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1

Directed assembly of discrete gold nanoparticle groupings usingbranched DNA scaffolds  

SciTech Connect

The concept of self-assembled dendrimers is explored for the creation of discrete nanoparticle assemblies. Hybridization of branched DNA trimers and nanoparticle-DNA conjugates results in the synthesis of nanoparticle trimer and tetramer complexes. Multiple tetramer architectures are investigated, utilizing Au-DNA conjugates with varying secondary structural motifs. Hybridization products are analyzed by gel electrophoresis, and discrete bands are observed corresponding to structures with increasing numbers of hybridization events. Samples extracted from each band are analyzed by transmission electron microscopy, and statistics compiled from micrographs are used to compare assembly characteristics for each architecture. Asymmetric structures are also produced in which both 5 and 10 nm Au particles are assembled on branched scaffolds.

Claridge, Shelley A.; Goh, Sarah L.; Frechet, Jean M.J.; Williams, Shara C.; Micheel, Christine M.; Alivisatos, A. Paul

2004-09-14

2

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.

2008-01-04

3

Group II Introns: Mobile Ribozymes that Invade DNA  

PubMed Central

SUMMARY Group II introns are mobile ribozymes that self-splice from precursor RNAs to yield excised intron lariat RNAs, which then invade new genomic DNA sites by reverse splicing. The introns encode a reverse transcriptase that stabilizes the catalytically active RNA structure for forward and reverse splicing, and afterwards converts the integrated intron RNA back into DNA. The characteristics of group II introns suggest that they or their close relatives were evolutionary ancestors of spliceosomal introns, the spliceosome, and retrotransposons in eukaryotes. Further, their ribozyme-based DNA integration mechanism enabled the development of group II introns into gene targeting vectors (“targetrons”), which have the unique feature of readily programmable DNA target specificity. PMID:20463000

Lambowitz, Alan M.; Zimmerly, Steven

2011-01-01

4

Human xeroderma pigmentosum group G gene encodes a DNA endonuclease.  

PubMed Central

Because of defective nucleotide excision repair of ultraviolet damaged DNA, xeroderma pigmentosum (XP) patients suffer from a high incidence of skin cancers. Cell fusion studies have identified seven XP complementation groups, A to G. Previous studies have implicated the products of these seven XP genes in the recognition of ultraviolet-induced DNA damage and in incision of the damage-containing DNA strand. Here, we express the XPG-encoded protein in Sf9 insect cells and purify it to homogeneity. We demonstrate that XPG is a single-strand specific DNA endonuclease, thus identifying the catalytic role of the protein in nucleotide excision repair. We suggest that XPG nuclease acts on the single-stranded region created as a result of the combined action of the XPB helicase and XPD helicase at the DNA damage site. Images PMID:8078765

Habraken, Y; Sung, P; Prakash, L; Prakash, S

1994-01-01

5

Mitochondrial DNA evolution in the Anaxyrus boreas species group  

Microsoft Academic Search

The Anaxyrus boreas species group currently comprises four species in western North America including the broadly distributed A. boreas, and three localized species, Anaxyrus nelsoni, Anaxyrusexsul and Anaxyrus canorus. Phylogenetic analyses of the mtDNA 12S rDNA, cytochrome oxidase I, control region, and restriction sites data, identified three major haplotype clades. The Northwest clade (NW) includes both subspecies of A. boreas

Anna M. Goebel; Tom A. Ranker; Paul Stephen Corn; Richard G. Olmstead

2009-01-01

6

Affine reflection groups for tiling applications: Knot theory and DNA  

NASA Astrophysics Data System (ADS)

We present in this paper some non-conventional applications of affine Weyl groups Waff of rank 2, the symmetry group of the tiling/lattice. We first develop and present the tools for applications requiring tilings of a real Euclidean plane {R}^2. We then elucidate the equivalence of these tilings with 2D projections of knots. The resulting mathematical structure provides a framework within which is encompassed recent work utilizing knot theory for modeling the structure and function of genetic molecules, specifically the action of particular enzymes in altering the topology of DNA in site-specific recombination.

Bodner, M.; Patera, J.; Peterson, M.

2012-01-01

7

Mitochondrial DNA evolution in the Anaxyrus boreas species group  

USGS Publications Warehouse

The Anaxyrus boreas species group currently comprises four species in western North America including the broadly distributed A. boreas, and three localized species, Anaxyrus nelsoni, Anaxyrus exsul and Anaxyrus canorus. Phylogenetic analyses of the mtDNA 12S rDNA, cytochrome oxidase I, control region, and restriction sites data, identified three major haplotype clades. The Northwest clade (NW) includes both subspecies of A. boreas and divergent minor clades in the middle Rocky Mountains, coastal, and central regions of the west and Pacific Northwest. The Southwest (SW) clade includes A. exsul, A. nelsoni, and minor clades in southern California. Anaxyrus canorus, previously identified as paraphyletic, has populations in both the NW and SW major clades. The Eastern major clade (E) includes three divergent lineages from southern Utah, the southern Rocky Mountains, and north of the Great Basin at the border of Utah and Nevada. These results identify new genetic variation in the eastern portion of the toad's range and are consistent with previous regional studies from the west coast. Low levels of control region sequence divergence between major clades (2.2-4.7% uncorrected pair-wise distances) are consistent with Pleistocene divergence and suggest that the phylogeographic history of the group was heavily influenced by dynamic Pleistocene glacial and climatic changes, and especially pluvial changes, in western North America. Results reported here may impact conservation plans in that the current taxonomy does not reflect the diversity in the group. ?? 2008 Elsevier Inc.

Goebel, A.M.; Ranker, T.A.; Corn, P.S.; Olmstead, R.G.

2009-01-01

8

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. PMID:22851931

Geserick, Gunther; Wirth, Ingo

2012-01-01

9

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

FELIX A. H. SPERLING

1993-01-01

10

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. PMID:11283033

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

2001-01-01

11

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

Melek ALTIPARMAK; Mahmure NAKIBOGLU TEZER

2009-01-01

12

Hands on Group Work Paper Model for Teaching DNA Structure, Central Dogma and Recombinant DNA  

ERIC Educational Resources Information Center

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…

Altiparmak, Melek; Nakiboglu Tezer, Mahmure

2009-01-01

13

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. PMID:3671088

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

1987-01-01

14

[Mitochondrial DNA variability in populations and ethnic groups of Tatars of the Tobol-Irtysh basin].  

PubMed

The data on mitochondrial DNA diversity in seven local populations (villages) and four territorial groups of Tatars of the Tobol-Irtysh basin are presented. In the Turkic-speaking populations from the Tobol and Irtysh river basins, high levels of intergroup and interpopulation mtDNA variation were observed. It was demonstrated that genetic diversity of the territorial groups of Tatars of the Tobol-Irtysh basin resulted from various interethnic relationships and different ethnic components integrated into these groups. PMID:19824547

Naumova, O Iu; Rychkov, S Iu; Zhukova, O V

2009-09-01

15

Identification of two groups of Mycobacterium paratuberculosis strains by restriction endonuclease analysis and DNA hybridization.  

PubMed Central

Genomic DNA was prepared from four reference strains of Mycobacterium paratuberculosis and 46 isolates of this organism from New Zealand, Australia, Canada, and Norway and also from two mycobactin-dependent "wood pigeon" strains. The DNA was characterized by restriction endonuclease analysis, both with and without DNA hybridization, with a probe specific to a repetitive DNA sequence in M. paratuberculosis. Both techniques differentiated M. paratuberculosis strains into two groups, but DNA hybridization revealed more differences between strains within the larger group. All the strains from cattle and many strains from other animals belonged to this group. The second group of nine strains included the Faroe Islands strain, all New Zealand sheep strains, and one New Zealand goat strain. Primary isolation of strains belonging to this group was difficult to achieve. DNA from acid-fast organisms harvested directly from intestinal tissues of sheep with Johne's disease was shown to have restriction and hybridization patterns identical to those of DNA obtained from M. paratuberculosis isolates cultured from the same tissues. Two Norwegian goat strains and the wood pigeon strains did not hybridize to the M. paratuberculosis probe and had restriction patterns very different from those of other M. paratuberculosis strains. The wood pigeon strains had restriction patterns very similar to those of strains of Mycobacterium avium, indicating that they should be classified as that species. The presence of two distinct groups of M. paratuberculosis strains and their predominant distribution in different host animals may be significant in management of mixed-animal farming operations. Images PMID:2166089

Collins, D M; Gabric, D M; de Lisle, G W

1990-01-01

16

Efimov like phase of a three stranded DNA (Efimov-DNA) and the renormalization group limit cycle  

E-print Network

A three-stranded DNA with short range base pairings only is known to exhibit a classical analog of the quantum Efimov effect, viz., a three chain bound state at the two chain melting point where no two are bound. By using a non-perturbative renormalization group method for a rigid duplex DNA and a flexible third strand, with base pairings and strand exchange, we show that the Efimov-DNA is associated with a limit cycle type behavior of the flow of an effective three chain interaction. The analysis also shows that thermally generated bubbles play an essential role in producing the effect. A toy model for the flow equations shows the limit cycle in an extended three dimensional parameter space of the two-chain coupling and a complex three chain interaction.

Tanmoy Pal; Poulomi Sadhukhan; Somendra M. Bhattacharjee

2014-09-29

17

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. PMID:23661683

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

2013-01-01

18

Phylogenetic relationship of the twenty-one DNA groups of the genus Acinetobacter as revealed by 16S ribosomal DNA sequence analysis.  

PubMed

The inter- and intrageneric relationships of members of the genus Acinetobacter were investigated by performing a comparative sequence analysis of PCR-amplified 16S ribosomal DNAs (rDNAs) from 21 strains representing all of the DNA groups that have been described. Phylogenetic treeing confirmed that Acinetobacter spp. form a coherent cluster within the gamma subdivision of the class Proteobacteria that includes strains with overall levels of 16S rDNA sequence similarity of more than 94%. The analysis of intrageneric relationships suggested that the majority of the strains cluster in five clearly distinguishable clusters, and this conclusion was supported by the results obtained with the different methods used for phylogenetic analysis (i.e., the maximum-likelihood, parsimony, and distance matrix methods). The first cluster contains the representatives of DNA groups 2 (Acinetobacter baumannii) and TU13, whereas the second cluster comprises representatives of DNA groups 3, "Close To TU13," and "between 1 and 3." The representatives of closely related Acinetobacter DNA groups 8 (Acinetobacter twoffii) and 9 belong to the third cluster, which includes the representative of DNA group 6 as well. The fourth cluster is formed by DNA groups BJ15, BJ16, and BJ17, and the fifth cluster comprises DNA groups 1 (Acinetobacter calcoaceticus), BJ14, 10, and 11. Within the fifth cluster the 16S rDNA sequences of DNA group 10 and 11 strains are nearly identical. The representatives of DNA groups 4 (Acinetobacter haemolyticus), 5 (Acinetobacter junii), 7 (Acinetobacter johnsonii), 12 (Acinetobacter radioresistens), TU14, and TU15 form individual branches that are not significantly affiliated with any of the five clusters identified. Apart from the clustering of the most closely related DNA groups, the general topology of the distance dendrogram revealed some discrepancy with previous DNA-DNA hybridization data, which may point to the inadequacy of comparative 16S rDNA sequence analysis for reflecting true evolutionary relationships of closely related bacterial taxa. Important, however, was the presence of unique sequence motifs in each of the 21 different DNA groups studied, which may be useful for rapid differentiation of DNA groups of the genus Acinetobacter. PMID:9226915

Ibrahim, A; Gerner-Smidt, P; Liesack, W

1997-07-01

19

Spy: A New Group of Eukaryotic DNA Transposons without Target Site Duplications  

PubMed Central

Class 2 or DNA transposons populate the genomes of most eukaryotes and like other mobile genetic elements have a profound impact on genome evolution. Most DNA transposons belong to the cut-and-paste types, which are relatively simple elements characterized by terminal-inverted repeats (TIRs) flanking a single gene encoding a transposase. All eukaryotic cut-and-paste transposons so far described are also characterized by target site duplications (TSDs) of host DNA generated upon chromosomal insertion. Here, we report a new group of evolutionarily related DNA transposons called Spy, which also include TIRs and DDE motif-containing transposase but surprisingly do not create TSDs upon insertion. Instead, Spy transposons appear to transpose precisely between 5?-AAA and TTT-3? host nucleotides, without duplication or modification of the AAATTT target sites. Spy transposons were identified in the genomes of diverse invertebrate species based on transposase homology searches and structure-based approaches. Phylogenetic analyses indicate that Spy transposases are distantly related to IS5, ISL2EU, and PIF/Harbinger transposases. However, Spy transposons are distinct from these and other DNA transposon superfamilies by their lack of TSD and their target site preference. Our findings expand the known diversity of DNA transposons and reveal a new group of eukaryotic DDE transposases with unusual catalytic properties. PMID:24966181

Han, Min-Jin; Xu, Hong-En; Zhang, Hua-Hao; Feschotte, Cedric; Zhang, Ze

2014-01-01

20

DNA DNA DNA (d)DNA DNA DNA  

E-print Network

DNA DNA DNA DNA DNA DNA DNA DNA [ 2008] (d)DNA DNA DNA DNA 2 3 DNA DNA DNA DNA DNA DNA DNA (a) (c) (b) (d) #12;DNA DNA DNA DNA DNA DNA DNA DNA (b) DNA [Tanaka et al.2008] DNA DNA DNA DNA DNA DNA DNA #12;iGEM MIT MIT

Hagiya, Masami

21

Effects of sugar functional groups, hydrophobicity, and fluorination on carbohydrate-DNA stacking interactions in water.  

PubMed

Carbohydrate-aromatic interactions are highly relevant for many biological processes. Nevertheless, experimental data in aqueous solution relating structure and energetics for sugar-arene stacking interactions are very scarce. Here, we evaluate how structural variations in a monosaccharide including carboxyl, N-acetyl, fluorine, and methyl groups affect stacking interactions with aromatic DNA bases. We find small differences on stacking interaction among the natural carbohydrates examined. The presence of fluorine atoms within the pyranose ring slightly increases the interaction with the C-G DNA base pair. Carbohydrate hydrophobicity is the most determinant factor. However, gradual increase in hydrophobicity of the carbohydrate does not translate directly into a steady growth in stacking interaction. The energetics correlates better with the amount of apolar surface buried upon sugar stacking on top of the aromatic DNA base pair. PMID:24552250

Lucas, Ricardo; Peñalver, Pablo; Gómez-Pinto, Irene; Vengut-Climent, Empar; Mtashobya, Lewis; Cousin, Jonathan; Maldonado, Olivia S; Perez, Violaine; Reynes, Virginie; Aviñó, Anna; Eritja, Ramón; González, Carlos; Linclau, Bruno; Morales, Juan C

2014-03-21

22

Multiparameter DNA content analysis identifies distinct groups in primary breast cancer  

PubMed Central

Background: Multiparameter flow cytometry is a robust and reliable method for determining tumour DNA content applicable to formalin-fixed paraffin-embedded (FFPE) tissue. This study examined the clinical and pathological associations of DNA content in primary breast cancer using an improved multiparametric technique. Methods: The FFPE tissue from 201 primary breast cancers was examined and the cancers categorised according to their DNA content using multiparametric flow cytometry incorporating differential labelling of stromal and tumour cell populations. Mathematical modelling software (ModFit 3.2.1) was used to calculate the DNA index (DI) and percentage S-phase fraction (SPF%) for each tumour. Independent associations with clinical and pathological parameters were sought using backward stepwise Binary Logistic Regression (BLR) and Cox's Regression (CR) analysis. Results: Tumours were grouped into four categories based on the DI of the tumour cell population. Low DI tumours (DI=0.76–1.14) associated with progesterone receptor-positive status (P=0.012, BLR), intermediate DI (DI=1.18–1.79) associated with p53 mutant tumours (P=0.001, BLR), high DI (DI?1.80) tumours with human epidermal growth factor receptor 2 (HER2)-positive status (P=0.004, BLR) and ‘multiploid tumours' (two or more tumour DNA peaks) did not show any significant associations. Tumours with high SPF% (?10%) independently associated with poor overall survival (P=0.027, CR). Conclusion: Multiparametric flow analysis of FFPE tissue can accurately assess tumour DNA content. Tumour sub-populations associated with biomarkers of prognosis or likely response to therapy. The alterations in DNA content present the potential for greater understanding of the mechanisms underlying clinically significant biomarker changes in primary breast cancer. PMID:23412097

Dayal, J H S; Sales, M J; Corver, W E; Purdie, C A; Jordan, L B; Quinlan, P R; Baker, L; ter Haar, N T; Pratt, N R; Thompson, A M

2013-01-01

23

Mitochondrial DNA control region analysis of three ethnic groups in the Republic of Macedonia.  

PubMed

A total of 444 individuals representing three ethnic groups (Albanians, Turks and Romanies) in the Republic of Macedonia were sequenced in the mitochondrial control region. The mtDNA haplogroup composition differed between the three groups. Our results showed relatively high frequencies of haplogroup H12 in Albanians (8.8%) and less in Turks (3.3%), while haplogroups M5a1 and H7a1a were dominant in Romanies (13.7% and 10.3%, respectively) but rare in the former two. This highlights the importance of regional sampling for forensic mtDNA databasing purposes. These population data will be available on EMPOP under accession numbers EMP00644 (Albanians), EMP00645 (Romanies) and EMP00646 (Turks). PMID:25051224

Jankova-Ajanovska, Renata; Zimmermann, Bettina; Huber, Gabriela; Röck, Alexander W; Bodner, Martin; Jakovski, Zlatko; Janeska, Biljana; Duma, Aleksej; Parson, Walther

2014-11-01

24

Mitochondrial DNA control region analysis of three ethnic groups in the Republic of Macedonia  

PubMed Central

A total of 444 individuals representing three ethnic groups (Albanians, Turks and Romanies) in the Republic of Macedonia were sequenced in the mitochondrial control region. The mtDNA haplogroup composition differed between the three groups. Our results showed relatively high frequencies of haplogroup H12 in Albanians (8.8%) and less in Turks (3.3%), while haplogroups M5a1 and H7a1a were dominant in Romanies (13.7% and 10.3%, respectively) but rare in the former two. This highlights the importance of regional sampling for forensic mtDNA databasing purposes. These population data will be available on EMPOP under accession numbers EMP00644 (Albanians), EMP00645 (Romanies) and EMP00646 (Turks). PMID:25051224

Jankova-Ajanovska, Renata; Zimmermann, Bettina; Huber, Gabriela; Röck, Alexander W.; Bodner, Martin; Jakovski, Zlatko; Janeska, Biljana; Duma, Aleksej; Parson, Walther

2014-01-01

25

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

VESNA RAPICOTRIN; ISAO KURAOKA; TIZIANA NARDO; MARY MCLENIGAN; A. P. M. EKER; MIRIA STEFANINI; ARTHUR S. LEVINE; RICHARD D. WOOD

1998-01-01

26

Specialization of the DNA-Cleaving Activity of a Group I Ribozyme Through In Vitro Evolution  

NASA Technical Reports Server (NTRS)

In an earlier study, an in vitro evolution procedure was applied to a large population of variants of the Tetrahymena group 1 ribozyme to obtain individuals with a 10(exp 5)-fold improved ability to cleave a target single-stranded DNA substrate under simulated physiological conditions. The evolved ribozymes also showed a twofold improvement, compared to the wild-type, in their ability to cleave a single-stranded RNA substrate. Here, we report continuation of the in vitro evolution process using a new selection strategy to achieve both enhanced DNA and diminished RNA-cleavage activity. Our strategy combines a positive selection for DNA cleavage with a negative selection against RNA binding. After 36 "generations" of in vitro evolution, the evolved population showed an approx. 100-fold increase in the ratio of DNA to RNA-cleavage activity. Site-directed mutagenesis experiment confirmed the selective advantage of two covarying mutations within the catalytic core of ribozyme that are largely responsible for this modified behavior. The population of ribozymes has now undergone a total of 63 successive generations of evolution, resulting in an average 28 mutations relative to the wild-type that are responsible for the altered phenotype.

Tsang, Joyce; Joyce, Gerald F.

1996-01-01

27

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

PubMed

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

2011-01-01

28

Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes  

NASA Technical Reports Server (NTRS)

We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.

Egli, M.; Usman, N.; Rich, A.

1993-01-01

29

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. PMID:21359176

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

2011-01-01

30

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.

DANIELE DAFFONCHIO; SARA BORIN; GIUSEPPE FROVA; ROMINA GALLO; ELENA MORI; RENATO FANI; CLAUDIA SORLINI

1999-01-01

31

Inhibition of DNA polymerase reactions by pyrimidine nucleotide analogues lacking the 2-keto group  

Microsoft Academic Search

To investigate the influence of the pyrimidine 2-keto group on selection of nucleotides for incorporation into DNA by polymerases, we have prepared two C nucleoside triphosphates that are analogues of dCTP and dTTP, namely 2-amino-5-(24-deoxy-?-D-ribofurano- syl)pyridine-54-triphosphate (d*CTP) and 5-(24-deoxy- ?-D-ribofuranosyl)-3-methyl-2-pyridone-54-triphosphate (d*TTP) respectively. Both proved strongly inhibitory to PCR catalysed by Taq polymerase; d*TTP rather more so than d*CTP. In primer

Mao-Jun Guo; Stefan Hildbrand; Christian J. Leumann; Larry W. McLaughlin; Michael J. Waring

1998-01-01

32

Role of Polycomb Group Proteins in the DNA Damage Response - A Reassessment  

PubMed Central

A growing body of evidence suggests that Polycomb group (PcG) proteins, key regulators of lineage specific gene expression, also participate in the repair of DNA double-strand breaks (DSBs) but evidence for direct recruitment of PcG proteins at specific breaks remains limited. Here we explore the association of Polycomb repressive complex 1 (PRC1) components with DSBs generated by inducible expression of the AsiSI restriction enzyme in normal human fibroblasts. Based on immunofluorescent staining, the co-localization of PRC1 proteins with components of the DNA damage response (DDR) in these primary cells is unconvincing. Moreover, using chromatin immunoprecipitation and deep sequencing (ChIP-seq), which detects PRC1 proteins at common sites throughout the genome, we did not find evidence for recruitment of PRC1 components to AsiSI-induced DSBs. In contrast, the S2056 phosphorylated form of DNA-PKcs and other DDR proteins were detected at a subset of AsiSI sites that are predominantly at the 5? ends of transcriptionally active genes. Our data question the idea that PcG protein recruitment provides a link between DSB repairs and transcriptional repression. PMID:25057768

Chandler, Hollie; Patel, Harshil; Palermo, Richard; Brookes, Sharon; Matthews, Nik; Peters, Gordon

2014-01-01

33

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

1989-01-01

34

Indirect Readout of DNA Sequence by P22 Repressor: Roles of DNA and Protein Functional Groups in  

E-print Network

, USA 2 - School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332­DNA complexes, the negatively charged E44 and E48 residues are provocatively positioned near the negatively charged DNA phosphates of the non-contacted nucleotides. The close proximity of the negatively charged

Williams, Loren

35

Cryptons: a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi.  

