on how to draw a picture using vocabulary and descriptive language. In the mailbox activity, children will be surprised to discover that they have mail at group time. Mailboxes can be used for…

Church, Ellen Booth



Nominal grouping sessions vs focus groups  

Microsoft Academic Search

These empirical results provide new and strong support for Langford’s 1994 quantitative demonstration that the qualitative results of nominal grouping sessions (NGS) are highly reliable and valid. We also show that NGS produces responses in greater depth and breadth than many years of research have demonstrated for focus groups. Since the NGS procedure provides broad, deep, reliable and valid results

Barry E. Langford; Gerald Schoenfeld; George Izzo



From Loop Groups to 2Groups  

Microsoft Academic Search

We describe an interesting relation between Lie 2-algebras, the Kac-Moody\\u000acentral extensions of loop groups, and the group String(n). A Lie 2-algebra is\\u000aa categorified version of a Lie algebra where the Jacobi identity holds up to a\\u000anatural isomorphism called the \\

John C. Baez; Danny Stevenson; Alissa S. Crans; Urs Schreiber



SYBR Green I: fluorescence properties and interaction with DNA.  


In this study, we have investigated the fluorescence properties of SYBR Green I (SG) dye and its interaction with double-stranded DNA (dsDNA). SG/dsDNA complexes were studied using various spectroscopic techniques, including fluorescence resonance energy transfer and time-resolved fluorescence techniques. It is shown that SG quenching in the free state has an intrinsic intramolecular origin; thus, the observed >1,000-fold SG fluorescence enhancement in complex with DNA can be explained by a dampening of its intra-molecular motions. Analysis of the obtained SG/DNA binding isotherms in solutions of different ionic strength and of SG/DNA association in the presence of a DNA minor groove binder, Hoechst 33258, revealed multiple modes of interaction of SG inner groups with DNA. In addition to interaction within the DNA minor groove, both intercalation between base pairs and stabilization of the electrostatic SG/DNA complex contributed to increased SG affinity to double-stranded DNA. We show that both fluorescence and the excited state lifetime of SG dramatically increase in viscous solvents, demonstrating an approximate 200-fold enhancement in 100 % glycerol, compared to water, which also makes SG a prospective fluorescent viscosity probe. A proposed structural model of the SG/DNA complex is compared and discussed with results recently reported for the closely related PicoGreen chromophore. PMID:22534954

Dragan, A I; Pavlovic, R; McGivney, J B; Casas-Finet, J R; Bishop, E S; Strouse, R J; Schenerman, M A; Geddes, C D



Forensic DNA analysis.  


Before the routine use of DNA profiling, blood typing was an important forensic tool. However, blood typing was not very discriminating. For example, roughly 30% of the United States population has type A-positive blood. Therefore, if A-positive blood were found at a crime scene, it could have come from 30% of the population. DNA profiling has a much better ability for discrimination. Forensic laboratories no longer routinely determine blood type. If blood is found at a crime scene, DNA profiling is performed. From Jeffrey's discovery of DNA fingerprinting to the development of PCR of STRs to the formation of DNA databases, our knowledge of DNA and DNA profiling have expanded greatly. Also, the applications for which we use DNA profiling have increased. DNA profiling is not just used for criminal case work, but it has expanded to encompass paternity testing, disaster victim identification, monitoring bone marrow transplants, detecting fetal cells in a mother's blood, tracing human history, and a multitude of other areas. The future of DNA profiling looks expansive with the development of newer instrumentation and techniques. PMID:22693781

McDonald, Jessica; Lehman, Donald C



Particle Assembly with Double-Helix DNA  

NASA Astrophysics Data System (ADS)

The use of DNA-functionalized particles and DNA motifs for programmable assembly has been extensively studied in the past decade. However, the majority of the previous successful efforts have been based on a paradigm in which a hybridization of single-stranded DNA(ssDNA)-functionalized particles is utilized to group particles into clusters or large scale assemblies. Here, we report a novel strategy that allows for controllable and programmable assembly of double-stranded DNA (dsDNA)-modified nanoparticles using molecular intercalators. Transmission electron microscopy (TEM), Atomic Force Microscopy (AFM) and dynamic light scattering (DLS), applied to assembled structures, confirm successful assembly of designed clusters using this approach. The efficiency of assembly and thermodynamic properties of formed structures have been also studied. The presented approach is broadly applicable to varieties of existing DNA-based nano-architectures and might provide a platform for development of novel assembly motifs. The potential utility of our approach for a fabrication of complex structures will be also discussed.

Sun, Dazhi Peter; Stadler, Andrea; van der Lelie, Daniel; Gang, Oleg



DNA damage phenotype and prostate cancer risk  

PubMed Central

The capacity of an individual to process DNA damage is considered a crucial factor in carcinogenesis. The comet assay is a phenotypic measure of the combined effects of sensitivity to a mutagen exposure and repair capacity. In this paper, we evaluate the association of the DNA repair kinetics, as measured by the comet assay, with prostate cancer risk. In a pilot study of 55 men with prostate cancer, 53 men without the disease, and 71 men free of cancer at biopsy, we investigated the association of DNA damage with prostate cancer risk at early (0-15 min) and later (15-45 min) stages following gamma-radiation exposure. Although residual damage within 45 min was the same for all groups (65% of DNA in comet tail disappeared), prostate cancer cases had a slower first phase (38% vs 41%) and faster second phase (27% vs 22%) of the repair response compared to controls. When subjects were categorized into quartiles, according to efficiency of repairing DNA damage, high repair-efficiency within the first 15 min after exposure was not associated with prostate cancer risk while higher at the 15-45 min period was associated with increased risk (OR for highest-to-lowest quartiles = 3.24, 95% CI=0.98-10.66, p-trend =0.04). Despite limited sample size, our data suggest that DNA repair kinetics marginally differ between prostate cancer cases and controls. This small difference could be associated with differential responses to DNA damage among susceptible individuals.