PubMed

A new group of transposable elements, which the authors have named cryptons, was detected in several pathogenic fungi, including the basidiomycete Cryptococcus neoformans, and the ascomycetes Coccidioides posadasii and Histoplasma capsulatum. These elements are unlike any previously described transposons. An archetypal member of the group, crypton Cn1, is 4 kb in length and is present at a low but variable copy number in a variety of C. neoformans strains. It displays interstrain variations in its insertion sites, suggesting recent mobility. The internal region contains a long gene, interrupted by several introns. The product of this gene contains a putative tyrosine recombinase near its middle, and a region similar in sequence to the DNA-binding domains of several fungal transcription factors near its C-terminus. The element contains no long repeat sequences, but is bordered by short direct repeats which may have been produced by its insertion into the host genome by recombination. Many of the structural features of crypton Cn1 are conserved in the other known cryptons, suggesting that these elements represent the functional forms. The presence of cryptons in ascomycetes and basidiomycetes suggests that this is an ancient group of elements (>400 million years old). Sequence comparisons suggest that cryptons may be related to the DIRS1 and Ngaro1 groups of tyrosine-recombinase-encoding retrotransposons. PMID:14600222

Goodwin, Timothy J D; Butler, Margaret I; Poulter, Russell T M

2003-11-01

36

The influence of the 2-amino group of guanine on DNA conformation. Uranyl and DNase I probing of inosine/diaminopurine substituted DNA.  

PubMed Central

The conformation of the DNA helix is supposed to be a critical element in site-specific recognition by ligands both large and small. Groove width is one important measure of the conformation which varies with the local nucleotide composition, perhaps because of the presence of a purine 2-amino group on G.C base pairs. We have probed DNA with G-->inosine (I) and/or A-->diaminopurine (DAP) substitutions to see whether the location of the purine 2-amino group can indeed affect the minor groove width. At acid pH, the reactivity towards uranyl nitrate is modulated in substituted DNA quite differently from natural DNA, consistent with a marked narrowing of the minor groove at sites of G-->I substitution and widening at sites of A-->DAP replacement. The latter exerts the dominant effect. The expected changes in conformation are equally evident in the patterns of susceptibility to DNase I cleavage, but not to hydroxyl radical attack. Nuclease cleavage is maximal in normal and substituted DNA at regions of inferred moderate groove width which are generally little affected by the nucleotide substitutions. Consistent with models of sequence-dependent cutting by DNase I we find that the presence of a purine 2-amino group on the base pair three places upstream of the cutting site has a profound influence on the rate of reaction. Images PMID:7744018

Bailly, C; Møllegaard, N E; Nielsen, P E; Waring, M J

1995-01-01

37

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. PMID:16214741

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

2005-01-01

38

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

PubMed Central

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. We show that this requirement leads to equivalency of the corresponding partition functions, resulting in a one-step renormalization. Compared to prior works exploiting similar ideas, the main novelty of this work is the introduction of a highly compact set of Hamiltonian basis functions, based on molecular interaction potentials. We demonstrate that such compactification allows us to reproduce many-body effects, generated by one-step renormalization, at low computational cost. In addition, compact Hamiltonians greatly increase the likelihood of finding unique solutions for the coarse-grained force-field parameter values. By successfully applying our molecular renormalization group coarse-graining technique to double-stranded DNA, we solved, for the first time, a long-standing problem in coarse-graining polymer systems, namely, how to accurately capture the correlations among various polymeric degrees of freedom. Excellent agreement is found among atomistic and coarse-grained distribution functions for various structural observables, including those not included in the Hamiltonian. We also suggest higher-order generalization of this method, which may allow capturing more subtle correlations in biopolymer dynamics. PMID:19450476

Savelyev, Alexey; Papoian, Garegin A.

2009-01-01

39

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

Microsoft Academic Search

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

Michael Balke; Ignacio Ribera; Alfried P. Vogler

2004-01-01

40

Chloroplast DNA variation and geographical structure of the Aristolochia kaempferi group (Aristolochiaceae).  

PubMed

The present study documents cpDNA variation in the Aristolochia kaempferi group (Aristolochiaceae), which consists of one Chinese and all Japanese and Taiwanese species of the subgenus Siphisia. In a phylogenetic analysis based on the nucleotide sequences of the matK gene, and the atpB-rbcL and trnS-trnG intergenic spacer regions, 38 haplotypes were recognized in the A. kaempferi group and as many as 24 within A. kaempferi. This is the most haplotypes reported for a single species to date. Although six highly significant major clades were identified in the phylogenetic analysis, they were not congruent with previous classifications. This might be attributed to the specific speciation process, such as convergent evolution, incomplete lineage sorting, and/or reticulate evolution. The six major clades had a clear geographical distribution pattern and were significantly associated with geographical distribution of haplotypes in a nested clade analysis and AMOVA. The results allow us to deduce a scenario in which multiple contractions and expansions of the geographical ranges brought about by Quaternary climatic oscillations affected the patterns of genetic diversity. The present geographic patterns of haplotype distribution within the A. kaempferi group can be explained by the last postglacial range expansion from different refugia, and the boundaries may be suture zones. PMID:21646203

Watanabe, Kana; Kajita, Tadashi; Murata, Jin

2006-03-01

41

A human ortholog of archaeal DNA repair protein Hef is defective in Fanconi anemia complementation group M.  

PubMed

Fanconi anemia is a genetic disease characterized by genomic instability and cancer predisposition. Nine genes involved in Fanconi anemia have been identified; their products participate in a DNA damage-response network involving BRCA1 and BRCA2 (refs. 2,3). We previously purified a Fanconi anemia core complex containing the FANCL ubiquitin ligase and six other Fanconi anemia-associated proteins. Each protein in this complex is essential for monoubiquitination of FANCD2, a key reaction in the Fanconi anemia DNA damage-response pathway. Here we show that another component of this complex, FAAP250, is mutant in individuals with Fanconi anemia of a new complementation group (FA-M). FAAP250 or FANCM has sequence similarity to known DNA-repair proteins, including archaeal Hef, yeast MPH1 and human ERCC4 or XPF. FANCM can dissociate DNA triplex, possibly owing to its ability to translocate on duplex DNA. FANCM is essential for monoubiquitination of FANCD2 and becomes hyperphosphorylated in response to DNA damage. Our data suggest an evolutionary link between Fanconi anemia-associated proteins and DNA repair; FANCM may act as an engine that translocates the Fanconi anemia core complex along DNA. PMID:16116422

Meetei, Amom Ruhikanta; Medhurst, Annette L; Ling, Chen; Xue, Yutong; Singh, Thiyam Ramsing; Bier, Patrick; Steltenpool, Jurgen; Stone, Stacie; Dokal, Inderjeet; Mathew, Christopher G; Hoatlin, Maureen; Joenje, Hans; de Winter, Johan P; Wang, Weidong

2005-09-01

42

An ancient DNA test of a founder effect in Native American ABO blood group frequencies.  

PubMed

Anthropologists have assumed that reduced genetic diversity in extant Native Americans is due to a founder effect that occurred during the initial peopling of the Americas. However, low diversity could also be the result of subsequent historical events, such as the population decline following European contact. In this study, we show that autosomal DNA from ancient Native American skeletal remains can be used to investigate the low level of ABO blood group diversity in the Americas. Extant Native Americans exhibit a high frequency of blood type O, which may reflect a founder effect, genetic drift associated with the historical population decline, or natural selection in response to the smallpox epidemics that occurred following European contact. To help distinguish between these possibilities, we determined the ABO genotypes of 15 precontact individuals from eastern North America. The precontact ABO frequencies were not significantly different from those observed in extant Native Americans from the same region, but they did differ significantly from the ABO frequencies in extant Siberian populations. Studies of other precontact populations are needed to better test the three hypotheses for low ABO blood group diversity in the Americas, but our findings are most consistent with the hypothesis of a founder effect during the initial settlement of this continent. PMID:18618657

Halverson, Melissa S; Bolnick, Deborah A

2008-11-01

43

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

1998-01-01

44

The Q motif of Fanconi anemia group J protein (FANCJ) DNA helicase regulates its dimerization, DNA binding, and DNA repair function.  

PubMed

The Q motif, conserved in a number of RNA and DNA helicases, is proposed to be important for ATP binding based on structural data, but its precise biochemical functions are less certain. FANCJ encodes a Q motif DEAH box DNA helicase implicated in Fanconi anemia and breast cancer. A Q25A mutation of the invariant glutamine in the Q motif abolished its ability to complement cisplatin or telomestatin sensitivity of a fancj null cell line and exerted a dominant negative effect. Biochemical characterization of the purified recombinant FANCJ-Q25A protein showed that the mutation disabled FANCJ helicase activity and the ability to disrupt protein-DNA interactions. FANCJ-Q25A showed impaired DNA binding and ATPase activity but displayed ATP binding and temperature-induced unfolding transition similar to FANCJ-WT. Size exclusion chromatography and sedimentation velocity analyses revealed that FANCJ-WT existed as molecular weight species corresponding to a monomer and a dimer, and the dimeric form displayed a higher specific activity for ATPase and helicase, as well as greater DNA binding. In contrast, FANCJ-Q25A existed only as a monomer, devoid of helicase activity. Thus, the Q motif is essential for FANCJ enzymatic activity in vitro and DNA repair function in vivo. PMID:22582397

Wu, Yuliang; Sommers, Joshua A; Loiland, Jason A; Kitao, Hiroyuki; Kuper, Jochen; Kisker, Caroline; Brosh, Robert M

2012-06-22

45

The Q Motif of Fanconi Anemia Group J Protein (FANCJ) DNA Helicase Regulates Its Dimerization, DNA Binding, and DNA Repair Function*  

PubMed Central

The Q motif, conserved in a number of RNA and DNA helicases, is proposed to be important for ATP binding based on structural data, but its precise biochemical functions are less certain. FANCJ encodes a Q motif DEAH box DNA helicase implicated in Fanconi anemia and breast cancer. A Q25A mutation of the invariant glutamine in the Q motif abolished its ability to complement cisplatin or telomestatin sensitivity of a fancj null cell line and exerted a dominant negative effect. Biochemical characterization of the purified recombinant FANCJ-Q25A protein showed that the mutation disabled FANCJ helicase activity and the ability to disrupt protein-DNA interactions. FANCJ-Q25A showed impaired DNA binding and ATPase activity but displayed ATP binding and temperature-induced unfolding transition similar to FANCJ-WT. Size exclusion chromatography and sedimentation velocity analyses revealed that FANCJ-WT existed as molecular weight species corresponding to a monomer and a dimer, and the dimeric form displayed a higher specific activity for ATPase and helicase, as well as greater DNA binding. In contrast, FANCJ-Q25A existed only as a monomer, devoid of helicase activity. Thus, the Q motif is essential for FANCJ enzymatic activity in vitro and DNA repair function in vivo. PMID:22582397

Wu, Yuliang; Sommers, Joshua A.; Loiland, Jason A.; Kitao, Hiroyuki; Kuper, Jochen; Kisker, Caroline; Brosh, Robert M.

2012-01-01

46

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. PMID:19170889

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

2011-01-01

47

Recovery of a Nitrosomonas-like 16S rDNA Sequence Group from Freshwater Habitats  

Microsoft Academic Search

In order to study the diversity of ammonia-oxidising bacteria in freshwater habitats, including sediments, a molecular approach focused on the sequencing of 16S rDNA was adopted. 16S rDNA sequences showing affinity with the beta-subgroup of ammonia-oxidising bacteria were recovered by specific PCR of directly isolated DNA from freshwater samples, and samples from brackish water and Glyceria maxima rhizosphere were included

Arjen G. C. L. Speksnijder; Georg A. Kowalchuk; Kees Roest; Hendrikus J. Laanbroek

1998-01-01

48

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

2009-03-30

49

DNA Sequence of the Serum Opacity Factor of Group A Streptococci: Identification of a Fibronectin-Binding Repeat Domain  

Microsoft Academic Search

The serum opacity factor (SOF) is a group A streptococcal protein that induces opacity of mammalian serum. The serum opacity factor 22 gene (sof22) from an M type 22 strain was cloned from an EMBL4 library by screening for plaques exhibiting serum opacity activity. DNA sequencing yielded an open reading frame of 3,075 bp. Its deduced amino acid sequence predicts

JASNA V. RAKONJAC; JOHN C. ROBBINS; ANDVINCENT A. FISCHETTI

50

Role of the Acidic Tail of High Mobility Group Protein B1 (HMGB1) in Protein Stability and DNA Bending  

PubMed Central

High mobility group box (HMGB) proteins are abundant nonhistone proteins found in all eukaryotic nuclei and are capable of binding/bending DNA. The human HMGB1 is composed of two binding motifs, known as Boxes A and B, are L-shaped alpha-helix structures, followed by a random-coil acidic tail that consists of 30 Asp and Glu residues. This work aimed at evaluating the role of the acidic tail of human HMGB1 in protein stability and DNA interactions. For this purpose, we cloned, expressed and purified HMGB1 and its tailless form, HMGB1?C, in E. coli strain. Tryptophan fluorescence spectroscopy and circular dichroism (CD) experiments clearly showed an increase in protein stability promoted by the acidic tail under different conditions, such as the presence of the chemical denaturant guanidine hydrochloride (Gdn.HCl), high temperature and low pH. Folding intermediates found at low pH for both proteins were denatured only in the presence of chemical denaturant, thus showing a relatively high stability. The acidic tail did not alter the DNA-binding properties of the protein, although it enhanced the DNA bending capability from 76° (HMGB1?C) to 91° (HMGB1), as measured using the fluorescence resonance energy transfer technique. A model of DNA bending in vivo was proposed, which might help to explain the interaction of HMGB1 with DNA and other proteins, i.e., histones, and the role of that protein in chromatin remodeling. PMID:24255708

Belgrano, Fabricio S.; de Abreu da Silva, Isabel C.; Bastos de Oliveira, Francisco M.; Fantappie, Marcelo R.; Mohana-Borges, Ronaldo

2013-01-01

51

A small insertion in the SSU rDNA of the lichen fungus Arthonia lapidicola is a degenerate group-I intron  

Microsoft Academic Search

Insertions of less than 100 nt occurring in highly conserved regions of the small subunit ribosomal DNA (SSU rDNA) may represent\\u000a degenerate forms of the group-I introns observed at the same positions in other organisms. A 63-nt insertion at SSU rDNA position\\u000a 1512 (relative to theEscherichia coli SSU rDNA) of the lichen-forming fungusArthonia lapidicola can be folded into a secondary

Martin Grube; Andrea Gargas; Paula T. DePriest

1996-01-01

52

Cockayne Syndrome group B protein stimulates NEIL2 DNA glycosylase activity.  

PubMed

Cockayne Syndrome is a segmental premature aging syndrome, which can be caused by loss of function of the CSB protein. CSB is essential for genome maintenance and has numerous interaction partners with established roles in different DNA repair pathways including transcription coupled nucleotide excision repair and base excision repair. Here, we describe a new interaction partner for CSB, the DNA glycosylase NEIL2. Using both cell extracts and recombinant proteins, CSB and NEIL2 were found to physically interact independently of DNA. We further found that CSB is able to stimulate NEIL2 glycosylase activity on a 5-hydroxyl uracil lesion in a DNA bubble structure substrate in vitro. A novel 4,6-diamino-5-formamidopyrimidine (FapyA) specific incision activity of NEIL2 was also stimulated by CSB. To further elucidate the biological role of the interaction, immunofluorescence studies were performed, showing an increase in cytoplasmic CSB and NEIL2 co-localization after oxidative stress. Additionally, stalling of the progression of the transcription bubble with ?-amanitin resulted in increased co-localization of CSB and NEIL2. Finally, CSB knockdown resulted in reduced incision of 8-hydroxyguanine in a DNA bubble structure using whole cell extracts. Taken together, our data supports a biological role for CSB and NEIL2 in transcription associated base excision repair. PMID:24406253

Aamann, Maria D; Hvitby, Christina; Popuri, Venkateswarlu; Muftuoglu, Meltem; Lemminger, Lasse; Skeby, Cecilie K; Keijzers, Guido; Ahn, Byungchan; Bjørås, Magnar; Bohr, Vilhelm A; Stevnsner, Tinna

2014-01-01

53

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 PMID:7937082

Goodrich-Blair, H; Shub, D A

1994-01-01

54

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

Microsoft Academic Search

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

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

2007-01-01

55

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

PubMed

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

2007-06-01

56

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

PubMed Central

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 used as the basis for phylogenetic analyses of genes related to DNA repair that were found duplicated. Although 16S rRNA phylogenetic analyses confirm their classification at the basis of the gamma proteobacteria subdivision, differences were found in the origin of the various genes investigated. Except for lexA, detected as a recent duplication, most of the genes in more than one copy are represented by two highly divergent orthologs. Basically, one of such duplications is frequently positioned close to other gamma proteobacteria, but the second is often positioned close to unrelated bacteria. These orthologs may have occurred from old duplication events, followed by extensive gene loss, or were originated from lateral gene transfer (LGT), as is the case of the uvrD homolog. Conclusions Duplications of DNA repair related genes may result in redundancy and also improve the organisms' responses to environmental challenges. Most of such duplications, in Xanthomonas, seem to have arisen from old events and possibly enlarge both functional and evolutionary genome potentiality. PMID:15333143

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

2004-01-01

57

The electrokinetic characterization of gold nanoparticles, functionalized with cationic functional groups, and its' interaction with DNA.  

PubMed

Gold nanoparticles have attracted strong biomedical interest for drug delivery due to their low toxic nature, surface plasmon resonance and capability of increasing the stability of the payload. However, gene transfection represents another important biological application. Considering that cellular barriers keep enclosed their secret to deliver genes using nanoparticles, an important step can be achieved by studying the functionalization of nanoparticles with DNA. In the present contribution the synthesis of nanoparticles consisting of a gold core coated with one or more layers of amino acid (l-lysine), and cationic polyelectrolytes (poly-ethyleneimine and poly-l-lysine) is reported. All nanoparticles were subjected to dynamic light scattering, electrophoretic mobility measurements, UV-vis optical spectrophotometry analysis and transmission electron microscopy imaging. In addition, the adsorption of DNA plasmid (pSGS) with linear and supercoiled configurations was studied for those gold nanoparticles under the most suitable surface modifications. Preliminary results showed that the gold nanoparticles functionalized with poly-ethyleneimine and poly-l-lysine, respectively, and bound to linear DNA configurations, present in absolute value a higher electrophoretic mobility irrespective of the pH of the media, compared to the supercoiled and nicked configuration. The findings from this study suggest that poly-ethyleneimine and poly-l-lysine functionalized gold nanoparticles are biocompatible and may be promising in the chemical design and future optimization of nanostructures for biomedical applications such as gene and drug delivery. PMID:25009100

Lazarus, Geraldine Genevive; Revaprasadu, Neerish; López-Viota, Julián; Singh, Moganavelli

2014-09-01

58

A long-lasting dendritic cell DNA vaccination system using lysinylated amphiphiles with mannose-mimicking head-groups.  

PubMed

Dendritic cells (DCs) pulsed/transduced with tumor-associated or viral antigens have shown promise in combating cancer and infectious diseases. Despite significant progresses, development of a biologically safe DC-based genetic immunization (DNA vaccination) system capable of providing truly long-lasting protective immunity remains a significant scientific challenge. Here we show that immunization with autologous DCs pre-transfected with electrostatic complexes (lipoplexes) of a plasmid DNA encoding melanoma tumor associated antigen and liposomes of two lysinylated cationic amphiphiles with mannose-mimicking quinic and shikimic acid head-groups provides long-lasting (300 days post tumor challenge) protective immunity with significant memory response (more than six months after the second tumor challenge) in more than 80% immunized mice. The presently described non-viral ex vivo DC-transfection system may be exploited in inducing long-lasting immune response in DC-based genetic immunization. PMID:22658799

Srinivas, Ramishetti; Garu, Arup; Moku, Gopikrishna; Agawane, Sachin B; Chaudhuri, Arabinda

2012-09-01

59

A small insertion in the SSU rDNA of the lichen fungus Arthonia lapidicola is a degenerate group-I intron.  

PubMed

Insertions of less than 100 nt occurring in highly conserved regions of the small subunit ribosomal DNA (SSU rDNA) may represent degenerate forms of the group-I introns observed at the same positions in other organisms. A 63-nt insertion at SSU rDNA position 1512 (relative to the Escherichia coli SSU rDNA) of the lichen-forming fungus Arthonia lapidicola can be folded into a secondary structure with two stem loops and a pairing of the insertion and flanking sequences. The two stem loops may correspond to the P1 and P2, and the insertion-flanking pairing to the P10, of a group-I intron. Considering these small insertions as degenerate introns provides important clues to the evolution and catalytic function of group-I introns. Keywords Ribosomal DNA middle dot Small subunit middle dot 18s middle dot Degenerate introns middle dot Ascomycetes PMID:8662198

Grube, M; Gargas, A; DePriest, P T

1996-05-01

60

Chromosome 9: gene for blood group, Matt RidleySite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: Matt Ridley DNAi Location:Genome>tour>genome spots>Blood groups Location: chromosome 9 gene name: ABO (galactosyl transferase) The ABO gene codes for an enzyme called galactosyl transferase and determines your blood group. In people with A and B blood groups, the gene differs by seven basepairs, four of which have an effect on the type, shape and activity of the enzyme. People with O blood group have a single deletion in the gene that causes an inactive protein to be made.

2008-10-06

61

Genome-Wide DNA Polymorphisms in Seven Rice Cultivars of Temperate and Tropical Japonica Groups  

PubMed Central

Elucidation of the rice genome is expected to broaden our understanding of genes related to the agronomic characteristics and the genetic relationship among cultivars. In this study, we conducted whole-genome sequencings of 6 cultivars, including 5 temperate japonica cultivars and 1 tropical japonica cultivar (Moroberekan), by using next-generation sequencing (NGS) with Nipponbare genome as a reference. The temperate japonica cultivars contained 2 sake brewing (Yamadanishiki and Gohyakumangoku), 1 landrace (Kameji), and 2 modern cultivars (Koshihikari and Norin 8). Almost >83% of the whole genome sequences of the Nipponbare genome could be covered by sequenced short-reads of each cultivar, including Omachi, which has previously been reported to be a temperate japonica cultivar. Numerous single nucleotide polymorphisms (SNPs), insertions, and deletions were detected among the various cultivars and the Nipponbare genomes. Comparison of SNPs detected in each cultivar suggested that Moroberekan had 5-fold more SNPs than the temperate japonica cultivars. Success of the 2 approaches to improve the efficacy of sequence data by using NGS revealed that sequencing depth was directly related to sequencing coverage of coding DNA sequences: in excess of 30× genome sequencing was required to cover approximately 80% of the genes in the rice genome. Further, the contigs prepared using the assembly of unmapped reads could increase the value of NGS short-reads and, consequently, cover previously unavailable sequences. These approaches facilitated the identification of new genes in coding DNA sequences and the increase of mapping efficiency in different regions. The DNA polymorphism information between the 7 cultivars and Nipponbare are available at NGRC_Rices_Build1.0 (http://www.nodai-genome.org/oryza_sativa_en.html). PMID:24466017

Arai-Kichise, Yuko; Shiwa, Yuh; Ebana, Kaworu; Shibata-Hatta, Mari; Yoshikawa, Hirofumi; Yano, Masahiro; Wakasa, Kyo

2014-01-01

62

DNA duplexes with reactive dialdehyde groups as novel reagents for cross-linking to restriction- modification enzymes.  

PubMed Central

To create new, effective reagents for affinity modification of restriction-modification (R-M) enzymes, a regioselective method for reactive dialdehyde group incorporation into oligonucleotides, based on insertion of a 1-beta-D-galactopyranosylthymine residue, has been developed. We synthesized DNA duplex analogs of the substrates of the Eco RII and Mva I R-M enzymes that contained a galactose or periodate-oxidized galactose residue as single substituents either in the center of the Eco RII (Mva I) recognition site or in the flanking nucleotide sequence. The dependence of binding, cleavage and methylation of these substrate analogs on the modified sugar location in the duplex was determined. Cross-linking of the reagents to the enzymes under different conditions was examined. M. Eco RII covalent attachment to periodate-oxidized substrate analogs proceeded in a specific way and to a large extent depended on the location of the reactive dialdehyde group in the substrate. The yield of covalent attachment to a DNA duplex with a dialdehyde group in the flanking sequence with Eco RII or Mva I methylases was 9-20% and did not exceed 4% for R. Eco RII. PMID:9241245

Brevnov, M G; Gritsenko, O M; Mikhailov, S N; Efimtseva, E V; Ermolinsky, B S; Van Aerschot, A; Herdewijn, P; Repyk, A V; Gromova, E S

1997-01-01

63

Variation in the small subunit ribosomal DNA confirms that Udonella (Monogenea: Udonellidae) is a species-rich group.  

PubMed

Numerous global reports of the species Udonella caligorum, currently thought to be a species complex, suggests that the group may be species-rich. Herein we describe Udonella fugu n. sp., previously described as U. caligorum, found on the parasitic copepod Pseudocaligus fugu infecting Takifugu spp. from Japan. Using morphological data U. fugu can be distinguished from the current valid species by at least one of the traditionally used characters in udonellid taxonomy, and phylogenetic analyses of ssrDNA sequence data for U. fugu and other udonellids confirm that U. fugu forms a distinct clade from other udonellids including U. caligorum. Variable regions in the ssrDNA demonstrated a range of between 2.75 and 5.5% difference between currently recognized species of Udonella. These differences in ssrDNA sequences are phylogenetically useful when distinguishing between morphologically similar udonellids and can be used in conjunction with other data (morphology, phylogeography and fish host) to help clarify udonellid systematics. Udonella fugu was also found to cause significant damage to farmed tiger puffers through their feeding activities. Individual skin lesions were round in shape but merged with adjoining lesions to form more extensive lacerations. In some of the specimens from P. fugu infecting Takifugu niphobles, the protozoan ciliate Trichodina was found on the udonellid body surface and in their intestinal contents. We conclude that the udonellids are a more species-rich group than currently recognized, that early descriptions of new species may have been synonymized with U. caligorum in error and that the frequent global reports of U. caligorum may actually represent new species. This has led to a wide range of morphological descriptions for U. caligorum, blurring the usefulness of morphological data for the group. PMID:19715695

Freeman, Mark A; Ogawa, Kazuo

2010-02-01

64

Chloroplast and nuclear DNA studies in a few members of the Brassica oleracea L. group using PCR-RFLP and ISSR-PCR markers: a population genetic analysis  

Microsoft Academic Search

A population genetic analysis of chloroplast and nuclear DNA was performed covering nine wild populations of Brassica oleracea. Three members of the n = 9 group, all close to B. oleracea, Brassica alboglabra Bailey, Brassica bourgeaui (Webb) O. Kuntze and Brassica montana Pourret, were also studied to better understand their relationship with B. oleracea. Chloroplast DNA was analysed using the

S. Panda; J. P. Martín; I. Aguinagalde

2003-01-01

65

Fanconi Anemia Group J Helicase and MRE11 Nuclease Interact To Facilitate the DNA Damage Response  

PubMed Central

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.

2013-01-01

66

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. PMID:22253728

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

2012-01-01

67

The RNA polymerase I transactivator upstream binding factor requires its dimerization domain and high-mobility-group (HMG) box 1 to bend, wrap, and positively supercoil enhancer DNA.  

PubMed Central

Upstream binding factor (UBF) is an important transactivator of RNA polymerase I and is a member of a family of proteins that contain nucleic acid binding domains named high-mobility-group (HMG) boxes because of their similarity to HMG chromosomal proteins. UBF is a highly sequence-tolerant DNA-binding protein for which no binding consensus sequence has been identified. Therefore, it has been suggested that UBF may recognize preformed structural features of DNA, a hypothesis supported by UBF's ability to bind synthetic DNA cruciforms, four-way junctions, and even tRNA. We show here that full-length UBF can also bend linear DNA to mediate circularization of probes as small as 102 bp in the presence of DNA ligase. Longer probes in the presence of UBF become positively supercoiled when ligated, suggesting that UBF wraps the DNA in a right-handed direction, opposite the direction of DNA wrapping around a nucleosome. The dimerization domain and HMG box 1 are necessary and sufficient to circularize short probes and supercoil longer probes in the presence of DNA ligase. UBF's sequence tolerance coupled with its ability to bend and wrap DNA makes UBF an unusual eukaryotic transcription factor. However, UBF's ability to bend DNA might explain how upstream and downstream rRNA gene promoter domains interact. UBF-induced DNA wrapping could also be a mechanism by which UBF counteracts histone-mediated gene repression. Images PMID:7935371

Putnam, C D; Copenhaver, G P; Denton, M L; Pikaard, C S

1994-01-01

68

Interrelationships of Staphyliniform groups inferred from 18S and 28S rDNA sequences, with special emphasis on Hydrophiloidea (Coleoptera, Staphyliniformia)  

Microsoft Academic Search

The series Staphyliniformia is one of the mega-diverse groups of Coleoptera, but the relationships among the main families are still poorly understood. In this paper we address the interrelationships of staphyliniform groups, with special emphasis on Hydrophiloidea and Hydraenidae, based on partial sequences of the ribosomal genes 18S rDNA and 28S rDNA. Sequence data were analysed with parsimony and Bayesian

A. Korte; I. Ribera; R. G. Beutel; D. Bernhard

2004-01-01

69

Testing the validity of Northern European species in the Chrysis ignita species group (Hymenoptera: Chrysididae) with DNA barcoding.  

PubMed

Containing more than a hundred species, the Chrysis ignita species group is the largest and one of the most taxonomically challenging groups in its genus. It has not been possible to resolve the taxonomy of the group using traditional methods due to the lack of robust diagnostic morphological characters. Here we present the results of a molecular analysis designed to delimit species in the Chrysis ignita group for the first time; using mitochondrial sequence data for 364 in-group specimens consisting of all 18 species known to occur in Northern Europe. Two mitochondrial loci were analysed: a COI gene fragment, and a continuous DNA sequence consisting of 16S rRNA, tRNAVal, 12S rRNA and ND4. Two approaches were employed for delimiting species: (1) genetic distance analysis based on the standard COI barcode sequences and; (2) phylogenetic analysis of the COI fragment together with rRNA genes. Both analyses yielded trees with similar topology, but support values for nodes were higher using the second approach. Fifteen species were distinguished in all analyses: Chrysis angustula Schenck, 1856, C. brevitarsis Thomson, 1870, C. clarinicollis Linsenmaier, 1951, C. corusca Valkeila, 1971, C. fulgida Linnaeus, 1761, C. ignita (Linnaeus, 1758), C. impressa Schenck, 1856, C. iris Christ, 1791, C. leptomandibularis Niehuis, 2000, C. longula Abeille de Perrin, 1879, C. ruddii Shuckard, 1837, C. schencki Linsenmaier, 1968, C. subcoriacea Linsenmaier, 1959, C. terminata Dahlbom, 1854 and C. vanlithi Linsenmaier, 1959. The specific status of C. mediata Linsenmaier, 1951 and C. solida Haupt, 1957 was not resolved. Included unidentified specimens grouped in three clusters, two of which are distinctly delimited and apparently represent cryptic species. The specific status of the unidentified samples in the third cluster remained unclear. Moreover, our data suggest the existence of additional cryptic species currently lumped under the names C. pseudobrevitarsis Linsenmaier, 1951 and C. schencki Linsenmaier, 1968. In conclusion, our results derived from analysis of mitochondrial loci strongly support the specific status of the majority of currently recognised species in the Chrysis ignita species group, and suggest the existence of additional cryptic species in Northern Europe. Thus, considering the difficulties that often arise during species determination based on morphological characters, the mtDNA loci used here appear highly suitable for assisting species delimitation in this group as well as identification of specimens.  PMID:24869539

Soon, Villu; Budrys, Eduardas; Orlovskyt?, Svetlana; Paukkunen, Juho; Odegaard, Frode; Ljubomirov, Toshko; Saarma, Urmas

2014-01-01

70

Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts.  

PubMed

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-, I-, and AI-tracts show almost identical structures, with high propeller twist and minor groove narrowing. G- and D-tracts have small propeller twisting and are partly shifted toward the A-form. The elastic properties also differ between the two groups. The sequence-dependent electrostatic component of base stacking seems to play a minor role. Our conclusions are entirely consistent with available experimental data. Nevertheless, the propeller twist and helical twist in the simulated A-tract appear to be underestimated compared to crystallographic studies. To obtain further insight into the possible force field deficiencies, additional multiple simulations have been made for d(A)10, systematically comparing four major force fields currently used in DNA simulations and utilizing B and A-DNA forms as the starting structure. This comparison shows that the conclusions of the present work are not influenced by the force field choice. PMID:11964246

Lankas, Filip; Cheatham, Thomas E; Spacková, Nad'a; Hobza, Pavel; Langowski, Jörg; Sponer, Jirí

2002-05-01

71

DNA fingerprinting and anastomosis grouping reveal similar genetic diversity in Rhizoctonia species infecting turfgrasses in the transition zone of USA.  

PubMed

Rhizoctonia blight is a common and serious disease of many turfgrass species. The most widespread causal agent, Thanatephorus cucumeris (anamorph: R. solani), consists of several genetically different subpopulations. In addition, Waitea circinata varieties zeae, oryzae and circinata (anamorph: Rhizoctonia spp.) also can cause the disease. Accurate identification of the causal pathogen is important for effective management of the disease. It is challenging to distinguish the specific causal pathogen based on disease symptoms or macroscopic and microscopic morphology. Traditional methods such as anastomosis reactions with tester isolates are time consuming and sometimes difficult to interpret. In the present study universally primed PCR (UP-PCR) fingerprinting was used to assess genetic diversity of Rhizoctonia spp. infecting turfgrasses. Eighty-four Rhizoctonia isolates were sampled from diseased turfgrass leaves from seven distinct geographic areas in Virginia and Maryland. Rhizoctonia isolates were characterized by ribosomal DNA internal transcribed spacer (rDNA-ITS) region and UP-PCR. The isolates formed seven clusters based on ITS sequences analysis and unweighted pair group method with arithmetic mean (UPGMA) clustering of UP-PCR markers, which corresponded well with anastomosis groups (AGs) of the isolates. Isolates of R. solani AG 1-IB (n = 18), AG 2-2IIIB (n = 30) and AG 5 (n = 1) clustered separately. Waitea circinata var. zeae (n = 9) and var. circinata (n = 4) grouped separately. A cluster of six isolates of Waitea (UWC) did not fall into any known Waitea variety. The binucleate Rhizoctonia-like fungi (BNR) (n = 16) clustered into two groups. Rhizoctonia solani AG 2-2IIIB was the most dominant pathogen in this study, followed by AG 1-IB. There was no relationship between the geographic origin of the isolates and clustering of isolates based on the genetic associations. To our knowledge this is the first time UP-PCR was used to characterize Rhizoctonia, Waitea and Ceratobasidium isolates to their infra-species level. PMID:23709576

Amaradasa, B S; Horvath, B J; Lakshman, D K; Warnke, S E

2013-01-01

72

Syntheses of Two 5-Hydroxymethyl-2?-DeoxyCytidine Phosphoramidites with TBDMS as the 5-hydroxyl protecting group and Their Incorporation into DNA  

PubMed Central

5-Hydroxymethylcytosine (5-hmC) is a newly discovered DNA base modification in mammalian genomic DNA that is proposed to be a major epigenetic mark. We report here the syntheses of two new versions of phosphoramidites III and IV from dU in 18 and 32% overall yields, respectively, with TBDMS as the 5-hydroxyl 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 ultra-mild DNA synthesis, which enables the synthesis of 5hmC-containing DNA with additional modifications. PMID:21462947

Song, Chun-Xiao; Pan, Tao; He, Chuan

2012-01-01

73

Microsatellite DNA analysis shows that greater sage grouse leks are not kin groups.  

PubMed

The spectacular social courtship displays of lekking birds are thought to evolve via sexual selection, but this view does not easily explain the participation of many males that apparently fail to mate. One of several proposed solutions to this 'lek skew paradox' is that kin selection favours low-ranking males joining leks to increase the fitness of closely related breeders. We investigated the potential for kin selection to operate in leks of the greater sage grouse, Centrocercus urophasianus, by estimating relatedness between lekking males using microsatellite DNA markers. We also calibrated these estimates using data from known families. Mean relatedness within leks was statistically indistinguishable from zero. We also found no evidence for local clustering of kin during lek display, although males tended to range closer to kin when off the lek. These results make kin selection an unlikely solution to the lek skew paradox in sage grouse. Together with other recent studies, they also raise the question of why kin selection apparently promotes social courtship in some lekking species, but not in others. PMID:16313605

Gibson, Robert M; Pires, Debra; Delaney, Kathleen S; Wayne, Robert K

2005-12-01

74

Grouping  

NSDL National Science Digital Library

This interactive Flash applet models the measurement interpretation of division. A child or teacher chooses a total number of objects and a divisor representing the size of equal groups. The applet allows the user to move the objects into equal groups and links the process to jumps on a number line. The applet can be used to introduce children to remainders and to reinforce the language and notation of division. It works well on an interactive white board or projector. A teacher's guide to this collection of applets is cataloged separately.

2006-01-01

75

Effect of point substitutions within the minimal DNA-binding domain of xeroderma pigmentosum group A protein on interaction with DNA intermediates of nucleotide excision repair.  

PubMed

Xeroderma pigmentosum factor A (XPA) is one of the key proteins in the nucleotide excision repair (NER) process. The effects of point substitutions in the DNA-binding domain of XPA (positively charged lysine residues replaced by negatively charged glutamate residues: XPA K204E, K179E, K141E, and tandem mutant K141E/K179E) on the interaction of the protein with DNA structures modeling intermediates of the damage recognition and pre-incision stages in NER were analyzed. All these mutations decreased the affinity of the protein to DNA, the effect depending on the substitution and the DNA structure. The mutant as well as wild-type proteins bind with highest efficiency partly open damaged DNA duplex, and the affinity of the mutants to this DNA is reduced in the order: K204E > K179E > K141E = K141/179E. For all the mutants, decrease in DNA binding efficiency was more pronounced in the case of full duplex and single-stranded DNA than with bubble-DNA structure, the difference between protein affinities to different DNA structures increasing as DNA binding activity of the mutant decreased. No effect of the studied XPA mutations on the location of the protein on the partially open DNA duplex was observed using photoinduced crosslinking with 5-I-dUMP in different positions of the damaged DNA strand. These results combined with earlier published data suggest no direct correlation between DNA binding and activity in NER for these XPA mutants. PMID:25100013

Maltseva, E A; Krasikova, Y S; Naegeli, H; Lavrik, O I; Rechkunova, N I

2014-06-01

76

Two group I ribozymes with different functions in a nuclear rDNA intron.  

PubMed Central

DiSSU1, a mobile intron in the nuclear rRNA gene of Didymium iridis, was previously reported to contain two independent catalytic RNA elements. We have found that both catalytic elements, renamed GIR1 and GIR2, are group I ribozymes, but with differing functionality. GIR2 carries out the several reactions associated with self-splicing. GIR1 carries out a hydrolysis reaction at an internal processing site (IPS-1). These conclusions are based on the catalytic properties of RNAs transcribed in vitro. Mutation of the P7 pairing segment of GIR2 abrogated self-splicing, while mutation of P7 in GIR1 abrogated hydrolysis at the IPS-1. Much of the P2 stem and all of the associated loop could be deleted without effect on self-splicing. These results are accounted for by a secondary structure model, in which a long P2 pairing segment brings the 5' splice site to the GIR2 catalytic core. GIR1 is the smallest natural group I ribozyme yet reported and is the first example of a group I ribozyme whose presumptive biological function is hydrolysis. We hypothesize that GIR1-mediated cleavage of the excised intron RNA functions in the generation and expression of the mRNA for the intron-encoded endonuclease I-DirI. Images PMID:7556099

Decatur, W A; Einvik, C; Johansen, S; Vogt, V M

1995-01-01

77

Effect of pendant group on pDNA delivery by cationic-?-cyclodextrin:alkyl-PVA-PEG pendant polymer complexes.  

PubMed

We have previously shown that cationic-?-cyclodextrin:R-poly(vinyl alcohol)-poly(ethylene glycol) (CD+:R-PVA-PEG) pendant polymer host:guest complexes are safe and efficient vehicles for nucleic acid delivery, where R = benzylidene-linked adamantyl or cholesteryl esters. Herein, we report the synthesis and biological performance of a family of PVA-PEG pendant polymers whose pendant groups have a wide range of different affinities for the ?-CD cavity. Cytotoxicity studies revealed that all of the cationic-?-CD:pendant polymer host:guest complexes have 100-1000-fold lower toxicity than branched polyethylenimine (bPEI), with pDNA transfection efficiencies that are comparable to bPEI and Lipofectamine 2000. Complexes formed with pDNA at N/P ratios greater than 5 produced particles with diameters in the 100-170 nm range and ?-potentials of 15-35 mV. Gel shift and heparin challenge experiments showed that the complexes are most stable at N/P ? 10, with adamantyl- and noradamantyl-modified complexes displaying the best resistance toward heparin-induced decomplexation. Disassembly rates of fluoresceinated-pDNA:CD(+):R-PVA-PEG-rhodamine complexes within HeLa cells showed a modest dependence on host:guest binding constant, with adamantyl-, noradamantyl-, and dodecyl-based complexes showing the highest loss in FRET efficiency 9 h after cellular exposure. These findings suggest that the host:guest binding constant has a significant impact on the colloidal stability in the presence of serum and cellular uptake efficiency, whereas endosomal disassembly and transfection performance of cationic-?-CD:R-poly(vinyl alcohol)-poly(ethylene glycol) pendant polymer complexes appears to be controlled by the hydrolysis rates of the acetal grafts onto the PVA main chain. PMID:24295406

Kulkarni, Aditya; Badwaik, Vivek; DeFrees, Kyle; Schuldt, Ryan A; Gunasekera, Dinara S; Powers, Cory; Vlahu, Alexander; VerHeul, Ross; Thompson, David H

2014-01-13

78

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

PubMed Central

The purpose of this study was to investigate mitochondrial DNA (mtDNA) hypervariable segment-I (HVS-I) C-stretch variations and explore the significance of these variations in forensic and population genetics studies. The C-stretch sequence variation was studied in 919 unrelated individuals from 8 Chinese ethnic groups using both direct and clone sequencing approaches. Thirty eight C-stretch haplotypes were identified, and some novel and population specific haplotypes were also detected. The C-stretch genetic diversity (GD) values were relatively high, and probability (P) values were low. Additionally, C-stretch length heteroplasmy was observed in approximately 9% of individuals studied. There was a significant correlation (r=?0.961, P<0.01) between the expansion of the cytosine sequence length in the C-stretch of HVS-I and a reduction in the number of upstream adenines. These results indicate that the C-stretch could be a useful genetic maker in forensic identification of Chinese populations. The results from the Fst and dA genetic distance matrix, neighbor-joining tree, and principal component map also suggest that C-stretch could be used as a reliable genetic marker in population genetics. PMID:19816995

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

2009-01-01

79

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

PubMed

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 A(2)B 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 N(6)-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 A(2)B protomers, which indicates that it requires an assembly containing at least two A(2)B units. PMID:23147004

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

2013-01-01

80

Drosophila Polycomb-group regulated chromatin inhibits the accessibility of a trans-activator to its target DNA.  

PubMed Central

The genes of the Polycomb-group (Pc-G) are responsible for maintaining the inactive expression state of homeotic genes. They act through specific cis-regulatory DNA elements termed PREs (Pc-G Response Elements). Multimeric complexes containing the Pc-G proteins are thought to induce heterochromatin-like structures, which stably and heritably inactivate transcription. We have tested the functional role of the FAB fragment, a PRE of the bithorax complex. We find that this element behaves as an orientation dependent silencer, capable of inducing mosaic gene expression on neighboring genes. Transgenic fly lines were constructed containing a PRE adjacent to a reporter gene inducible by the yeast GAL4 trans-activator. The competition between the activator and Pc-G-containing chromatin was visualized on polytene chromosomes using immunocytochemistry. The Pc-G protein Polycomb and GAL4 have mutually exclusive binding patterns, supporting the notion that Pc-G-induced chromatin structures can prevent activators from binding to their target sequences. However, this antagonistic function can be overcome by high doses of GAL4, even in the absence of DNA replication. Images PMID:8521823

Zink, D; Paro, R

1995-01-01

81

Survey of chimeric IStron elements in bacterial genomes: multiple molecular symbioses between group I intron ribozymes and DNA transposons.  

PubMed

IStrons are chimeric genetic elements composed of a group I intron associated with an insertion sequence (IS). The group I intron is a catalytic RNA providing the IStron with self-splicing ability, which renders IStron insertions harmless to the host genome. The IS element is a DNA transposon conferring mobility, and thus allowing the IStron to spread in genomes. IStrons are therefore a striking example of a molecular symbiosis between unrelated genetic elements endowed with different functions. In this study, we have conducted the first comprehensive survey of IStrons in sequenced genomes that provides insights into the distribution, diversity, origin and evolution of IStrons. We show that IStrons have a restricted phylogenetic distribution limited to two bacterial phyla, the Firmicutes and the Fusobacteria. Nevertheless, diverse IStrons representing two major groups targeting different insertion site motifs were identified. This taken with the finding that while the intron components of all IStrons belong to the same structural class, they are fused to different IS families, indicates that multiple intron-IS symbioses have occurred during evolution. In addition, introns and IS elements related to those that were at the origin of IStrons were also identified. PMID:25324310

Tourasse, Nicolas J; Stabell, Fredrik B; Kolstø, Anne-Brit

2014-11-10

82

Autonomously replicating macronuclear DNA pieces are the physical basis of genetic coassortment groups in Tetrahymena thermophila.  