Kosti, O.; Goldman, L.; Saha, D.T.; Orden, R.A.; Pollock, A.J.; Madej, H.L.; Hsing, A.W.; Chu, L.W.; Lynch, J.H.; Goldman, R.



Realizations of Continuous Groups  

NASA Astrophysics Data System (ADS)

General relativity replaces the flat spacetime of special relativity by a curved Riemannian manifold and extends the invariance group of the theory (i.e., the group of transformations that leave the forms of all dynamical equations invariant) from the Poincaré group to the group of general differentiable coordinate transformations, known to mathematicians as the diffeomorphism group. It will be helpful, in introducing the formal apparatus of general relativity, to develop first a little of the theory of groups of continuous transformations.

Dewitt, Bryce; Christensen, Steven M.


DNA content in radiation-associated thyroid cancer  

SciTech Connect

DNA content has been reported to be of prognostic significance in differentiated thyroid carcinoma. Since malignant tumors with irradiation as an initiator often contain DNA aberrations, the DNA content of well-differentiated thyroid carcinoma in patients with a prior history of low-dose head and neck irradiation was determined and compared with similar nonradiation-associated lesions. The DNA content of thyroid cancers from 53 patients was determined with use of flow cytometry. Sixteen radiation-associated thyroid carcinomas (11 papillary, 3 follicular, and 2 medullary) all were diploid. In a group of 37 nonradiation-associated tumors, 10 were aneuploid (10 of 29 papillary carcinomas and 0 of 2 follicular or 6 medullary carcinomas). This difference in DNA content is significant (p less than 0.02, Fisher's exact test). These findings were unexpected and suggest that if the initiating irradiation causes a DNA aberration, this aberration is not reflected in DNA content as measured by means of flow cytometry.

Komorowski, R.A.; Deaconson, T.F.; Vetsch, R.; Cerletty, J.M.; Wilson, S.D.



Sequence specificity of DNA cleavage by Micrococcus luteus gamma endonuclease.  


DNA fragments of defined sequence have been used to determine the sites of cleavage by gamma-endonuclease activity in extracts prepared from Micrococcus luteus. End-labeled DNA restriction fragments of pBR322 DNA that had been irradiated under nitrogen in the presence of potassium iodide or t-butanol were treated with M. luteus gamma endonuclease and analyzed on high resolution, denaturing, polyacrylamide gels. Gamma endonuclease was found to cleave irradiated DNA preferentially at the positions of cytosines and thymines. DNA cleavage occurred immediately to the 3' side of pyrimidines in irradiated DNA and resulted in fragments that terminate in a 5'-phosphoryl group. These studies indicate that both altered cytosines and thymines may be important DNA lesions requiring repair after exposure to gamma radiation. PMID:3983367

Hentosh, P; Henner, W D; Reynolds, R J



Sequence specificity of DNA cleavage by Micrococcus luteus. gamma. endonuclease  

SciTech Connect

DNA fragments of defined sequence have been used to determine the sites of cleavage by ..gamma..-endonuclease activity in extracts prepared from Micrococcus luteus. End-labeled DNA restriction fragments of pBR322 DNA that had been irradiated under nitrogen in the presence of potassium iodide or t-butanol were treated with M. luteus ..gamma.. endonuclease and analyzed on irradiated DNA preferentially at the positions of cytosines and thymines. DNA cleavage occurred immediately to the 3' side of pyrimidines in irradiated DNA and resulted in fragments that terminate in a 5'-phosphoryl group. These studies indicate that both altered cytosines and thymines may be important DNA lesions requiring repair after exposure to ..gamma.. radiation.

Hentosh, P.; Henner, W.D.; Reynolds, R.J.



Mechanism of DNA Translocation in a Replicative Hexameric Helicase  

SciTech Connect

The E1 protein of papillomavirus is a hexameric ring helicase belonging to the AAA + family. The mechanism that couples the ATP cycle to DNA translocation has been unclear. Here we present the crystal structure of the E1 hexamer with single-stranded DNA discretely bound within the hexamer channel and nucleotides at the subunit interfaces. This structure demonstrates that only one strand of DNA passes through the hexamer channel and that the DNA-binding hairpins of each subunit form a spiral 'staircase' that sequentially tracks the oligonucleotide backbone. Consecutively grouped ATP, ADP and apo configurations correlate with the height of the hairpin, suggesting a straightforward DNA translocation mechanism. Each subunit sequentially progresses through ATP, ADP and apo states while the associated DNA-binding hairpin travels from the top staircase position to the bottom, escorting one nucleotide of single-stranded DNA through the channel. These events permute sequentially around the ring from one subunit to the next.

Enemark,E.; Joshua-Tor, L.



Method for producing intact plants containing foreign DNA  

SciTech Connect

An in vivo method is described for transforming and regenerating whole dicotyledenous plants comprising: infecting a dicotyledenous plant (P) with Rhizobiaceae bacteria containing virulence functions; a first plasmid containing T-DNA terminal sequences flanking oncogenic factors capable of inducing a shoot-bearing shooty tumor on plant (P), and a second plasmid containing T-DNA