PubMed Central

The macronucleus of the ciliate Tetrahymena thermophila contains a fragmented somatic genome consisting of several hundred identifiable chromosome pieces. These pieces are generated by site-specific fragmentation of the germline chromosomes and most of them are represented at an average of 45 copies per macronucleus. In the course of successive divisions of an initially heterozygous macronucleus, the random distribution of alleles of loci carried on these copies eventually generates macronuclei that are pure for one allele or the other. This phenomenon is called phenotypic assortment. We have previously reported the existence of loci that assort together (coassort) and hypothesized that these loci reside on the same macronuclear piece. The work reported here provides new, rigorous genetic support for the hypothesis that macronuclear autonomously replicating chromosome pieces are the physical basis of coassortment groups. Thus, coassortment allows the mapping of the somatic genome by purely genetic means. The data also strongly suggest that the random distribution of alleles in the Tetrahymena macronucleus is due to the random distribution of the MAC chromosome pieces that carry them. PMID:10880474

Wong, L; Klionsky, L; Wickert, S; Merriam, V; Orias, E; Hamilton, E P

2000-01-01

83

High mobility group 1 and 2 proteins bind preferentially to DNA that contains bulky adducts induced by benzo(a)pyrene diol epoxide and N-acetoxy-acetylaminofluorene  

Microsoft Academic Search

High mobility group (HMG) proteins 1 and 2 are abundant non-histone chromosomal proteins that bind preferentially DNA that is bent or underwound. Previous studies have shown that these proteins preferentially bind to DNA damaged by the crosslinking agents cis-diammine-dichloro-platinum(II), chromium(III) and UV-C radiation. Here we have studied the binding of HMG-1\\/2 proteins to a duplex oligonucleotide damaged by benzo(a)pyrene diol

Piotr Widak

2000-01-01

84

SSX2 is a novel DNA-binding protein that antagonizes polycomb group body formation and gene repression.  

PubMed

Polycomb group (PcG) complexes regulate cellular identity through epigenetic programming of chromatin. Here, we show that SSX2, a germline-specific protein ectopically expressed in melanoma and other types of human cancers, is a chromatin-associated protein that antagonizes BMI1 and EZH2 PcG body formation and derepresses PcG target genes. SSX2 further negatively regulates the level of the PcG-associated histone mark H3K27me3 in melanoma cells, and there is a clear inverse correlation between SSX2/3 expression and H3K27me3 in spermatogenesis. However, SSX2 does not affect the overall composition and stability of PcG complexes, and there is no direct concordance between SSX2 and BMI1/H3K27me3 presence at regulated genes. This suggests that SSX2 antagonizes PcG function through an indirect mechanism, such as modulation of chromatin structure. SSX2 binds double-stranded DNA in a sequence non-specific manner in agreement with the observed widespread association with chromatin. Our results implicate SSX2 in regulation of chromatin structure and function. PMID:25249625

Gjerstorff, Morten Frier; Relster, Mette Marie; Greve, Katrine Buch Viden; Moeller, Jesper Bonnet; Elias, Daniel; Lindgreen, Jonas Nørrelund; Schmidt, Steffen; Mollenhauer, Jan; Voldborg, Bjørn; Pedersen, Christina Bøg; Brückmann, Nadine Heidi; Møllegaard, Niels Erik; Ditzel, Henrik Jørn

2015-02-01

85

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

PubMed

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

2009-06-01

86

No Differences in DNA Damage and Antioxidant Capacity Between Intervention Groups of Healthy, Nonsmoking Men Receiving 2, 5, or 8 Servings\\/Day of Vegetables and Fruit  

Microsoft Academic Search

The effects of different intake levels of vegetables and fruit (VF) on some cancer-relevant biomarkers such as DNA damage and oxidative stress were investigated. In a randomized controlled trial, 64 nonsmoking male subjects were asked to consume a diet with 2 servings of VF\\/day for 4 wk. Then subjects were randomly assigned to 1 of 3 groups with either a

Karlis Briviba; Achim Bub; Jutta Möseneder; Tanja Schwerdtle; Andrea Hartwig; Sabine Kulling; Bernhard Watzl

2008-01-01

87

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  

Microsoft Academic Search

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

Ronald D. Snyder; James D. Regan

1982-01-01

88

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

1995-01-01

89

Phylogenetic Evidence for Horizontal Transmission of Group I Introns in the Nuclear Ribosomal DNA of Mushroom-Forming Fungi  

E-print Network

of Mushroom-Forming Fungi David S. Hibbett Harvard University Herbaria, Department of Organismic in the nuclear small-subunit ribosomal DNA (nuc- ssu-rDNA) in several species of homobasidiomycetes (mushroom of intron sequences suggest that the mushroom introns are monophyletic, and are nested within a clade

Hibbett, David S.

90

A DNA vaccine encoding a chimeric allergen derived from major group 1 allergens of dust mite can be used for specific immunotherapy  

PubMed Central

Immunization with DNA-based constructs has been shown to be against the antigen and the response is skewed in such a way as to ameliorate the symptoms of allergic disease. This approach is particularly useful in the treatment of allergic inflammatory diseases, such as asthma. The major group 1 allergen from house dust mites is one of the triggers of allergic asthma. This study explores whether a chimeric gene R8, derived from the major group 1 allergen of house dust mite species (Dermatophagoides farinae and Dermatophagoides pteronyssinus), can be expressed in Human Embryonic Kidney 293 cells (HEK 293T) and whether such a construct can be used as a DNA vaccine in asthma therapy. The eukaryotic expression vector pcDNA3.1 was used to express the R8 molecule in HEK 293T cells and successful expression of R8 was confirmed using a fluorescence microscope and western blot analysis. The efficacy of R8 as DNA vaccine was also assessed in a mouse asthma model. The in vivo data showed that R8 rectified the TH1/TH2 imbalance typical of allergic inflammation and stimulated the proliferation of regulatory T (Treg) cells. Immunization with the R8 construct also decreased serum allergen-specific IgE production in this mouse asthma model. Our findings suggest that R8 may be a feasible potential DNA vaccine for specific immunotherapy (SIT) in the treatment of allergic asthma. PMID:25337189

Sun, Tong; Yin, Kang; Wu, Lu-Yi; Jin, Wen-Jie; Li, Yang; Sheng, Bin; Jiang, Yu-Xin

2014-01-01

91

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 PMID:8265659

King, C Y; Weiss, M A

1993-01-01

92

Spectroscopic study on the interaction of ct-DNA with manganese Salen complex containing triphenyl phosphonium groups.  

PubMed

The DNA binding properties of a bulky and hydrophobic Schiff base complex of manganese(III) [N,N'-bis(5-(triphenyl phosphonium methyl)salicylidene)-1,2-ethylene diamine chloride Mn(III) acetate] was examined by spectroscopic techniques. UV-vis titration data indicate both hypo and hyperchromic effect with addition of DNA to complex. A competitive binding study showed that the enhanced emission intensity of ethidium bromide (EB) in the presence of DNA was quenched by adding Mn Salen complex. This finding indicates that Mn Salen complex displaces EB from its binding site in DNA. Helix melting studies indicate improvement in the helix stability, and an increase in the melting temperature. The analysis of CD spectra represents the structural changes in DNA due to the binding of Mn Salen complex. The binding constant has been calculated using absorbance and fluorescence data. The results also represent that the binding process proceeds by strong electrostatic and hydrophobic interactions. PMID:22306451

Dehkordi, Maryam Nejat; Bordbar, Abdol-Khalegh; Lincoln, Per; Mirkhani, Valiollah

2012-05-01

93

Checkpoint Kinase ATR Promotes Nucleotide Excision Repair of UV-induced DNA Damage via Physical Interaction with Xeroderma Pigmentosum Group A*  

PubMed Central

In response to DNA damage, eukaryotic cells activate a series of DNA damage-dependent pathways that serve to arrest cell cycle progression and remove DNA damage. Coordination of cell cycle arrest and damage repair is critical for maintenance of genomic stability. However, this process is still poorly understood. Nucleotide excision repair (NER) and the ATR-dependent cell cycle checkpoint are the major pathways responsible for repair of UV-induced DNA damage. Here we show that ATR physically interacts with the NER factor Xeroderma pigmentosum group A (XPA). Using a mass spectrometry-based protein footprinting method, we found that ATR interacts with a helix-turn-helix motif in the minimal DNA-binding domain of XPA where an ATR phosphorylation site (serine 196) is located. XPA-deficient cells complemented with XPA containing a point mutation of S196A displayed a reduced repair efficiency of cyclobutane pyrimidine dimers as compared with cells complemented with wild-type XPA, although no effect was observed for repair of (6-4) photoproducts. This suggests that the ATR-dependent phosphorylation of XPA may promote NER repair of persistent DNA damage. In addition, a K188A point mutation of XPA that disrupts the ATR-XPA interaction inhibits the nuclear import of XPA after UV irradiation and, thus, significantly reduced DNA repair efficiency. By contrast, the S196A mutation has no effect on XPA nuclear translocation. Taken together, our results suggest that the ATR-XPA interaction mediated by the helix-turn-helix motif of XPA plays an important role in DNA-damage responses to promote cell survival and genomic stability after UV irradiation. PMID:19586908

Shell, Steven M.; Li, Zhengke; Shkriabai, Nikolozi; Kvaratskhelia, Mamuka; Brosey, Chris; Serrano, Moises A.; Chazin, Walter J.; Musich, Phillip R.; Zou, Yue

2009-01-01

94

Polyphyletic origin of the genus Physarum (Physarales, Myxomycetes) revealed by nuclear rDNA mini-chromosome analysis and group I intron synapomorphy  

PubMed Central

Background Physarales represents the largest taxonomic order among the plasmodial slime molds (myxomycetes). Physarales is of particular interest since the two best-studied myxomycete species, Physarum polycephalum and Didymium iridis, belong to this order and are currently subjected to whole genome and transcriptome analyses. Here we report molecular phylogeny based on ribosomal DNA (rDNA) sequences that includes 57 Physarales isolates. Results The Physarales nuclear rDNA sequences were found to be loaded with 222 autocatalytic group I introns, which may complicate correct alignments and subsequent phylogenetic tree constructions. Phylogenetic analysis of rDNA sequences depleted of introns confirmed monophyly of the Physarales families Didymiaceae and Physaraceae. Whereas good correlation was noted between phylogeny and taxonomy among the Didymiaceae isolates, significant deviations were seen in Physaraceae. The largest genus, Physarum, was found to be polyphyletic consisting of at least three well supported clades. A synapomorphy, located at the highly conserved G-binding site of L2449 group I intron ribozymes further supported the Physarum clades. Conclusions Our results provide molecular relationship of Physarales genera, species, and isolates. This information is important in further interpretations of comparative genomics nd transcriptomics. In addition, the result supports a polyphyletic origin of the genus Physarum and calls for a reevaluation of current taxonomy. PMID:22938158

2012-01-01

95

Hoechst 33258, distamycin A, and high mobility group protein I (HMG-I) compete for binding to mouse satellite DNA.  

PubMed

The experiments described were designed to test the hypothesis that the (A+T)-specific DNA binding ligands Hoechst 33258 and distamycin A affect the condensation of mouse centromeric heterochromatin by competing for binding to satellite DNA with one or more chromosomal proteins. The studies focused on the nonhistone chromosomal protein HMG-I since its binding properties predict it would be a target for competition. Gel mobility shift assays show that HMG-I forms specific complexes with satellite DNA and that the formation of these complexes is competed for by both Hoechst and distamycin. In addition, methidium propyl EDTA Fe(II) [MPE Fe(II)] footprints of ligand-satellite DNA complexes showed essentially the same protection pattern for both drugs and a similar, but not identical, HMG-I footprint. If these in vitro results reflect the in vivo situation then the incomplete condensation of centromeric heterochromatin observed when mouse cells are grown in the presence of either chemical ligand could be a consequence of competition for binding of HMG-I (and possibly other proteins) to satellite DNA. PMID:1385053

Radic, M Z; Saghbini, M; Elton, T S; Reeves, R; Hamkalo, B A

1992-10-01

96

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

PubMed

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

2011-01-01

97

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

1993-01-01

98

DNA Build  

NSDL National Science Digital Library

Students reinforce their knowledge that DNA is the genetic material for all living things by modeling it using toothpicks and gumdrops that represent the four biochemicals (adenine, thiamine, guanine, and cytosine) that pair with each other in a specific pattern, making a double helix. They investigate specific DNA sequences that code for certain physical characteristics such as eye and hair color. Student teams trade DNA "strands" and de-code the genetic sequences to determine the physical characteristics (phenotype) displayed by the strands (genotype) from other groups. Students extend their knowledge to learn about DNA fingerprinting and recognizing DNA alterations that may result in genetic disorders.

Integrated Teaching And Learning Program

99

A high mobility group box 1 (HMGB1) gene from Chlamys farreri and the DNA-binding ability and pro-inflammatory activity of its recombinant protein.  

PubMed

High-mobility group box 1 (HMGB1) protein, a highly conserved DNA binding protein, plays an important role in maintaining nucleosome structures, transcription, and inflammation. In the present research, a cDNA of 1268 bp for the Zhikong scallop Chlamys farreri HMGB1 (designed as CfHMGB1) was cloned via rapid amplification of cDNA ends (RACE) technique and expression sequence tag (EST) analysis. The complete cDNA sequence of CfHMGB1 contained an open reading frame (ORF) of 648 bp, which encoded a protein of 215 amino acids. The amino acid sequence of CfHMGB1 shared 53-57% similarity with other identified HMGB1s. There were two HMG domains, two low complexity regions and a conserved acidic tail in the amino acid sequence of CfHMGB1. The mRNA transcripts of CfHMGB1 were constitutively expressed in all the tested tissues, including haemocytes, muscle, mantle, gill, hepatopancreas, kidney and gonad, with the highest expression level in hepatopancreas. The mRNA expression profiles of CfHMGB1 in haemocytes after the stimulation with different pathogen-associated molecular patterns (PAMPs), including lipopolysaccharide (LPS), peptidoglycan (PGN) and glucan (Glu), were similar with an up-regulation in the early stage and then recovered to the original level. The recombinant CfHMGB1 protein could bind double-stranded DNA and induce the release of TNF-? activity in mixed primary culture of scallop haemocytes. These results collectively indicated that CfHMGB1, with DNA-binding ability and pro-inflammatory activity, could play an important role in the immune response of scallops. PMID:24378681

Wang, Mengqiang; Wang, Lingling; Guo, Ying; Zhou, Zhi; Yi, Qilin; Zhang, Daoxiang; Zhang, Huan; Liu, Rui; Song, Linsheng

2014-02-01

100

Additional data for nuclear DNA give new insights into the phylogenetic position of Sorex granarius within the Sorex araneus group  

E-print Network

microsatellites. These analyses revealed that all markers apart from mtDNA showed similar patterns, suggesting phylogenetic relationship and their close geographic distribution, the most likely explanation for this pattern reserved. 1. Introduction The climatic oscillations that characterized the Pleistocene im- posed important

Alvarez, Nadir

101

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

PubMed

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

2012-06-01

102

DNA conjugation andDNA conjugation and reversibility onreversibility on  

E-print Network

DNA conjugation andDNA conjugation and reversibility onreversibility on chitosan surfaceschitosan surfaceschitosan surfaceschitosan surfaces Rubloff Research Group Accomplishments #12;DNA conjugation and reversibility onDNA conjugation and reversibility on chitosan surfaceschitosan surfaces Accomplishment Single

Rubloff, Gary W.

103

Phosphate-group of DNA as a potential target for RSU-1069, a nitroimidazole-aziridine radiosensitizer  

Microsoft Academic Search

Strand breakage of plasmid DNA by parent and radiation-reduced RSU-1069 (2.0-8.0 mmol dm-3) has been measured in air over 4 hr at 310K. Reduced RSU-1069 was shown to be approximately 4 times as efficient as the parent compound at causing strand breakage. The aziridine moiety of both parent and reduced RSU-1069 is required for strand break production and, furthermore, is

Andrew R. J. Silver; P. ONeill; Terence C. Jenkins; Shona S. McNeil

1986-01-01

104

Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing  

PubMed Central

Mobile group II introns encode reverse transcriptases (RTs) that function in intron mobility (“retrohoming”) by a process that requires reverse transcription of a highly structured, 2–2.5-kb intron RNA with high processivity and fidelity. Although the latter properties are potentially useful for applications in cDNA synthesis and next-generation RNA sequencing (RNA-seq), group II intron RTs have been difficult to purify free of the intron RNA, and their utility as research tools has not been investigated systematically. Here, we developed general methods for the high-level expression and purification of group II intron-encoded RTs as fusion proteins with a rigidly linked, noncleavable solubility tag, and we applied them to group II intron RTs from bacterial thermophiles. We thus obtained thermostable group II intron RT fusion proteins that have higher processivity, fidelity, and thermostability than retroviral RTs, synthesize cDNAs at temperatures up to 81°C, and have significant advantages for qRT-PCR, capillary electrophoresis for RNA-structure mapping, and next-generation RNA sequencing. Further, we find that group II intron RTs differ from the retroviral enzymes in template switching with minimal base-pairing to the 3? ends of new RNA templates, making it possible to efficiently and seamlessly link adaptors containing PCR-primer binding sites to cDNA ends without an RNA ligase step. This novel template-switching activity enables facile and less biased cloning of nonpolyadenylated RNAs, such as miRNAs or protein-bound RNA fragments. Our findings demonstrate novel biochemical activities and inherent advantages of group II intron RTs for research, biotechnological, and diagnostic methods, with potentially wide applications. PMID:23697550

Mohr, Sabine; Ghanem, Eman; Smith, Whitney; Sheeter, Dennis; Qin, Yidan; King, Olga; Polioudakis, Damon; Iyer, Vishwanath R.; Hunicke-Smith, Scott; Swamy, Sajani; Kuersten, Scott; Lambowitz, Alan M.

2013-01-01

105

Evidence for chromosome and Pst I satellite DNA family evolutionary stasis in the Bufo viridis group (Amphibia, Anura).  

PubMed

The West Palearctic green toads, Bufo viridis , represent a species complex. Apart from tetraploid populations, which form at least one separate species, evidence exists for relevant differentiation among diploid populations. We present the results of a chromosomal (C-, Ag-NOR-, Replication pattern, DAPI and CMA3 banding) and molecular study (isolation and characterization of a satellite DNA family) carried out on a number of Central Asian, European and North African populations. For comparative purposes, our molecular analysis was also extended to specimens of three additional Bufo species (B. bufo, B. mauritanicus and B. cf. regularis ), as well as two rare African bufonids (Werneria mertensis and Wolterstoffina sp.). Our results demonstrate a remarkable karyological and molecular evolutionary stasis in the Bufo viridis complex. In fact, all chromatinic markers showed the same pattern and/or composition in all specimens, independently of their origin and ploidy levels. Even the NOR loci were invariably two and located on the telomeric regions of two chromosomes of the sixth pair, or quartet. Furthermore, very similar patterns of genomic hybridization of a monomeric unit of the Pst I satellite DNA family (named pBv) were observed in all diploid and tetraploid populations, as well as in B. bufo and B. mauritanicus . Finally, pBv hybridizes with monomeric units of Pst I satellite DNA in all species studied, including Werneria and Wolterstorffina, which are thought to have separated from Bufo as early as in the Mesozoic. PMID:15505402

Odierna, Gaetano; Aprea, Gennaro; Capriglione, Teresa; Castellano, Sergio; Balletto, Emilio

2004-01-01

106

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. PMID:23733431

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

2013-01-01

107

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

PubMed

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. PMID:23733431

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

2013-06-01

108

Identification of Optimal Protocols for Sequencing Difficult Templates: Results of the 2008 ABRF DNA Sequencing Research Group Difficult Template Study 2008  

PubMed Central

The 2008 ABRF DNA Sequencing Research Group (DSRG) difficult template sequencing study was designed to identify a general set of guidelines that would constitute the best approaches for sequencing difficult templates. This was a continuation of previous DSRG difficult template studies performed in 1996, 1997, and 2003. The distinguishing factors in the present study were the number of DNA templates used, the number of different types of difficult regions tested, and the inclusion of a follow-up phase of the study to identify optimal protocols for each type of difficult template. DNA templates with associated sequencing primers were distributed to participating laboratories and each laboratory returned their sequencing results along with descriptions of the experimental conditions used. The data were analyzed and the best protocols were identified for each difficult template. This information was subsequently distributed to the participating laboratories for a second round of sequencing to evaluate the general applicability of the optimized protocols. The average improvements in sequencing results were 11% overall, with a range of ?25% to +43% using the optimized protocols. The full results from this study are presented here and they demonstrate that general experimental protocols and common additives can be used to improve the sequencing success for many difficult templates. PMID:19503623

Kieleczawa, Jan; Adam, Debbie; Bintzler, Doug; Detwiler, Michelle; Needleman, David; Schweitzer, Peter; Singh, Sushmita; Steen, Robert; Zianni, Michael

2009-01-01

109

Universal Plant DNA Barcode Loci May Not Work in Complex Groups: A Case Study with Indian Berberis Species  

PubMed Central

Background The concept of DNA barcoding for species identification has gained considerable momentum in animals because of fairly successful species identification using cytochrome oxidase I (COI). In plants, matK and rbcL have been proposed as standard barcodes. However, barcoding in complex genera is a challenging task. Methodology and Principal Findings We investigated the species discriminatory power of four reportedly most promising plant DNA barcoding loci (one from nuclear genome- ITS, and three from plastid genome- trnH-psbA, rbcL and matK) in species of Indian Berberis L. (Berberidaceae) and two other genera, Ficus L. (Moraceae) and Gossypium L. (Malvaceae). Berberis species were delineated using morphological characters. These characters resulted in a well resolved species tree. Applying both nucleotide distance and nucleotide character-based approaches, we found that none of the loci, either singly or in combinations, could discriminate the species of Berberis. ITS resolved all the tested species of Ficus and Gossypium and trnH-psbA resolved 82% of the tested species in Ficus. The highly regarded matK and rbcL could not resolve all the species. Finally, we employed amplified fragment length polymorphism test in species of Berberis to determine their relationships. Using ten primer pair combinations in AFLP, the data demonstrated incomplete species resolution. Further, AFLP analysis showed that there was a tendency of the Berberis accessions to cluster according to their geographic origin rather than species affiliation. Conclusions/Significance We reconfirm the earlier reports that the concept of universal barcode in plants may not work in a number of genera. Our results also suggest that the matK and rbcL, recommended as universal barcode loci for plants, may not work in all the genera of land plants. Morphological, geographical and molecular data analyses of Indian species of Berberis suggest probable reticulate evolution and thus barcode markers may not work in this case. PMID:21060687

Roy, Sribash; Tyagi, Antariksh; Shukla, Virendra; Kumar, Anil; Singh, Uma M.; Chaudhary, Lal Babu; Datt, Bhaskar; Bag, Sumit K.; Singh, Pradhyumna K.; Nair, Narayanan K.; Husain, Tariq; Tuli, Rakesh

2010-01-01

110

Polymorphisms and allele frequencies of the ABO blood group gene among the Jomon, Epi-Jomon and Okhotsk people in Hokkaido, northern Japan, revealed by ancient DNA analysis.  

PubMed

To investigate the genetic characteristics of the ancient populations of Hokkaido, northern Japan, polymorphisms of the ABO blood group gene were analyzed for 17 Jomon/Epi-Jomon specimens and 15 Okhotsk specimens using amplified product-length polymorphism and restriction fragment length polymorphism analyses. Five ABO alleles were identified from the Jomon/ Epi-Jomon and Okhotsk people. Allele frequencies of the Jomon/Epi-Jomon and Okhotsk people were compared with those of the modern Asian, European and Oceanic populations. The genetic relationships inferred from principal component analyses indicated that both Jomon/Epi-Jomon and Okhotsk people are included in the same group as modern Asian populations. However, the genetic characteristics of these ancient populations in Hokkaido were significantly different from each other, which is in agreement with the conclusions from mitochondrial DNA and ABCC11 gene analyses that were previously reported. PMID:20703243

Sato, Takehiro; Kazuta, Hisako; Amano, Tetsuya; Ono, Hiroko; Ishida, Hajime; Kodera, Haruto; Matsumura, Hirofumi; Yoneda, Minoru; Dodo, Yukio; Masuda, Ryuichi

2010-10-01

111

Phosphate-group of DNA as a potential target for RSU-1069, a nitroimidazole-aziridine radiosensitizer  

SciTech Connect

Strand breakage of plasmid DNA by parent and radiation-reduced RSU-1069 (2.0-8.0 mmol dm-3) has been measured in air over 4 hr at 310K. Reduced RSU-1069 was shown to be approximately 4 times as efficient as the parent compound at causing strand breakage. The aziridine moiety of both parent and reduced RSU-1069 is required for strand break production and, furthermore, is capable of alkylating inorganic phosphate (k = 1.0 X 10(-3) dm3 mol-1 s-1) and a series of nucleotides (k = 0.8 - 2.1 X 10(-3) dm3 mol-1 s-1) at pH 7.0. From the determined rate constants and the nature of the adducts observed, it was shown that phosphate is a target on nucleotides, although additional sites probably exist particularly, on dGMP and dAMP. The mechanism of action of RSU-1069 is discussed in terms of its ability to act as a cytotoxic agent, radiosensitizer and bioreductive drug.

Silver, A.R.; O'Neill, P.; Jenkins, T.C.; McNeil, S.S.

1986-07-01

112

Longitudinal Changes in Total, 2-LTR Circular, and Integrated HIV-1 DNA During the First Year of HIV-1 Infection in CD4Low and CD4High Patient Groups with HIV-1 Subtype AE.  

PubMed

Abstract The level of viral DNA in early HIV-1 infection is an important parameter in the prediction of disease progression. Few data have been published on the dynamics of HIV-1 DNA during the first year of HIV infection. In this study, two distinct HIV-1 patient groups were enrolled. Group 1 (CD4High group) maintained their CD4 above 450 cells/?L within 1 year, while Group 2 (CD4Low group) progressed to CD4 below 300 cells/?L. The amounts of total, 2-long terminal repeat (2-LTR) circular, and integrated HIV-1 DNA were determined in the peripheral blood mononuclear cells at 1, 3, 6, and 12 months after HIV infection. Reductions in the amount of total and integrated HIV-1 DNA were detected in the CD4High group during the first year of HIV infection but not in the CD4Low group. Disease progression may be related to the body's ability to control HIV-1 DNA during early HIV-1 infection. PMID:25188292

Zhang, Haihong; Jiao, Yanmei; Li, Hongjun; Zhu, Weijun; Li, Wei; Huang, Xiaojie; Zhang, Yonghong; Zhang, Tong; Lian, Shi; Wu, Hao

2014-11-01

113

PolA1, a Putative DNA Polymerase I, Is Coexpressed with PerR and Contributes to Peroxide Stress Defenses of Group A Streptococcus  

PubMed Central

The peroxide stress response regulator PerR coordinates the oxidative-stress defenses of group A Streptococcus (GAS). We now show that PerR is expressed from an operon encoding a putative DNA polymerase I (PolA1), among other GAS products. A polA1 deletion mutant exhibited wild-type growth but showed reduced capacity to repair DNA damage caused by UV light or ciprofloxacin. Mutant bacteria were hypersensitive to H2O2, compared with the wild type or a complemented mutant strain, and remained severely attenuated even after adaptation at sublethal H2O2 levels, whereas wild-type bacteria could adapt to withstand peroxide challenge under identical conditions. The hypersensitivity of the mutant was reversed when bacteria were grown in iron-depleted medium and challenged in the presence of a hydroxyl radical scavenger, results that indicated sensitivity to hydroxyl radicals generated by Fenton chemistry. The peroxide resistance of a perR polA1 double mutant following adaptation at sublethal H2O2 levels was decreased 9-fold relative to a perR single mutant, thus implicating PolA1 in PerR-mediated defenses against peroxide stress. Cultures of the polA1 mutant grown with or without prior H2O2 exposure yielded considerably lower numbers of rifampin-resistant mutants than cultures of the wild type or the complemented mutant strain, a finding consistent with PolA1 lacking proofreading activity. We conclude that PolA1 promotes genome sequence diversity while playing an essential role in oxidative DNA damage repair mechanisms of GAS, dual functions predicted to confer optimal adaptive capacity and fitness in the host. Together, our studies reveal a unique genetic and functional relationship between PerR and PolA1 in streptococci. PMID:23204468

Toukoki, Chadia

2013-01-01

114

The varying frequencies of five DNA polymorphisms of X-linked coagulant factor IX in eight ethnic groups.  

PubMed Central

Five RFLPS of X-linked coagulation factor IX were evaluated in more than 500 normal persons (723-804 X chromosomes) of both sexes who belonged to eight ethnic groups: Anglo-Americans, Basques, Swedes, African-Americans, East Africans, East Indians, Chinese, and Malays. The polymorphisms, 5' to 3', were BamHI, XmnI, TaqI, MnlI, and HhaI. A PCR procedure was developed for three previously described RFLPs-XmnI, TaqI, and MnlI; a PCRP procedure was developed for BamHI, and a PCRP which had been described by others was used for HhaI. Europeans were the most polymorphic, African-Americans and East Africans were intermediate, and Orientals were the least polymorphic. Extragenic 3' HhaI was highly polymorphic in most groups, and extragenic 5' BamHI was polymorphic only in persons with African ancestry. Two major haplotypes predominated among 247 men, and the expected and observed heterozygosities were concordant among women. Allelic association was very strong between the three intragenic PCRPs; it was present but weak between 5' extragenic BamHI and XmnI. No association was found between 3' extragenic HhaI and MnlI. Images Figure 2 PMID:1679290

Graham, J B; Kunkel, G R; Egilmez, N K; Wallmark, A; Fowlkes, D M; Lord, S T

1991-01-01

115

Functional constraints and evolutionary dynamics of the repeats in the rDNA internal transcribed spacer 2 of members of the Anopheles barbirostris group  

PubMed Central

Background The Anopheles barbirostris group is widely distributed in Southeast Asia. Although seven species have been formally described, a molecular analysis of the rDNA ITS2 and the mitochondrial cytochrome oxidase I gene suggests that the group includes species that are morphologically very similar or identical. We have previously shown that species in the Anopheles barbirostris Subgroup have an exceptionally large ITS2 (>1.5 kb), greater than in any other Anopheline group. However, the molecular processes responsible for generating such a large ITS2 have not previously been explored. Methods To determine the processes by which this large ITS2 is generated, we examined the sequence and secondary structure of the ITS2 of 51 specimens from five species of the Anopheles barbirostris Subgroup. These include the anthropophilic species An. campestris and three morphospecies of the Barbirostris Complex: An. vanderwulpi, An. barbirostris I and III, together with a previously undescribed member of this group (Clade IV). Results and conclusions All the specimens were found to have an ITS2 greater than 1.5 kb in length. The possibility that the spacer sequences amplified were pseudogenes was examined and discarded. The large size of ITS2 in the species studied is due to the presence of internal repeats of approximately 110 bp in length, confined to the central region of the spacer. Repeats varied markedly between the species examined, with respect to their organization, number and sequence similarity. The nucleotide diversity increased in direct relation to size variation and the presence of non-repeated elements. A secondary structure analysis showed that the repeats form hairpin structures with a wide range of free energy values. These hairpin structures are known to facilitate the subsequent processing of mature rRNA. An analysis of the repeats from the different species suggests they originate from a common ancestor, with the repeats appearing before speciation of the Barbirostris Group. PMID:24646478

2014-01-01

116

Design, synthesis, and DNA binding characteristics of a group of orthogonally positioned diamino, N-formamido, pyrrole- and imidazole-containing polyamides.  

PubMed

Orthogonally positioned diamino/dicationic polyamides (PAs) have good water solubility and enhanced binding affinity, whilst retaining DNA minor groove and sequence specificity compared to their monoamino/monocationic counterparts. The synthesis and DNA binding properties of the following diamino PAs: f-IPI (3a), f-IPP (4), f-PIP (5), and f-PPP (6) are described. P denotes the site where a 1-propylamino group is attached to the N1-position of the heterocycle. Binding of the diamino PAs to DNA was assessed by DNase I footprinting, thermal denaturation, circular dichroism titration, biosensor surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC) studies. According to SPR studies, f-IPI (3a) bound more strongly (K(eq)=2.4×10(8) M(-1)) and with comparable sequence selectivity to its cognate sequence 5'-ACGCGT-3' when compared to its monoamino analog f-IPI (1). The binding of f-IPI (3a) to 5'-ACGCGT-3' via the stacked dimer motif was balanced between enthalpy and entropy, and that was quite different from the enthalpy-driven binding of its monoamino parent f-IPI (1). f-IPP (4) also bound more strongly to its cognate sequence 5'-ATGCAT-3' (K(eq)=7.4×10(6) M(-1)) via the side-by-side stacked motif than its monoamino analog f-IPP (2a). Although f-PPP (6) bound via a 1:1 motif, it bound strongly to its cognate sequence 5'-AAATTT-3' (K(eq)=4.8×10(7) M(-1)), 15-times higher than the binding of its monoamino analog f-PPP (2c), albeit f-PPP bound via the stacked motif. Finally, f-PIP (5) bound to its target sequence 5'-ATCGAT-3' as a stacked dimer and it has the lowest affinity among the diamino PAs tested (Keq <1×10(5) M(-1)). This was about two times lower in affinity than the binding of its monoamino analog f-PIP (2b). The results further demonstrated that the 'core rules' of DNA recognition by monoamino PAs also apply to their diamino analogs. Specifically, PAs that contain a stacked IP core structure bind most strongly (highest binding constants) to their cognate GC doublet, followed by the binding of PAs with a stacked PP structure to two degenerate AT base pairs, and finally the binding of PAs with a PI core to their cognate CG doublet. PMID:23647824

Chavda, Sameer; Babu, Balaji; Patil, Pravin; Plaunt, Adam; Ferguson, Amanda; Lee, Megan; Tzou, Samuel; Sjoholm, Robert; Rice, Toni; Mackay, Hilary; Ramos, Joseph; Wang, Shuo; Lin, Shicai; Kiakos, Konstantinos; Wilson, W David; Hartley, John A; Lee, Moses

2013-07-01

117

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. PMID:22718771

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

2012-01-01

118

DNA Fingerprinting  

NSDL National Science Digital Library

In this forensics activity, learners solve a mystery using âDNAâ taken from the scene of the crime. This activity describes how to collect a âDNA sampleâ (learner-invented DNA sequence on a roll of paper) from the culprit and from each learner in the group, then run the DNA on a âgelâ that covers the floor of the classroom, a hallway, or gymnasium. The crime-scene investigation aspect can become as elaborate as you wish by including additional âcluesâ such as fingerprints, a ransom note written in a specific type of ink, cloth fibers, eyewitness accounts and more.

Salter, Irene

2012-06-26

119

DNA barcoding for the identification of eight species members of the Thai Hyrcanus Group and investigation of their stenogamous behavior.  

PubMed

Eight species members of the Thai Hyrcanus Group were identified based on the intact morphology and molecular analysis (COI barcoding, 658 bp) of F1-progenies. Five iso-female lines of each species were pooled in order to establish stock colonies. A stenogamous colony of each species was investigated by making 200 and 300 newly emerged adult females and males co-habit in a 30 cm cubic cage for one week. After ovipositon, the spermathecae of females were examined for sperms. The results revealed that Anopheles argyropus, Anopheles crawfordi, Anopheles nitidus, Anopheles pursati, Anopheles sinensis, Anopheles nigerrimus, Anopheles paraliae and Anopheles peditaeniatus yielded insemination rates of 0%, 0%, 0%, 31%, 33%, 42%, 50% and 77%, respectively. Continuous selection to establish stenogamous colonies indicated that An. sinensis, An. pursati, An. nigerrimus, An. paraliae and An. peditaeniatus provided insemination rates of 33-34%, 27-31%, 42-58%, 43-57% and 61-86% in 1, 2, 5, 6 and 20 generations of passages, respectively. PMID:24161242

Wijit, Adulsak; Saeung, Atiporn; Baimai, Visut; Otsuka, Yasushi; Thongsahuan, Sorawat; Taai, Kritsana; Srisuka, Wichai; Songsawatkiat, Siripan; Sor-suwan, Sriwatapron; Hempolchom, Chayanit; Somboon, Pradya; Choochote, Wej

2013-09-01

120

The LEF-1 High-Mobility Group Domain Undergoes a Disorder-to-Order Transition upon Formation of a Complex with Cognate DNA  

E-print Network

of the DNA- bound state is retained in the free protein. Heteronuclear NMR experiments performed on the free an important role in regulation of the T cell receptor (TCR)-R gene enhancer (1-3). By bending DNA through with little or no specificity, and are found in most cell types. Proteins in this subclass recognize DNA

Love, John J.

121

Molecular cloning, sequence, and expression of a human GDP-L-fucose:. beta. -D-galactoside 2-. alpha. -L-fucosyltransferase cDNA that can form the H blood group antigen  

SciTech Connect

The authors have previously used a gene-transfer scheme to isolate a human genomic DNA fragment that determines expression of a GDP-L-fucose:{beta}D-galactoside 2-{alpha}-L-fucosyltransferase. Although this fragment determined expression of an {alpha}(1,2)FT whose kinetic properties mirror those of the human H blood group {alpha}(1,2)FT, their precise nature remained undefined. They describe here the molecular cloning, sequence, and expression of a human of cDNA corresponding to these human genomic sequences. When expressed in COS-1 cells, the cDNA directs expression of cell surface H structures and a cognate {alpha}(1,2)FT activity with properties analogous to the human H blood group {alpha}(1,2)FT. The cDNA sequence predicts a 365-amino acid polypeptide characteristic of a type II transmembrane glycoprotein with a domain structure analogous to that of other glycosyltransferases but without significant primary sequence similarity to these or other known proteins. To directly demonstrate that the cDNA encodes an {alpha}(1,2)FT, the COOH-terminal domain predicted to be Golgi-resident was expressed in COS-1 cells as a catalytically active, secreted, and soluble protein A fusion peptide. Southern blot analysis showed that this cDNA identified DNA sequences syntenic to the human H locus on chromosome 19. These results strongly suggest that this cloned {alpha}(1,2)FT cDNA represents the product of the human H blood group locus.

Larsen, R.D.; Ernst, L.K.; Nair, R.P.; Lowe, J.B. (Univ. of Michigan, Ann Arbor (USA))

1990-09-01

122

Variations of SSU rDNA group I introns in different isolates of Cordyceps militaris and the loss of an intron during cross-mating.  

PubMed

Cordyceps militaris, the type species of genus Cordyceps, is one of the most popular mushrooms and a nutraceutical in eastern Asia. It is considered a model organism for the study of Cordyceps species because it can complete its life cycle when cultured in vitro. In the present study, the occurrence and sequence variation of SSU rDNA group I introns, Cmi.S943 and Cmi.S1199, among different isolates of C. militaris were analyzed. Based on the secondary structure predictions, the Cmi.S943 intron has been placed in subgroup IC1, and the Cmi.S1199 intron has been placed in subgroup IE. No significant similarity between Cmi.S943 and Cmi.S1199 suggested different origins. Three genotypes, based on the frequency and distribution of introns, were described to discriminate the 57 surveyed C. militaris strains. It was found that the genotype was related to the stroma characteristics. The stromata of all of the genotype II strains, which possessed only Cmi.S943, could produce perithecium. In contrast, the stromata of all genotype III strains, which had both Cmi.S943 and Cmi.S1199, could not produce perithecium. Cmi.S1199 showed the lowest level of intra-specific variation among the tested strains. Group I introns can be lost during strain cross-mating. Therefore, we presumed that during cross-mating and recombination, intron loss could be driven by positive Darwinian selection due to the energetic cost of transcribing long introns. PMID:24996897

Lian, Tiantian; Yang, Tao; Sun, Junde; Guo, Suping; Yang, Huaijun; Dong, Caihong

2014-08-01

123

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

2013-10-01

124

Long-range repression by multiple polycomb group (PcG) proteins targeted by fusion to a defined DNA-binding domain in Drosophila.  

PubMed Central

A tethering assay was developed to study the effects of Polycomb group (PcG) proteins on gene expression in vivo. This system employed the Su(Hw) DNA-binding domain (ZnF) to direct PcG proteins to transposons that carried the white and yellow reporter genes. These reporters constituted naive sensors of PcG effects, as bona fide PcG response elements (PREs) were absent from the constructs. To assess the effects of different genomic environments, reporter transposons integrated at nearly 40 chromosomal sites were analyzed. Three PcG fusion proteins, ZnF-PC, ZnF-SCM, and ZnF-ESC, were studied, since biochemical analyses place these PcG proteins in distinct complexes. Tethered ZnF-PcG proteins repressed white and yellow expression at the majority of sites tested, with each fusion protein displaying a characteristic degree of silencing. Repression by ZnF-PC was stronger than ZnF-SCM, which was stronger than ZnF-ESC, as judged by the percentage of insertion lines affected and the magnitude of the conferred repression. ZnF-PcG repression was more effective at centric and telomeric reporter insertion sites, as compared to euchromatic sites. ZnF-PcG proteins tethered as far as 3.0 kb away from the target promoter produced silencing, indicating that these effects were long range. Repression by ZnF-SCM required a protein interaction domain, the SPM domain, which suggests that this domain is not primarily used to direct SCM to chromosomal loci. This targeting system is useful for studying protein domains and mechanisms involved in PcG repression in vivo. PMID:11333237

Roseman, R R; Morgan, K; Mallin, D R; Roberson, R; Parnell, T J; Bornemann, D J; Simon, J A; Geyer, P K

2001-01-01

125

Interactions of the RAD7 and RAD23 excision repair genes of Saccharomyces cerevisiae with DNA repair genes in different epistasis groups  

Microsoft Academic Search

The RAD7 and RAD23 genes of S. cerevisiae affect the efficiency of excision repair of UV-damaged DNA. We have examined the UV survival of strains carrying the rad7 or rad23 deletion mutation in combination with deletion mutations in genes affecting different DNA repair pathways. As expected, the rad7? and rad23? mutations interact epistatically with the excision repair defective rad1? mutation,

Robert H. Schiestl; Satya Prakash

1989-01-01

126

Changes in Fat Mitochondrial DNA and Function in Subjects Randomized to Abacavir-Lamivudine or Tenofovir DF-Emtricitabine With Atazanavir-Ritonavir or Efavirenz: AIDS Clinical Trials Group Study A5224s, Substudy of A5202  

PubMed Central

Background.?The effect of nonthymidine nucleoside reverse-transcriptase inhibitors (NRTIs) on fat mitochondrial DNA (mtDNA) content and function is unclear. Methods.?A5202 randomized antiretroviral therapy–naive human immunodeficiency virus–infected subjects to abacavir-lamivudine (ABC/3TC) versus tenofovir DF–emtricitabine (TDF/FTC) with efavirenz (EFV) or atazanavir-ritonavir (ATV/r). A5224s, substudy of A5202, enrolled 269 subjects with fat measurements by dual-energy x-ray absorptiometry and computed tomography. A subset of subjects underwent fat biopsies at baseline and week 96 for mtDNA content (real-time polymerase chain reaction) and oxidative phosphorylation nicotinamide adenine dinucleotide (reduced) dehydrogenase (complex I) and cytochrome c oxidase (complex IV) activity levels (immunoassays). Intent-to-treat analyses were performed using analysis of variance and paired t tests. Results.?Fifty-six subjects (87% male; median age, 39 years) were included; their median body mass index, CD4 cell count, and fat mtDNA level were 26 kg/m2, 227 cells/?L, and 1197 copies/cell, respectively. Fat mtDNA content decreased within the ABC/3TC and TDF/FTC groups (combining EFV and ATV/r arms; median change, ?341 [interquartile range, ?848 to 190; P = .03] and ?400 [?661 to ?221; P < .001] copies/cell, respectively), but these changes did not differ significantly between the 2 groups (P = .57). Complex I and IV activity decreased significantly in the TDF/FTC group (median change, ?12.45 [interquartile range, ?24.70 to 2.90; P = .003] and ?8.25 [?13.90 to ?1.30; P < .001], optical density × 103/µg, respectively) but not the ABC/3TC group. Differences between the ABC/3TC and TDF/FTC groups were significant for complex I (P = .03). Conclusions.?ABC/3TC and TDF/FTC significantly and similarly decreased fat mtDNA content, but only TDF/FTC decreased complex I and complex IV activity levels. Clinical Trials Registration.?NCT00118898. PMID:23204164

McComsey, Grace A.; Daar, Eric S.; O'Riordan, MaryAnn; Collier, Ann C.; Kosmiski, Lisa; Santana, Jorge L.; Fichtenbaum, Carl J.; Fink, Heidi; Sax, Paul E.; Libutti, Daniel E.; Gerschenson, Mariana

2013-01-01

127

Exploring DNA  

NSDL National Science Digital Library

Get ready to learn an explore DNA, genes and proteins. By moving through the different topics, you will hopefully gain greater understanding of how DNA, genes, and proteins are all related. DNA to Protein Module You will zoom into the human body to see and read more about DNA. The Journey Into DNA DNA Workshop Activity- You try it! More DNA and Protein Synthesis ...

Flitton, Mrs.

2008-08-13

128

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. PMID:22970105

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

2012-01-01

129

Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses  

PubMed Central

Single-stranded (ss)DNA viruses are extremely widespread, infect diverse hosts from all three domains of life and include important pathogens. Most ssDNA viruses possess small genomes that replicate by the rolling-circle-like mechanism initiated by a distinct virus-encoded endonuclease. However, viruses of the family Bidnaviridae, instead of the endonuclease, encode a protein-primed type B DNA polymerase (PolB) and hence break this pattern. We investigated the provenance of all bidnavirus genes and uncover an unexpected turbulent evolutionary history of these unique viruses. Our analysis strongly suggests that bidnaviruses evolved from a parvovirus ancestor from which they inherit a jelly-roll capsid protein and a superfamily 3 helicase. The radiation of bidnaviruses from parvoviruses was probably triggered by integration of the ancestral parvovirus genome into a large virus-derived DNA transposon of the Polinton (polintovirus) family resulting in the acquisition of the polintovirus PolB gene along with terminal inverted repeats. Bidnavirus genes for a receptor-binding protein and a potential novel antiviral defense modulator are derived from dsRNA viruses (Reoviridae) and dsDNA viruses (Baculoviridae), respectively. The unusual evolutionary history of bidnaviruses emphasizes the key role of horizontal gene transfer, sometimes between viruses with completely different genomes but occupying the same niche, in the emergence of new viral types. PMID:24939392

Krupovic, Mart; Koonin, Eugene V.

2014-01-01

130

Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses.  

PubMed

Single-stranded (ss)DNA viruses are extremely widespread, infect diverse hosts from all three domains of life and include important pathogens. Most ssDNA viruses possess small genomes that replicate by the rolling-circle-like mechanism initiated by a distinct virus-encoded endonuclease. However, viruses of the family Bidnaviridae, instead of the endonuclease, encode a protein-primed type B DNA polymerase (PolB) and hence break this pattern. We investigated the provenance of all bidnavirus genes and uncover an unexpected turbulent evolutionary history of these unique viruses. Our analysis strongly suggests that bidnaviruses evolved from a parvovirus ancestor from which they inherit a jelly-roll capsid protein and a superfamily 3 helicase. The radiation of bidnaviruses from parvoviruses was probably triggered by integration of the ancestral parvovirus genome into a large virus-derived DNA transposon of the Polinton (polintovirus) family resulting in the acquisition of the polintovirus PolB gene along with terminal inverted repeats. Bidnavirus genes for a receptor-binding protein and a potential novel antiviral defense modulator are derived from dsRNA viruses (Reoviridae) and dsDNA viruses (Baculoviridae), respectively. The unusual evolutionary history of bidnaviruses emphasizes the key role of horizontal gene transfer, sometimes between viruses with completely different genomes but occupying the same niche, in the emergence of new viral types. PMID:24939392

Krupovic, Mart; Koonin, Eugene V

2014-01-01

131

Nanotechnology with DNA DNA Nanodevices  

E-print Network

Nanotechnology with DNA DNA Nanodevices Friedrich C. Simmel* and Wendy U. Dittmer A DNA actuator. Introduction.............285 2. Overview: DNA Nanotechnology.......285 3. Prototypes of Nanomechanical DNA overview of DNA nanotechnology as a whole is given. The most important properties of DNA molecules

Ludwig-Maximilians-Universität, München

132

The ITS2 ribosomal DNA of Anopheles beklemishevi and further remarks on the phylogenetic relationships within the Anopheles maculipennis group of species (Diptera: Culicidae)  

Microsoft Academic Search

Anopheles beklemishevi specimens from Russia were analysed by their ITS2 ribosomal DNA sequence to amend and to specify the phylogenetic tree of the Anopheles maculipennis species complex. Surprisingly, with 638 base pairs, the ITS2 regions of all the 34 An beklemishevi specimens examined were considerably longer than those of all their sibling species. Sequence alignment with GenBank derived sequences of

Helge Kampen

2005-01-01

133

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

1997-01-01

134

DNA microarray (spot) .  

E-print Network

1. DNA microarray DNA (spot) . DNA probe , probe (hybridization) . DNA microarray cDNA oligonucleotide oligonucleotide cDNA probe . oligonucleotide microarray , DNA , probe . oligonucleotide microarray probe

135

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.

1998-03-01

136

5 Mechanisms for Priming DNA Synthesis  

E-print Network

DNA replication is a semiconservative process in which a DNA polymerase uses one DNA strand as a template for the synthesis of a second, complementary, DNA strand. However, in contrast to RNA polymerases, which can initiate RNA synthesis on a DNA template de novo, all DNA polymerases require a preexisting primer on which to initiate DNA synthesis (Kornberg and Baker 1992). One apparent exception to this rule is a mitochondria1 DNA (mtDNA)-encoded reverse transcriptase (RT) in Neurospora (Wang and Lambowitz 1993). Preexisting primers can be classified into four groups. The simplest primer consists of the 3'-hydroxyl (3'-OH) termini of DNA chains that are complementary to the DNA template and thereby form a stable duplex structure at the site where DNA synthesis begins. This primer is used for DNA repair (Friedberg and Wood, this volume), parvovirus DNA replication (Brush and Kelly; Cotmore and Tattersall; both this volume), some RTs. The second type of primer consists of a deoxyribonucleoside

Margarita Salas; Jennifer T. Miller; Jonathan Leis; Melvin L. Depamphilis

137

Systematics and evolutionary history of the Asterotricha group of the genus Onosma (Boraginaceae) in central and southern Europe inferred from AFLP and nrDNA ITS data  

Microsoft Academic Search

Onosma is a species-rich genus with complicated patterns of morphological and karyological variation, and controversial taxonomic\\u000a treatments. In the present study we focused on the Asterotricha group, one of three major infrageneric groups, in the area\\u000a of central and southern Europe. Ribosomal internal transcribed spacer (ITS) sequences and amplified fragment length polymorphism\\u000a (AFLP) markers were used to assess species differentiation

V. Kolar?ik; J. Zozomová-Lihová; P. Mártonfi

2010-01-01

138

DNA Computing Hamiltonian path  

E-print Network

2014 DNA DNA #12;DNA Computing · Feynman · Adleman · DNASIMD · ... · · · · · DNADNA #12;DNA · DNA · · · · DNA · · #12;2000 2005 2010 1995 Hamiltonian path DNA tweezers DNA tile DNA origami DNA box Sierpinski DNA tile self assembly DNA logic gates Whiplash PCR DNA automaton DNA spider MAYA

Hagiya, Masami

139

DNA Restriction  

NSDL National Science Digital Library

The discovery of enzymes that could cut and paste DNA made genetic engineering possible. Restriction enzymes, found naturally in bacteria, can be used to cut DNA fragment at specific sequences, while another enzyme, DNA ligase, can attach or rejoin DNA fragments with complementary ends. This animation from Cold Spring Harbor Laboratory's Dolan DNA Learning Center presents DNA restriction through a series of illustrations of processes involved.

2011-11-25

140

DNA Structural Nanotechnology Duke University  

E-print Network

DNA Structural Nanotechnology John Reif Duke University Graduate Students: Harish Chandran and Nikhil Gopalkrishnan Recent Graduated Phds: Urmi Majumder, Sudheer Sahu, & Peng Yin DNA Nanostructure Group John Reif & Thomas H. LaBean #12;Introduction to DNA Self-Assembly #12;Self-Assembly in Nature

Reif, John H.

141

Nuclear DNA PCR-RFLPs that distinguish African and European honey bee groups of subspecies. II: Conversion of long PCR markers to standard PCR.  

PubMed

Nuclear DNA PCR-RFLPs previously found in amplifications of three long (> 5 kbp) anonymous regions of DNA were made analyzable using standard PCR procedures. RFLP analyses were simplified by restricting the amplifications to sections, within each locus, that contained most of the informative polymorphic sites. AluI digests of locus L-1 section 2 (L-1S2) revealed three suballeles of which one was African-specific (Apis mellifera scutellata Lepeletier) and one was east European-predominant (A. m. ligustica Spinola, A. m. carnica Pollman, and A. m. caucasica Gorbachev). Alleles found originally at locus L-2 with AvaI were determined in RFLP analysis of two sections, L-2S1int and L-2S2, resulting in two African-specific and two east European-predominant suballeles. Suballele identity was determined by the combination of banding patterns from both fragments. Polymorphisms revealed by HaeIII in locus L-2 were analyzed in amplifications and digests of L-2SM1int. an 830 bpfragment within L-2S1. Seven suballeles were found of which two were African-specific and three were east European-specific or predominant, including one suballele specific to the east European subspecies A. m. caucasica. In locus L-5, RFLPs were detected with HaeIII, DdeI, and SpeI. HaeIII polymorphisms were analyzed by amplification and digestion offragments L-5S1xt and L-5S1ter: Five suballeles were found of which three were African-specific and one east European-predominant. For DdeI, all five alleles originally found with long PCR could be identified in RFLP analyses of three sections. Two African-specific, one east European-specific, and one west European-predominant (A. m. mellifera L. and A. m. iberica Goetze) suballeles were found. A west European-predominant suballele was also found in RFLP analysis of L-5S3 with SpeI. Allele frequency data from Old World and US. populations are presented. PMID:12296627

Suazo, Alonso; Hall, H Glenn

2002-08-01

142

Genetic variation and demographic history of the Haplochromis laparogramma group of Lake Victoria--An analysis based on SINEs and mitochondrial DNA  

E-print Network

Genetic variation and demographic history of the Haplochromis laparogramma group of Lake Victoria More than 500 endemic haplochromine cichlid species inhabit Lake Victoria. This striking species and population structure of closely related Lake Victoria cichlids and in showing the importance of applying

143

DNA and DNA Extraction  

NSDL National Science Digital Library

The DNA structure and how it makes up genes and chromosomes in the cell. This is the second of a series of seven animations that detail the process of crop genetic engineering. To begin at the beginning, see Overview of Crop Genetic Engineering. (To go to the next animation, go to Gene Cloning.)

144

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

1996-01-01

145

Polymorphisms and allele frequencies of the ABO blood group gene among the Jomon, Epi-Jomon and Okhotsk people in Hokkaido, northern Japan, revealed by ancient DNA analysis  

Microsoft Academic Search

To investigate the genetic characteristics of the ancient populations of Hokkaido, northern Japan, polymorphisms of the ABO blood group gene were analyzed for 17 Jomon\\/Epi-Jomon specimens and 15 Okhotsk specimens using amplified product-length polymorphism and restriction fragment length polymorphism analyses. Five ABO alleles were identified from the Jomon\\/ Epi-Jomon and Okhotsk people. Allele frequencies of the Jomon\\/Epi-Jomon and Okhotsk people

Takehiro Sato; Hisako Kazuta; Tetsuya Amano; Hiroko Ono; Hajime Ishida; Haruto Kodera; Hirofumi Matsumura; Minoru Yoneda; Yukio Dodo; Ryuichi Masuda

2010-01-01

146

Internal Repetition and Intraindividual Variation in the rDNA ITS1 of the Anopheles punctulatus Group (Diptera: Culicidae): Multiple Units and Rates of Turnover  

Microsoft Academic Search

The rapid divergence of repetitive sequences makes them desirable markers for phylogenetic studies of closely related groups,\\u000a provided that a high level of sequence homogeneity has been maintained within species. Intraspecific polymorphisms are found\\u000a in an increasing number of studies now, and this highlights the need to determine why these occur. In this study we examined\\u000a intraindividual variation present in

James E. Bower; Robert D. Cooper; Nigel W. Beebe

2009-01-01

147

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

1997-01-01

148

Partial mitochondrial DNA sequences suggest the existence of a cryptic species within the Leucosphyrus group of the genus Anopheles (Diptera: Culicidae), forest malaria vectors, in northern Vietnam  

PubMed Central

Background During the last decade, Southeast Asian countries have been very successful in reducing the burden of malaria. However, malaria remains endemic in these countries, especially in remote and forested areas. The Leucosphyrus group of the genus Anopheles harbors the most important malaria vectors in forested areas of Southeast Asia. In Vietnam, previous molecular studies have resulted in the identification of only Anopheles dirus sensu stricto (previously known as An. dirus species A) among the Leucosphyrus group members. However, Vietnamese entomologists have recognized that mosquitoes belonging to the Leucosphyrus group in northern Vietnam exhibit morphological characteristics similar to those of Anopheles takasagoensis, which has been reported only from Taiwan. Here, we aimed to confirm the genetic and morphological identities of the members of the Leucosphyrus group in Vietnam. Results In the molecular phylogenetic trees reconstructed using partial COI and ND6 mitochondrial gene sequences, samples collected from southern and central Vietnam clustered together with GenBank sequences of An. dirus that were obtained from Thailand. However, samples from northern Vietnam formed a distinct clade separated from both An. dirus and An. takasagoensis by other valid species. Conclusions The results suggest the existence of a cryptic species in northern Vietnam that is morphologically similar to, but phylogenetically distant from both An. dirus and An. takasagoensis. We have tentatively designated this possible cryptic species as Anopheles aff. takasagoensis for convenience, until a valid name is assigned. However, it is difficult to distinguish the species solely on the basis of morphological characteristics. Further studies on such as karyotypes and polytene chromosome banding patterns are necessary to confirm whether An. aff. takasagoensis is a valid species. Moreover, studies on (1) the geographic distribution, which is potentially spreading along the Vietnam, China, Laos, and Myanmar borders; (2) morphological and ecological characteristics; and (3) vectorial capacity of this newly identified cryptic species of An. dirus, which is one of the most important malaria vectors in the mainland of Southeast Asia, are necessary for planning efficient malaria vector control programs in this region. PMID:20433694

2010-01-01

149

Local Group(s)  

E-print Network

The properties of the galaxies of the Local Group are reviewed, followed by a brief discussion of nearby groups. The galaxy groups in our vicinity - the M81 group, the Cen A group, and the IC 342/Maffei group - are in many respects Local Group analogs: Their luminosity functions, galaxy content, fractional galaxy type distribution, crossing times, masses, and zero-velocity surface radii are similar to those of the Local Group. Also, the nearby groups usually consist of two subgroups, some of which approach each other and may ultimately merge to form a fossil group. These poor groups contrast with the less evolved, loose and extended galaxy ``clouds'' such as the Scl group and the CVn I cloud. These are characterized by long crossing times, are dominated by gas-rich, late-type galaxies, and lack gas-deficient, low luminosity early-type dwarfs. These clouds may be groups still in formation. The local Hubble flow derived from the clouds and groups is very cold.

Eva K. Grebel

2006-05-22

150

Identification of group-I introns at three different positions within the 28S rDNA gene of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae.  

PubMed

Using a set of heterologous primers designed from the 3'-end of the 28S rRNA gene of Verticillium dahliae the corresponding gene region of 30 isolates of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae was amplified. The polymerase chain reaction products obtained could be classified into four groups varying in size from 1.0 to 2.2 kb. Sequence analyses of representative PCR products revealed the presence of five distinct introns, positioned in three different insertion sites. Fungal isolates 316 and 11 both harbored one intron each (374 and 337 bp in size, respectively), whereas isolate 33 harbored three introns (436, 334, and 412 bp) within the relevant 28S rRNA region. All five introns shared the conserved P, Q, R, S elements and all the other characteristic features of group-I introns in their deduced secondary structure; three (316-int, 33-int1, and 33-int3) belong to subgroup IC1 and two (33-int2 and 11-int) belong to subgroup IE. Further, reverse transcription polymerase chain reactions indicated that all these introns were absent from the mature RNA molecules. The appearance of the five introns at identical positions with those from other organisms belonging to various phyla is discussed. PMID:11170737

Mavridou, A; Cannone, J; Typas, M A

2000-11-01

151

PCR and recombinant DNA Cristiano V. Bizarro  

E-print Network

PCR and recombinant DNA techniques Cristiano V. Bizarro Joan Camuñas Felix Ritort Group Small enzymes) PCR DNA Electrophoresis Recombinant DNA technology Applications in single-molecule biophysics:Chloroform extraction Ethanol precipitationIsolated plasmid 4. 5. 6. #12;Recombinant DNA technology Source:Color Atlas

Ritort, Felix

152

Identification of novel cluster groups in pediatric high-risk B-precursor acute lymphoblastic leukemia with gene expression profiling: correlation with genome-wide DNA copy number alterations, clinical characteristics, and outcome  

PubMed Central

To resolve the genetic heterogeneity within pediatric high-risk B-precursor acute lymphoblastic leukemia (ALL), a clinically defined poor-risk group with few known recurring cytogenetic abnormalities, we performed gene expression profiling in a cohort of 207 uniformly treated children with high-risk ALL. Expression profiles were correlated with genome-wide DNA copy number abnormalities and clinical and outcome features. Unsupervised clustering of gene expression profiling data revealed 8 unique cluster groups within these high-risk ALL patients, 2 of which were associated with known chromosomal translocations (t(1;19)(TCF3-PBX1) or MLL), and 6 of which lacked any previously known cytogenetic lesion. One unique cluster was characterized by high expression of distinct outlier genes AGAP1, CCNJ, CHST2/7, CLEC12A/B, and PTPRM; ERG DNA deletions; and 4-year relapse-free survival of 94.7% ± 5.1%, compared with 63.5% ± 3.7% for the cohort (P = .01). A second cluster, characterized by high expression of BMPR1B, CRLF2, GPR110, and MUC4; frequent deletion of EBF1, IKZF1, RAG1-2, and IL3RA-CSF2RA; JAK mutations and CRLF2 rearrangements (P < .0001); and Hispanic ethnicity (P < .001) had a very poor 4-year relapse-free survival (21.0% ± 9.5%; P < .001). These studies reveal striking clinical and genetic heterogeneity in high-risk ALL and point to novel genes that may serve as new targets for diagnosis, risk classification, and therapy. PMID:20699438

Harvey, Richard C.; Mullighan, Charles G.; Wang, Xuefei; Dobbin, Kevin K.; Davidson, George S.; Bedrick, Edward J.; Chen, I-Ming; Atlas, Susan R.; Kang, Huining; Ar, Kerem; Wilson, Carla S.; Wharton, Walker; Murphy, Maurice; Devidas, Meenakshi; Carroll, Andrew J.; Borowitz, Michael J.; Bowman, W. Paul; Downing, James R.; Relling, Mary; Yang, Jun; Bhojwani, Deepa; Carroll, William L.; Camitta, Bruce; Reaman, Gregory H.; Smith, Malcolm; Hunger, Stephen P.

2010-01-01

153

Conformation-dependent DNA attraction  

NASA Astrophysics Data System (ADS)

Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg2+ ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg2+ or Na+, benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg2+ bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription.Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg2+ ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg2+ or Na+, benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg2+ bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr03235c

Li, Weifeng; Nordenskiöld, Lars; Zhou, Ruhong; Mu, Yuguang

2014-05-01

154

CSI: DNA  

NSDL National Science Digital Library

CSI: DNA provides DNA fingerprints in the form of fluorescent electrophoregrams for use as evidence in crime scenes. It includes explanations of fluorescent genotyping, variable number tandem repeats (VNTRs), and probability in forensics.

Rebecca Reiss (New Mexico Tech;); Scotia Kurwoski (Rio Rancho High School;); Mary Robinson (Rio Rancho High School;)

2007-08-17

155

DNA Replication  

NSDL National Science Digital Library

This animation, which shows DNA replication and the interactions of the various enzymes, can be used to illustrate to students the order of events in DNA replication, as well as emphasize which enzymes are involved in the process.

American Society For Microbiology;

2002-01-01

156

DNA Detectives  

NSDL National Science Digital Library

Many of the revolutionary changes that have occurred in biology since 1970 can be attributed directly to the ability to manipulate DNA in defined ways. The principal tools for this recombinant DNA technology are enzymes that can "cut and "paste" DNA. Restriction enzymes are the "chemical scissors" of the molecular biologist; these enzymes cut DNA at specific nucleotide sequences. A sample of someone's DNA, incubated with restriction enzymes, is reduced to millions of DNA fragments of varying sizes. A DNA sample from a different person would have a different nucleotide sequence and would thus be enzymatically "chopped up" into a very different collection of fragments. We have been asked to apply DNA fingerprinting to determine which suspect should be charged with a crime perpetrated in our city.

BEGIN:VCARD VERSION:2.1 FN:Suzanne Black N:Black;Suzanne ORG:Inglemoor High School REV:2005-04-09 END:VCARD

1995-06-30

157

DNA Copyright  

E-print Network

of architecture and computer software. Sequences of DNA should also be acknowledged as eligible for copyright protection. Unaltered genomic DNA sequences would seem poor candidates for copyright protection. The case is stronger for copyright protection...

Torrance, Andrew W.

2011-01-01

158

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.

2012-04-10

159

DNA Nanotechnology  

NSDL National Science Digital Library

In this activity, learners explore deoxyribonucleic acid (DNA), a nanoscale structure that occurs in nature. Learners extract a sample of DNA from split peas and put the sample in an Eppendorf tube to take home. Learners discover that nanoscientists study DNA to understand its biological function and use it to make other nanoscale materials and devices.

Network, Nanoscale I.; Sciencenter

2014-06-10

160

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

2007-12-01

161

DNA demethylation by DNA repair  

E-print Network

Active DNA demethylation underlies key facets of reproduction in flowering plants and mammals and serves a general genome housekeeping function in plants. A family of 5-methylcytosine DNA glycosylases catalyzes plant ...

Gehring, Mary

162

Dna Sequencing  

DOEpatents

A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)

1995-04-25

163

Cinnamate-based DNA photolithography  

NASA Astrophysics Data System (ADS)

As demonstrated by means of DNA nanoconstructs, as well as DNA functionalization of nanoparticles and micrometre-scale colloids, complex self-assembly processes require components to associate with particular partners in a programmable fashion. In many cases the reversibility of the interactions between complementary DNA sequences is an advantage. However, permanently bonding some or all of the complementary pairs may allow for flexibility in design and construction. Here, we show that the substitution of a cinnamate group for a pair of complementary bases provides an efficient, addressable, ultraviolet light-based method to bond complementary DNA covalently. To show the potential of this approach, we wrote micrometre-scale patterns on a surface using ultraviolet light and demonstrated the reversible attachment of conjugated DNA and DNA-coated colloids. Our strategy enables both functional DNA photolithography and multistep, specific binding in self-assembly processes.

Feng, Lang; Romulus, Joy; Li, Minfeng; Sha, Ruojie; Royer, John; Wu, Kun-Ta; Xu, Qin; Seeman, Nadrian C.; Weck, Marcus; Chaikin, Paul

2013-08-01

164

Hypermodified bases in DNA.  

PubMed

Modified DNA bases are widespread in nature. They can be found in eukaryotes, prokaryotes, and bacteriophages. They may completely replace the standard base or replace only a small fraction. Their substituents vary from simple methyl or hydroxy groups to large moieties like amino acids and multiply hexosylated side chains. This review gives an overview of the modified DNA bases identified thus far, with emphasis on the "very unusual" or hypermodified DNA bases. Although these have been detected mainly in bacteriophages, recent work has shown the presence of a novel hypermodified DNA base in the eukaryote Trypanosoma brucei. We speculate on the biosynthesis and function of this novel base beta-D-glucosyl-hydroxymethyluracil. PMID:7649402

Gommers-Ampt, J H; Borst, P

1995-08-01

165

DNA Immunization  

PubMed Central

DNA immunization was discovered in early 1990s and its use has been expanded from vaccine studies to a broader range of biomedical research, such as the generation of high quality polyclonal and monoclonal antibodies as research reagents. In this unit, three common DNA immunization methods are described: needle injection, electroporation and gene gun. In addition, several common considerations related to DNA immunization are discussed. PMID:24510291

Wang, Shixia; Lu, Shan

2013-01-01

166

DNA Extraction  

NSDL National Science Digital Library

In this activity related to plant biotechnology, learners extract DNA from fruit to investigate how it looks and feels. The procedure is similar to what scientists have to do before they can use information contained in this DNA. This lesson guide includes procedure and discussion questions to help learners reflect on the process and purpose of DNA extraction. Modifications for younger learners are included in a related PDF (see related resources).

Stephens, Janice; Leach, Jan

2011-01-01

167

DNA Chips  

NSDL National Science Digital Library

In this lesson from Science NetLinks, students will conduct activities from a module called "DNA Chips: A Genetics Lab in the Palm of Your Hand." This module is part of the National Institutes of Health Snapshots series, which focuses on a single area of biomedical research to help students understand how science, people, ethics, and history all fit together. The module for this lesson is about the DNA microarray, also known as a DNA chip.

Science Netlinks;

2003-02-23

168

DNA Libraries  

NSDL National Science Digital Library

Teachers' Domain presents this interactive, adapted from the Dolan DNA Learning Center, to help students learn about DNA Libraries, "the tools scientists use to store and reproduce genetic information that they can later access for their research." After an introduction, students can explore more about the different types of DNA libraries by clicking on any of the five DNA vectors: Yeast Artificial Chromosomes, Bacterial Artificial Chromosomes, Cosmids, Bacteriophage Lambda, and Plasmids. On the site, visitors will also find a supplemental background essay, discussion questions, and standards alignment from Teachers' Domain.

2010-10-06

169

Group Assignment-1 Group A Group B Group C  

E-print Network

Group Assignment-1 Group A Group B Group C Shirkhodai, Arta ( artashir ) Kurozumi, Dean ( kurozumi ) Trang, Derrick ( trangd ) Yim, Gilbert ( gyim ) Marchant, Richard ( rmarchan) Young, Garrett ( garrettz

Zhang, Rui

170

Group Assignment-2 Group A Group B Group C  

E-print Network

Group Assignment-2 Group A Group B Group C Shirkhodai, Arta ( artashir ) Kurozumi, Dean ( kurozumi ( cobatake ) Shultz, Allen ( shultzam ) Yamakawa, Kelsie ( kayama ) Young, Garrett ( garrettz ) Walser, Ryan

Zhang, Rui

171

Patterning nanocrystals using DNA  

NASA Astrophysics Data System (ADS)

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. Here, we have sought to assemble larger and more complex nanostructures. Cold-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 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 mum, and collecting atomic force microscopy (AFM) images up to 30 mum. 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

172

Recombinant DNA means and method  

SciTech Connect

This patent describes a transformed living cell selected from the group consisting of fungi, yeast and bacteria, and containing genetic material derived from recombinant DNA material and coding for bovine rennin.

Alford, B.L.; Mao, J.I.; Moir, D.T.; Taunton-Rigby, A.; Vovis, G.F.

1987-05-19

173

DNA ALTERATIONS  

EPA Science Inventory

The exposure of an organism to genotoxic chemicals may induce a cascade of genetic events. nitially, structural alterations to DNA are formed. ext, the DNA damage is processed and subsequently expressed in mutant gene products. inally, diseases result from the genetic damage. he ...

174

DNA Pendant  

E-print Network

Broadcast Transcript: It's a symbol of commitment. It's a memento mori. It's the DNA pendant offered by Japan's Eiwa Industry and it's two, two, two things in one. Using genetic extraction, Eiwa removes the DNA from, say, a strand of hair or a...

Hacker, Randi; Tsutsui, William

2007-11-14

175

DNA Barcoding  

NSDL National Science Digital Library

This is a two-part animation. ÃÂDNA Barcoding, Part 1,ÃÂ provides an overview of how DNA barcoding of animals can be used to identify an unknown sample or discover a new species. Cytochrome c oxidase subunit 1 (COI) is found in the mitochondria as part of the electron transport chain. The COI gene is used for DNA barcoding. Just like a barcode on an item in a grocery store identifies a product, a DNA barcode (determined by DNA sequencing) is used to identify species. Part 1 run time: 1 minute, 40 seconds. ÃÂDNA Barcoding, Part 2ÃÂ details how small tissue samples are used for DNA barcoding, including a review of the laboratory and bioinformatics steps used in barcoding: DNA purification, polymerase chain reaction (PCR), agarose gel electrophoresis, DNA sequencing and analysis, and DNA sequence identification using the Basic Local Alignment Search Tool (BLAST) or the Barcode of Life Database (BOLD). Part 2 run time: 4 minutes, 15 seconds. Animation is closed captioned.

2012-10-22

176

DNA nanotechnology  

Microsoft Academic Search

Since Watson and Crick’s determination of its structure nearly 50 years ago, DNA has come to fill our lives in many areas, from genetic counseling to forensics, from genomics to gene therapy. These, and other ways in which DNA affects human activities, are related to its function as genetic material, not just our genetic material, but the genetic material of

Nadrian C Seeman

2003-01-01

177

DNA Vaccines  

Microsoft Academic Search

In just a few years, injection of plasmid DNA to elicit immune responses in vivo has developed from an interesting observation to a viable vaccine strategy. DNA vaccines have been shown to elicit both cellular and humoral immune responses and to be effective in a variety of preclinical bacterial, viral, and parasitic animal models. This review will discuss the current

Donna L. Montgomery; Jeffrey B. Ulmer; John J. Donnelly; Margaret A. Liu

1997-01-01

178

DNA Tutorial  

NSDL National Science Digital Library

This site is an excellent resource on the structure and function of DNA as well as its role in genes and chromosomes. It also covers DNA replication, RNA structure and function, RNA synthesis, the genetic code, and protein synthesis. The site includes a tutorial that tests comprehension of the covered subjects.

Yvette; Cf

179

PCR and recombinant DNA Joan Camuas  

E-print Network

PCR and recombinant DNA techniques Joan Camuñas Felix Ritort Group Small Biosystems Lab Universitat Electrophoresis Recombinant DNA technology Applications in single-molecule biophysics #12;Zooming in on cellular precipitationIsolated plasmid 4. 5. 6. #12;Recombinant DNA technology Source:Color Atlas Of Biochemistry 2d ed

Ritort, Felix

180

Interstrand DNA-DNA cross-link formation between adenine residues and abasic sites in duplex DNA.  

PubMed

The loss of a coding nucleobase from the structure of DNA is a common event that generates an abasic (Ap) site (1). Ap sites exist as an equilibrating mixture of a cyclic hemiacetal and a ring-opened aldehyde. Aldehydes are electrophilic functional groups that can form covalent adducts with nucleophilic sites in DNA. Thus, Ap sites present a potentially reactive aldehyde as part of the internal structure of DNA. Here we report evidence that the aldehyde group of Ap sites in duplex DNA can form a covalent adduct with the N(6)-amino group of adenine residues on the opposing strand. The resulting interstrand DNA-DNA cross-link occurs at 5'-ApT/5'-AA sequences in remarkably high yields (15-70%) under physiologically relevant conditions. This naturally occurring DNA-templated reaction has the potential to generate cross-links in the genetic material of living cells. PMID:24506784

Price, Nathan E; Johnson, Kevin M; Wang, Jin; Fekry, Mostafa I; Wang, Yinsheng; Gates, Kent S

2014-03-01

181

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

2009-08-01

182

Inside DNA  

NSDL National Science Digital Library

In this activity (on pages 34-39), learners make a fairly detailed model of DNA using licorice and gumdrops. The sugar and phosphate backbone of DNA is represented by alternating red and black licorice, and the base pairs are represented by gumdrops arranged so that gumdrop colors are paired. After a pair of learners have made a DNA section, they find another team and link them up to make a model of a gene. They then split the model and "copy" it using the base pair rules from earlier, comparing their copy to the original to see if there are any differences (mutations).

Museum, University O.; Nebraska Cooperative Extension 4-H Youth Development

2002-01-01

183

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.

2010-10-07

184

DNA adductomics.  

PubMed

Systems toxicology is a broad-based approach to describe many of the toxicological features that occur within a living system under stress or subjected to exogenous or endogenous exposures. The ultimate goal is to capture an overview of all exposures and the ensuing biological responses of the body. The term exposome has been employed to refer to the totality of all exposures, and systems toxicology investigates how the exposome influences health effects and consequences of exposures over a lifetime. The tools to advance systems toxicology include high-throughput transcriptomics, proteomics, metabolomics, and adductomics, which is still in its infancy. A well-established methodology for the comprehensive measurement of DNA damage resulting from every day exposures is not fully developed. During the past several decades, the (32)P-postlabeling technique has been employed to screen the damage to DNA induced by multiple classes of genotoxicants; however, more robust, specific, and quantitative methods have been sought to identify and quantify DNA adducts. Although triple quadrupole and ion trap mass spectrometry, particularly when using multistage scanning (LC-MS(n)), have shown promise in the field of DNA adductomics, it is anticipated that high-resolution and accurate-mass LC-MS(n) instrumentation will play a major role in assessing global DNA damage. Targeted adductomics should also benefit greatly from improved triple quadrupole technology. Once the analytical MS methods are fully mature, DNA adductomics along with other -omics tools will contribute greatly to the field of systems toxicology. PMID:24437709

Balbo, Silvia; Turesky, Robert J; Villalta, Peter W

2014-03-17

185

DNA behind bars: other ways of knowing forensic DNA technologies.  

PubMed

This paper explores 'other' ways of knowing DNA in the field of criminal investigation. Drawing upon 26 in-depth interviews with prisoners in Austria, it illustrates how this group knows and conceptualizes DNA traces and forensic DNA technologies. These understandings and conceptualizations are both nuanced and ambiguous. While on the one hand, DNA traces and forensic DNA technologies were not treated as categorically different from other types of traces and technologies in the prisoners' accounts, they were seen as 'unique' in one respect: respondents experienced DNA traces as beyond their control because they were virtually impossible to avoid (in contrast to, for example, fingerprints). Furthermore, the scientific rigour that our interviewees assumed to underpin forensic DNA technologies rendered these technologies as impenetrable and intimidating, and as effectively challenging many offenders' expert knowledge on how to manage crime scenes and avoid convictions. Finally, due to coming 'from the inside' of the body, forensic DNA technologies were seen as 'deepening' the stigma of delinquency in many of our interviewees' bodies and selves. For our interviewees, forensic DNA technologies assumed the role of institutionalized memories of their delinquency. PMID:19569425

Prainsack, Barbara; Kitzberger, Martin

2009-02-01

186

DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics  

E-print Network

DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics Soo-Yong Shin1 , Eun Jeong of DNA computing. The complexity of any computational algorithm is typically measured in terms of time and space. In DNA computing, the time complexity can be measured by the total reaction time

187

DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics  

E-print Network

DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics Soo­Yong Shin 1 , Eun Jeong the complexity of DNA computing. The complexity of any computational algorithm is typically measured in terms of time and space. In DNA computing, the time complexity can be measured by the total reaction time

188

Ancient DNA  

PubMed Central

In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets. PMID:15875564

Willerslev, Eske; Cooper, Alan

2004-01-01

189

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

2001-12-01

190

DNA Methylation and Its Basic Function  

PubMed Central

In the mammalian genome, DNA methylation is an epigenetic mechanism involving the transfer of a methyl group onto the C5 position of the cytosine to form 5-methylcytosine. DNA methylation regulates gene expression by recruiting proteins involved in gene repression or by inhibiting the binding of transcription factor(s) to DNA. During development, the pattern of DNA methylation in the genome changes as a result of a dynamic process involving both de novo DNA methylation and demethylation. As a consequence, differentiated cells develop a stable and unique DNA methylation pattern that regulates tissue-specific gene transcription. In this chapter, we will review the process of DNA methylation and demethylation in the nervous system. We will describe the DNA (de)methylation machinery and its association with other epigenetic mechanisms such as histone modifications and noncoding RNAs. Intriguingly, postmitotic neurons still express DNA methyltransferases and components involved in DNA demethylation. Moreover, neuronal activity can modulate their pattern of DNA methylation in response to physiological and environmental stimuli. The precise regulation of DNA methylation is essential for normal cognitive function. Indeed, when DNA methylation is altered as a result of developmental mutations or environmental risk factors, such as drug exposure and neural injury, mental impairment is a common side effect. The investigation into DNA methylation continues to show a rich and complex picture about epigenetic gene regulation in the central nervous system and provides possible therapeutic targets for the treatment of neuropsychiatric disorders. PMID:22781841

Moore, Lisa D; Le, Thuc; Fan, Guoping

2013-01-01

191

DNA methylation and its basic function.  

PubMed

In the mammalian genome, DNA methylation is an epigenetic mechanism involving the transfer of a methyl group onto the C5 position of the cytosine to form 5-methylcytosine. DNA methylation regulates gene expression by recruiting proteins involved in gene repression or by inhibiting the binding of transcription factor(s) to DNA. During development, the pattern of DNA methylation in the genome changes as a result of a dynamic process involving both de novo DNA methylation and demethylation. As a consequence, differentiated cells develop a stable and unique DNA methylation pattern that regulates tissue-specific gene transcription. In this chapter, we will review the process of DNA methylation and demethylation in the nervous system. We will describe the DNA (de)methylation machinery and its association with other epigenetic mechanisms such as histone modifications and noncoding RNAs. Intriguingly, postmitotic neurons still express DNA methyltransferases and components involved in DNA demethylation. Moreover, neuronal activity can modulate their pattern of DNA methylation in response to physiological and environmental stimuli. The precise regulation of DNA methylation is essential for normal cognitive function. Indeed, when DNA methylation is altered as a result of developmental mutations or environmental risk factors, such as drug exposure and neural injury, mental impairment is a common side effect. The investigation into DNA methylation continues to show a rich and complex picture about epigenetic gene regulation in the central nervous system and provides possible therapeutic targets for the treatment of neuropsychiatric disorders. PMID:22781841

Moore, Lisa D; Le, Thuc; Fan, Guoping

2013-01-01

192

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

2005-01-01

193

[Repair of ionizing radiation induced DNA double strand breaks].  

PubMed

DNA double-strand breaks (DSB) are created by ionizing radiation, an important environmental genotoxic agent. DSB are repaired by two mechanisms associated with recombination. In eukaryotic cells homologous recombination depends on genes belonging to the RAD52 epistatic group. Alternative pathway, DNA end-joining in non-homologous recombination involves DNA-dependent protein kinase (DNA-PK). PMID:10857377

Wid?ak, P

2000-01-01

194

Alternative nucleotide incision repair pathway for oxidative DNA damage  

Microsoft Academic Search

The DNA glycosylase pathway, which requires the sequential action of two enzymes for the incision of DNA, presents a serious problem for the efficient repair of oxidative DNA damage, because it generates genotoxic intermediates such as abasic sites and\\/or blocking 3'-end groups that must be eliminated by additional steps before DNA repair synthesis can be initiated. Besides the logistical problems,

Alexander A. Ischenko; Murat K. Saparbaev

2002-01-01

195

Groups32  

NSDL National Science Digital Library

A group theory calculator. Groups32 computes information about groups of orders 1-32; has a permutation group package; and provides a search for groups with given generators and relations. Site includes documentation as well as course handouts in PDF format.

2007-11-08

196

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.

1997-01-01

197

DNA origami nanopores for controlling DNA translocation.  

PubMed

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

2013-07-23

198

Original article Ribosomal DNA and chloroplast DNA  

E-print Network

Original article Ribosomal DNA and chloroplast DNA polymorphisms in a mixed stand of Quercus robur. However, recent studies of chloroplast DNA (cpDNA) variation in plants indicate that some species may of migration at 1 V/cm. Negatives of the gels were taken under UV illumi- nation at 254 nm. Two chloroplast DNA

Boyer, Edmond

199

##### SAT Engine ####### _ ############ DNA ###### _  

E-print Network

##### SAT Engine ####### _ ############ DNA ###### _ # # # #y # # #yy # # # #yy ###### DNA #################################### ############### ##################### 6 ## 10 ##### ### DNA ############### (Sakamoto et al., Science, Vol.288, pp.1223-122* *6

Hagiya, Masami

200

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

2012-06-26

201

DNA Music.  

ERIC Educational Resources Information Center

Describes an activity in which students reverse-translate proteins from their amino acid sequences back to their DNA sequences then assign musical notes to represent the adenine, guanine, cytosine, and thymine bases. Data is obtained from the National Institutes of Health (NIH) on the Internet. (DDR)

Miner, Carol; della Villa, Paula

1997-01-01

202

DNA vaccines  

Microsoft Academic Search

Preclinical DNA vaccine development has continued apace during the past year, with the investigation of several new infectious and non-infectious disease targets as well as advances in our understanding of some of the basic immunologic mechanisms, such as effector cells, responsible for conferring protection. The coming year promises to be at least as exciting, as initial human clinical studies have

Jeffrey B Ulmer; Jerald C Sadoff; Margaret A Liu

1996-01-01

203

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.

1991-01-01

204

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. PMID:8760891

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

1996-01-01

205

Fabrication of patterned DNA surfaces.  

PubMed

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. PMID:8760891

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

1996-08-01

206

DNA phosphorothioate modifications influence the global transcriptional response and protect DNA from double-stranded breaks  

PubMed Central

The modification of DNA by phosphorothioate (PT) occurs when the non-bridging oxygen in the sugar-phosphate backbone of DNA is replaced with sulfur. This DNA backbone modification was recently discovered and is governed by the dndABCDE genes in a diverse group of bacteria and archaea. However, the biological function of DNA PT modifications is poorly understood. In this study, we employed the RNA-seq analysis to characterize the global transcriptional changes in response to PT modifications. Our results show that DNA without PT protection is susceptible to DNA damage caused by the dndFGHI gene products. The DNA double-stranded breaks then trigger the SOS response, cell filamentation and prophage induction. Heterologous expression of dndBCDE conferring DNA PT modifications at GPSA and GPST prevented the damage in Salmonella enterica. Our data provide insights into the physiological role of the DNA PT system. PMID:25319634

Gan, Rui; Wu, Xiaolin; He, Wei; Liu, Zhenhua; Wu, Shuangju; Chen, Chao; Chen, Si; Xiang, Qianrong; Deng, Zixin; Liang, Dequan; Chen, Shi; Wang, Lianrong

2014-01-01

207

Anthraquinones quinizarin and danthron unwind negatively supercoiled DNA and lengthen linear DNA.  

PubMed

The intercalating drugs possess a planar aromatic chromophore unit by which they insert between DNA bases causing the distortion of classical B-DNA form. The planar tricyclic structure of anthraquinones belongs to the group of chromophore units and enables anthraquinones to bind to DNA by intercalating mode. The interactions of simple derivatives of anthraquinone, quinizarin (1,4-dihydroxyanthraquinone) and danthron (1,8-dihydroxyanthraquinone), with negatively supercoiled and linear DNA were investigated using a combination of the electrophoretic methods, fluorescence spectrophotometry and single molecule technique an atomic force microscopy. The detection of the topological change of negatively supercoiled plasmid DNA, unwinding of negatively supercoiled DNA, corresponding to appearance of DNA topoisomers with the low superhelicity and an increase of the contour length of linear DNA in the presence of quinizarin and danthron indicate the binding of both anthraquinones to DNA by intercalating mode. PMID:24434150

Verebová, Valéria; Adamcik, Jozef; Danko, Patrik; Podhradský, Dušan; Miškovský, Pavol; Stani?ová, Jana

2014-01-31

208

DNA phosphorothioate modifications influence the global transcriptional response and protect DNA from double-stranded breaks.  

PubMed

The modification of DNA by phosphorothioate (PT) occurs when the non-bridging oxygen in the sugar-phosphate backbone of DNA is replaced with sulfur. This DNA backbone modification was recently discovered and is governed by the dndABCDE genes in a diverse group of bacteria and archaea. However, the biological function of DNA PT modifications is poorly understood. In this study, we employed the RNA-seq analysis to characterize the global transcriptional changes in response to PT modifications. Our results show that DNA without PT protection is susceptible to DNA damage caused by the dndFGHI gene products. The DNA double-stranded breaks then trigger the SOS response, cell filamentation and prophage induction. Heterologous expression of dndBCDE conferring DNA PT modifications at GPSA and GPST prevented the damage in Salmonella enterica. Our data provide insights into the physiological role of the DNA PT system. PMID:25319634

Gan, Rui; Wu, Xiaolin; He, Wei; Liu, Zhenhua; Wu, Shuangju; Chen, Chao; Chen, Si; Xiang, Qianrong; Deng, Zixin; Liang, Dequan; Chen, Shi; Wang, Lianrong

2014-01-01

209

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.

210

Genetics, Linguistics, and Prehistoric Migrations: An Analysis of California Indian Mitochondrial DNA Lineages  

E-print Network

2001 Ancient Mitochondrial DNA Evidence for a PrehistoricMitochondrial DNA Lineages {Jolinson / Lorenz evidence of aDNA Lineages | Jotinson / Lorenz as weU as those of some other Central CaUfomia groups, show evidence

Johnson, John R; Lorenz, Joseph G

2006-01-01

211

PhD studentship in DNA biophysics Imperial College London  

E-print Network

PhD studentship in DNA biophysics Imperial College London Department of Chemistry, Faculty groups on chemical biology, chemical physics and biophysics, complex fluids, liquid crystals, nanoscience unique experience in DNA biophysics, doing research and attending lecture courses of choice

van der Heijden, Gert

212

Synthesizing human insulin using recombinant DNA, 3D animation with no audioSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

DNAi Location: Manipulation>Production>pieces of the puzzle>Synthesizing the DNA In order to synthesize human insulin using recombinant DNA technology, the human DNA sequence for insulin was needed. The amino acid sequence of human insulin was known. The Genentech group deduced the human DNA sequence of insulin based on its amino acid sequence. They then used the DNA nucleotides and synthesized the human DNA sequence. This sequence was then inserted into a plasmid and transformed into bacteria to produce insulin. By synthesizing the DNA sequence, the Genentech group assembled a human DNA sequence of insulin without ever having to use \\"real\\" human DNA. They thus bypassed some of the restrictions on human recombinant DNA work resulting from the Asilomar conference.

2008-10-06

213

Recombinant dna technical bulletin. Volume 12, Number 3, September 1989  

SciTech Connect

The Recombinant DNA Technical Bulletin is a publication of the Office of Recombinant DNA Activities (ORDA), National Institutes of Health (NIH). The Bulletin attempts to link investigators involved in recombinant DNA research with organizations active in this area. It is sent to the chairmen of Institutional Biosafety Committees registered with ORDA, to principal investigators of NIH grants and contracts involving recombinant DNA, to the chairmen of genetic manipulation advisory committees, and to other individuals and groups interested in recombinant DNA activities.

Not Available

1989-09-01

214

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

2007-08-16

215

DNA Topology: Fundamentals  

E-print Network

DNA Topology: Fundamentals Sergei M Mirkin, University of Illinois at Chicago, Illinois, USA Topological characteristics of DNA and specifically DNA supercoiling influence all major DNA transactions in living cells. DNA supercoiling induces the formation of unusual secondary structure by specific DNA

Mirkin, Sergei

216

Adleman[1] 1994 DNA Hamiltonian Path Problem , DNA  

E-print Network

1. Adleman[1] 1994 DNA Hamiltonian Path Problem , DNA DNA [2]. DNA DNA , . , , 2 , DNA 4 . DNA 4 A(Adenine), C(Cytosine), G(Guanine), T(Thymine) 2 4 . , . 1 mole 6x10 23 DNA DNA . , . DNA NP-complete [1, 2], [2

217

Group Signatures  

Microsoft Academic Search

Abstract. In this paper we present a new type of signature for a group of persons, called a group signature, which has the following propertjes: (i) only members,of the group can sign messages; (ii) the receiver can verify that it is a valid group signaa~e, but cannot discover which gr~up member made (i) if necessary, the signature can be \\

David Chaum; Eugène Van Heyst

1991-01-01

218

Aminoglycoside antibiotic-derived anion-exchange microbeads for plasmid DNA binding and in situ DNA capture.  

PubMed

Plasmid DNA (pDNA) therapeutics are being investigated for gene therapy and DNA vaccines against diseases including cancer, cystic fibrosis and AIDS. In addition, several applications in modern biotechnology require pDNA for transient protein production. Here, we describe the synthesis, characterization, and evaluation of microbeads ("Amikabeads") derived from the aminoglycoside antibiotic amikacin for pDNA binding and in situ DNA capture from mammalian cells. The parental aminoglycoside-derived microbeads (Amikabeads-P) acted as anion-exchange materials, and demonstrated high capacities for binding pDNA. Binding of pDNA was significantly enhanced following quaternization of the amines on the microbeads (Amikabeads-Q). Amikabeads were further employed for the disruption and extraction of DNA from mammalian cells, indicating their utility for in situ DNA capture. Our results indicate that Amikabeads are a novel material, with multiple reactive groups for further conjugation, and can have several applications in plasmid DNA biotechnology. PMID:25314226

Grandhi, Taraka Sai Pavan; Mallik, Amrita; Lin, Nan; Miryala, Bhavani; Potta, Thrimoorthy; Tian, Yifan; Rege, Kaushal

2014-11-12

219

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.

220

Separation Group.  

ERIC Educational Resources Information Center

Describes eight-week short-term group designed to help separated or divorced men and women move through related adjustment phase in focused group setting. Discusses constructs that form the foundations of this short-term psychoeducational and support group and presents brief overview of psychological difficulties that occur as result of marital…

Addington, Jean

1992-01-01

221

DNA denaturation in the rodlike polyelectrolyte model  

NASA Astrophysics Data System (ADS)

The denaturation of the DNA is analyzed using an analytic model. The DNA molecules are described in the Primitive Model of Polyelectrolytes (PMP), where the polyelectrolyte molecules are cylinders with charged sites. We show that the DNA stabilization arises as the result of the competition between the electrostatic repulsion of the phosphate groups and the attractive forces of the H-bonds. We also show that the addition of salt in the system screens the electrostatic interactions and favors the double strand configuration.

Passos, C. B.; Kuhn, P. S.; Barbosa, M. C.

2014-11-01

222

Automata groups  

E-print Network

of Mihailova normal form concerns only free groups, it can be useful for any group G, and we will use the following natural 11 definition: Definition II.12. Let G be a group with non-trivial generators{a1,...,an}, and H be a subgroup of the direct product G... to show that the defining relators in the group ?? are mapped to the trivial element of the group ???. In all three cases we have ??(a)2 = ((1,1)?)2 = (1,1), ??(x)2 = (1,?x2) = (1,1), ??(y)2 = (?a2,?y2) = (1,1), ??(z)2 = (?a2,?z2) = (1,1), ??(x...

Muntyan, Yevgen

2010-01-16

223

Polymer microspheres carrying fluorescent DNA probes  

NASA Astrophysics Data System (ADS)

A polymer microspheres carried DNA probe, which was based on resonance energy transfer, was presented in this paper when CdTe quantum dots(QDs) were as energy donors, Au nanoparticles were as energy accepters and poly(4- vinylpyrindine-co-ethylene glycol dimethacrylate) microspheres were as carriers. Polymer microspheres with functional group on surfaces were prepared by distillation-precipitation polymerization when ethylene glycol dimethacrylate was as crosslinker in acetonitrile. CdTe QDs were prepared when 3-mercaptopropionic acid(MPA) was as the stabilizer in aqueous solution. Because of the hydrogen-bonding between the carboxyl groups of MPA on QDs and the pyrindine groups on the microspheres, the QDs were self-assembled onto the surfaces of microspheres. Then, the other parts of DNA probe were finished according to the classic method. The DNA detection results indicated that this novel fluorescent DNA probe system could recognize the existence of complementary target DNA or not.

Chen, Xiaoyu; Dai, Zhao; Zhang, Jimei; Xu, Shichao; Wu, Chunrong; Zheng, Guo

2010-07-01

224

DNA Microarrays  

NASA Astrophysics Data System (ADS)

Genomics has revolutionised biological and biomedical research. This revolution was predictable on the basis of its two driving forces: the ever increasing availability of genome sequences and the development of new technology able to exploit them. Up until now, technical limitations meant that molecular biology could only analyse one or two parameters per experiment, providing relatively little information compared with the great complexity of the systems under investigation. This gene by gene approach is inadequate to understand biological systems containing several thousand genes. It is essential to have an overall view of the DNA, RNA, and relevant proteins. A simple inventory of the genome is not sufficient to understand the functions of the genes, or indeed the way that cells and organisms work. For this purpose, functional studies based on whole genomes are needed. Among these new large-scale methods of molecular analysis, DNA microarrays provide a way of studying the genome and the transcriptome. The idea of integrating a large amount of data derived from a support with very small area has led biologists to call these chips, borrowing the term from the microelectronics industry. At the beginning of the 1990s, the development of DNA chips on nylon membranes [1, 2], then on glass [3] and silicon [4] supports, made it possible for the first time to carry out simultaneous measurements of the equilibrium concentration of all the messenger RNA (mRNA) or transcribed RNA in a cell. These microarrays offer a wide range of applications, in both fundamental and clinical research, providing a method for genome-wide characterisation of changes occurring within a cell or tissue, as for example in polymorphism studies, detection of mutations, and quantitative assays of gene copies. With regard to the transcriptome, it provides a way of characterising differentially expressed genes, profiling given biological states, and identifying regulatory channels.

Nguyen, C.; Gidrol, X.

225

STRBase and Information Resources on Forensic DNA  

E-print Network

Applied Genetics STRBase and Information Resources on Forensic DNA John M. Butler NIST Fellow & Applied Genetics Group Leader Forensics@NIST 2012 Meeting Gaithersburg, MD November 28, 2012 #12;Applied of the technique · DNA is often referred to as the "gold standard" in forensic science because of the scientific

Perkins, Richard A.

226

Optical DNA  

NASA Astrophysics Data System (ADS)

A certificate of authenticity (COA) is an inexpensive physical object with a random and unique structure S which is hard to near-exactly replicate. An inexpensive device should be able to scan object’s physical “fingerprint,” a set of features that represents S. In this paper, we explore one set of requirements that optical media such as DVDs should satisfy, to be considered as COAs. As manufacturing of such media produces inevitable errors, we use the locations and count of these errors as a “fingerprint” for each optical disc: its optical DNA. The “fingerprint” is signed using publisher’s private-key and the resulting signature is stored onto the optical medium using a post-production process. Standard DVD players with altered firmware that includes publisher’s public-key, should be able to verify the authenticity of DVDs protected with optical DNA. Our key finding is that for the proposed protocol, only DVDs with exceptional wear-and-tear characteristics would result in an inexpensive and viable anti-counterfeiting technology.

Vijaywargi, Deepak; Lewis, Dave; Kirovski, Darko

227

Contribution of hydrophobicity to thermodynamics of ligand-DNA binding and DNA collapse.  

PubMed

The importance of understanding the dynamics of DNA condensation is inherent in the biological significance of DNA packaging in cell nuclei, as well as for gene therapy applications. Specifically, the role of ligand hydrophobicity in DNA condensation has received little attention. Considering that only multivalent cations can induce true DNA condensation, previous studies exploring monovalent lipids have been unable to address this question. In this study we have elucidated the contribution of the hydrophobic effect to multivalent cation- and cationic lipid-DNA binding and DNA collapse by studying the thermodynamics of cobalt hexammine-, spermine-, and lipospermine-plasmid DNA binding at different temperatures. Comparable molar heat capacity changes (DeltaC(p)) associated with cobalt hexammine- and spermine-DNA binding (-23.39 cal/mol K and -17.98 cal/mol K, respectively) suggest that upon binding to DNA, there are insignificant changes in the hydration state of the methylene groups in spermine. In contrast, the acyl chain contribution to the DeltaC(p) of lipospermine-DNA binding (DeltaC(p ) = DeltaC(p lipospermine) - DeltaC(p spermine)) is significant (-220.94 cal/mol K). Although lipopermine induces DNA ordering into "tubular" suprastructures, such structures do not assume toroidal dimensions as observed for spermine-DNA complexes. We postulate that a steric barrier posed by the acyl chains in lipospermine precludes packaging of DNA into dimensions comparable to those found in nature. PMID:15653734

Patel, Mayank M; Anchordoquy, Thomas J

2005-03-01

228

PNA Beacons for Duplex DNA  

Microsoft Academic Search

ABSTRACT We report here on the hybridization of peptide nucleic acid (PNA)-based molecular beacons (MB) directly to duplex DNA sites locally exposed by PNA openers. Two stemless PNA beacons were tested, both featuring the same recognition sequence and fluorophore-quencher pair (Fluorescein and DABCYL, respectively) but dif- fering in arrangement of these groups and net electrostatic charge. It was found that

Heiko Kuhn; Vadim V. Demidov; Brian D. Gildea; Mark J. Fiandaca; James C. Coull; Maxim D. Frank-Kamenetskii

2001-01-01

229

Simulation of Adsorption of DNA on Carbon Nanotubes  

SciTech Connect

We report molecular dynamics simulations of DNA adsorption on a single-walled carbon nanotube (SWNT) in an aqueous environment. We have modeled a DNA segment with 12 base pairs (Dickerson dodecamer) and a (8,8) SWNT in water, with counterions to maintain total charge neutrality. Simulations show that DNA binds to the external surface of an uncharged or positively charged SWNT on a time scale of a few hundred picoseconds. The hydrophobic end groups of DNA are attracted to the hydrophobic SWNT surface of uncharged SWNTs, while the hydrophilic backbone of DNA does not bind to the uncharged SWNT. The binding mode of DNA to charged SWNTs is qualitatively different from uncharged SWNTs. The phosphodiester groups of the DNA backbone are attracted to a positively charged SWNT surface while DNA does not adsorb on negatively charged SWNTs. There is no evidence for canonical doublestranded DNA wrapping around either charged or uncharged SWNTs on the very short time scales of the simulations. The adsorption process appears to have negligible effect on the internal stacking structure of the DNA molecule but significantly affects the A to B form conversion of A-DNA. The adsorption of A-DNA onto an uncharged SWNT inhibits the complete relaxation of A-DNA to B-DNA within the time scale of the simulations. In contrast, binding of the A-DNA onto a positively charged SWNT may promote slightly the A to B conversion.

Zhao, X.; Johnson, J.K.

2007-08-29

230

SUPPLEMENTARY NOTES DNA Fragmentation  

E-print Network

cycles of MagNA and DNA, a 4- 5min incubation period for DNA precipitation on the beads is performed1 SUPPLEMENTARY NOTES DNA Fragmentation Human solution hybrid selection For the 189 human DNA samples for the hybrid selection (application 1), between 200 and 4,800 ng genomic DNA (final volume 200ul

Reich, David

231

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

J. L. JOHNSON; C. F. PHELPS; C. S. CUMMINS; F. GASSER

1980-01-01

232

Photosensitive interaction of RSU 1069 with DNA  

Microsoft Academic Search

RSU 1069 is a 2-nitroimidazole radiosensitizer with an aziridine-containing side chain. In light (360 nm) the absorbance maximum of the nitro group at 325 nm disappears, which is accompanied by expulsion of the nitro group as the nitrite ion. This photosensitive effect was used to determine separately the damage of DNA induced by the reduced nitro group and the alkylating

D. I. Edwards; R. J. Knox; I. M. Skolimowski; A. Zahoor; R. C. Knight

1984-01-01

233

Photosensitive interaction of RSU 1069 with DNA  

SciTech Connect

RSU 1069 is a 2-nitroimidazole radiosensitizer with an aziridine-containing side chain. In light (360 nm) the absorbance maximum of the nitro group at 325 nm disappears, which is accompanied by expulsion of the nitro group as the nitrite ion. This photosensitive effect was used to determine separately the damage of DNA induced by the reduced nitro group and the alkylating property of the aziridine. The aziridine-induced DNA damage is maximized in the dark when the nitro group is either absent (electrolytically reduced prior to the addition of DNA) or non functional (unreduced). In the light, damage is reduced. Typical DNA damage includes helix disruption leading to single strand breaks and the release of thymidine. Alkaline filter elution studies show evidence only for strand breakage and none for cross-linking indicating the drug is capable of mono-functional alkylation only.

Edwards, D.I.; Knox, R.J.; Skolimowski, I.M.; Zahoor, A.; Knight, R.C.

1984-08-01

234

Prognostic Significance of DNA and Histone Methylation  

Cancer.gov

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

235

Grouping Fireflies  

NSDL National Science Digital Library

In this lesson, students will explore the way fireflies are grouped in the text Ten Flashing Fireflies by Philomen Sturges. Students will represent all of the ways fireflies can be grouped so that some are in a jar and some are left to fly in the night sky.

Brown, Kathleen

2012-07-25

236

DNA, Genes and Chromosomes  

NSDL National Science Digital Library

Today you will learn about the parts of DNA and what DNA, genes and chromosomes are. Today you will learn what DNA, genes and chromosomes are and the parts of the DNA molecule. Look at all of the websites, take whatever notes you need to. At the end of the assignment, be able to describle DNA, the parts of DNA, genes and chromosomes. Covers Biology Core Curriculum, ...

Fomby, Mrs.

2007-11-07

237

Synthesis of DNA  

DOEpatents

A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

Mariella, Jr., Raymond P. (Danville, CA)

2008-11-18

238

An overview of the structures of protein-DNA complexes  

Microsoft Academic Search

On the basis of a structural analysis of 240 protein-DNA complexes contained in the Protein Data Bank (PDB), we have classified the DNA-binding proteins involved into eight different structural\\/functional groups, which are further classified into 54 structural families. Here we present this classification and review the functions, structures and binding interactions of these protein-DNA complexes.

Nicholas M Luscombe; Susan E Austin; Helen M Berman; Janet M Thornton

2000-01-01

239

Compaction of DNA by Gemini Surfactants: Effects of Surfactant Architecture  

Microsoft Academic Search

The interaction between bacteriophage T4 DNA and cationic gemini surfactants was studied by the use of fluorescence microscopy. Upon addition of surfactant, DNA undergoes a transition from random coil to globule, with an intermediate coexistence region. The state behavior of a DNA–gemini surfactant system was found to depend on spacer length, valency, head group size, and tail length. A series

Lisa Karlsson; Marcel C. P. van Eijk; Olle Söderman

2002-01-01

240

Energy transport in crystalline DNA composites  

NASA Astrophysics Data System (ADS)

This work reports on the synthesis of crystalline DNA-composited films and microfibers, and details the study of thermal energy transport in them. The transient electro-thermal technique is used to characterize the thermal transport in DNA composite microfibers, and the photothermal technique is used to explore the thermal transport in the thickness direction of DNA films. Compared with microfibers, the DNA films are found to have a higher thermal transport capacity, largely due to the carefully controlled crystallization process in film synthesis. In high NaCl concentration solutions, the bond of the Na+ ion and phosphate group aligns the DNA molecules with the NaCl crystal structure during crystallization. This results in significant enhancement of thermal transport in the DNA films with aligned structure.

Xu, Zaoli; Xu, Shen; Tang, Xiaoduan; Wang, Xinwei

2014-01-01

241

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

242

Research Groups  

Cancer.gov

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.

243

DNA extraction techniques for use in education.  

PubMed

DNA extraction provides a hands-on introduction to DNA and enables students to gain real life experience and practical knowledge of DNA. Students gain a sense of ownership and are more enthusiastic when they use their own DNA. A cost effective, simple protocol for DNA extraction and visualization was devised. Buccal mucosal epithelia provide a readily available source of cells for DNA extraction and can be harvested in a painless, noninvasive manner. Seven criteria were established to evaluate the protocol: Safety, DNA yield, DNA quality/stability, cost, user friendliness, reliability, and time. To identify the optimum conditions for each stage of the protocol (cell harvest, lysis, purification, and precipitation), each was investigated separately, and an adaptation of the fast-boiling protocol was used for the remaining stages. A validation study was undertaken with the optimized protocol to assess its performance when conducted by a group of students in a classroom setting. The optimum protocol used an isotonic Lucozade Hydro Active Fitness Water (HAFW) mouthwash. Lysis was achieved using a TE (10 mM Tris-HCl, 1 mM EDTA, pH 8) + 1% Sodium Dodecyl Sulphate (SDS) buffer. Protein was then digested using Proteinase K (Qiagen Inc., UK) at 56°C for 10 min. The DNA was then precipitated with sodium chloride and absolute ethanol. This protocol achieved an increase in DNA yield using readily available equipment and reagents at a lower per capita cost and is simple to use. PMID:21567818

Hearn, R P; Arblaster, K E

2010-05-01

244

A Partial Denaturation Map of Herpes Simplex Virus Type 1 DNA: Evidence for Inversions of the Unique DNA Regions  

Microsoft Academic Search

SUMMARY Partial denaturation maps of 30 HSV-I DNA molecules have been obtained using a procedure designed to avoid possible hydrolysis of the DNA at alkali- labile bonds. From the denaturation pattern of the long unique DNA region these molecules were divided into two groups comprised of 16 and 14 molecules. Histo- gram plots relating the percentage denaturation to position on

H. Delius; J. B. Clements

1976-01-01

245

mtDNA / Y chromosome pedigree, animated imageSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

DNAi location:Applications>gene genealogy>Tracing ancestries>Using genetic tools together Studies following the male lineage (using the Y chromosome) have been compared to studies following the female lineage (using mitochondrial DNA (mtDNA)). The results suggest that men and women have had different roles in the peopling of the planet and in the mixing of genes among population groups. A pedigree illustrating maternal inheritance of mtDNA and paternal inheritance of the Y chromosome.

2008-10-06

246

DNA adsorption characteristics of hollow spherical allophane nano-particles  

NASA Astrophysics Data System (ADS)

To understand the propensity of the natural allophane to adsorb the DNA molecules, the adsorption characteristics were assessed against a natural allophane, 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 deprotonation, 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 allophane clustered particle was successfully observed through TEM analysis.

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

2014-05-01

247

Group dynamics.  

PubMed

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

1990-12-01

248

Molecular DNA switches and DNA chips  

NASA Astrophysics Data System (ADS)

We present an assay to detect single-nucleotide polymorphisms on a chip using molecular DNA switches and isothermal rolling- circle amplification. The basic principle behind the switch is an allele-specific oligonucleotide circularization, mediated by DNA ligase. A DNA switch is closed when perfect hybridization between the probe oligonucleotide and target DNA allows ligase to covalently circularize the probe. Mismatches around the ligation site prevent probe circularization, resulting in an open switch. DNA polymerase is then used to preferentially amplify the closed switches, via rolling-circle amplification. The stringency of the molecular switches yields 102 - 103 fold discrimination between matched and mismatched sequences.

Sabanayagam, Chandran R.; Berkey, Cristin; Lavi, Uri; Cantor, Charles R.; Smith, Cassandra L.

1999-06-01

249

Abelian groups  

E-print Network

of G . Therefore x is the sum of elements in the G 's, pi p To finish our proof we wish to show this expression is unique. Suppose x ~ yl + y 2 + ~ ~ ~ + yg and m zl + s2 + ~ ~ ~ + s~o Then yl + y 2 + ~ ~ ~ + yy sl + $2 + ~ ~ ~ + zygo so that s... groups. In order to d. o this, we will need the aid. of some vector space theorys D~ef ~tp 4s10 A vector ~sac 7 over the field. P is an abelian group which admits mult1plicatlon by elements of t' he field. such that, for a, b e P and. x, y s V& (l) a...

Bolen, James Cordell

2012-06-07

250

DNA Binding Hydroxyl Radical Probes  

PubMed Central

The hydroxyl radical is the primary mediator of DNA damage by the indirect effect of ionizing radiation. It is a powerful oxidizing agent produced by the radiolysis of water and is responsible for a significant fraction of the DNA damage associated with ionizing radiation. There is therefore an interest in the development of sensitive assays for its detection. The hydroxylation of aromatic groups to produce fluorescent products has been used for this purpose. We have examined four different chromophores which produce fluorescent products when hydroxylated. Of these, the coumarin system suffers from the fewest disadvantages. We have therefore examined its behavior when linked to a cationic peptide ligand designed to bind strongly to DNA. PMID:22125376

Tang, Vicky J; Konigsfeld, Katie M; Aguilera, Joe A; Milligan, Jamie R

2011-01-01

251

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

2011-01-01

252

Triplex DNA Structures  

Microsoft Academic Search

A DNA triplex is formed when pyrimidine or purine bases occupy the major groove of the DNA double Helix forming Hoogsteen pairs with purines of the Watson-Crick basepairs. Intermolecular triplexes are formed between triplex forming oligonucleotides (TFO) and target sequences on duplex DNA. Intra- molecular triplexes are the major elements of H-DNAs, unusual DNA struc- tures, which are formed in

Maxim D. Frank-Kamenetskii; Sergei M. Mirkin

1995-01-01

253

DNA excision repair pathways  

Microsoft Academic Search

The major DNA excision repair pathways of base excision repair for endogenous DNA lesions and nucleotide excision repair for DNA damage inflicted by ultraviolet light have been reconstructed with purified mammalian proteins and details of these repair mechanisms are emerging. Similar data are becoming available with regard to mismatch repair for correction of replication errors. Deletion of individual DNA repair

Tomas Lindahl; Peter Karran; Richard D Wood

1997-01-01

254

Quantitative DNA fiber mapping  

DOEpatents

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)

1998-01-01

255

Melanesian mtDNA Complexity  

PubMed Central

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 inland Papuan-speaking groups on the largest islands have the greatest distinctions, while shore dwelling populations are considerably less diverse (at the same time, within-group haplotype diversity is less in the most isolated groups). Persistent differences between shore and inland groups in effective population sizes and marital migration rates probably cause these differences. We also add 16 whole sequences to the Melanesian mtDNA phylogenies. We identify the likely origins of a number of the haplogroups and ancient branches in specific islands, point to some ancient mtDNA connections between Near Oceania and Australia, and show additional Holocene connections between Island Southeast Asia/Taiwan and Island Melanesia with branches of haplogroup E. Coalescence estimates based on synonymous transitions in the coding region suggest an initial settlement and expansion in the region at ?30–50,000 years before present (YBP), and a second important expansion from Island Southeast Asia/Taiwan during the interval ?3,500–8,000 YBP. However, there are some important variance components in molecular dating that have been overlooked, and the specific nature of ancestral (maternal) Austronesian influence in this region remains unresolved. PMID:17327912

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

2007-01-01

256

Variation in mitochondrial DNA levels in muscle from normal controls. Is depletion of mtDNA in patients with mitochondrial myopathy a distinct clinical syndrome?  

Microsoft Academic Search

Recent studies have identified a group of patients with cytochrome oxidase (COX) deficiency presenting in infancy associated with a deficiency of mtDNA in muscle or other affected tissue (Moraes et al 1991). We used a novel approach to compare the level of mitochondrial (mtDNA) compared to nuclear DNA in skeletal muscle from a group of patients and controls, based on

J. Poulton; C. Sewry; C. G. Potter; T. Bougeron; D. Chretien; F. A. Wijburg; K. J. Morten; G. Brown

1995-01-01

257

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

258

newDNA-Prot: Prediction of DNA-binding proteins by employing support vector machine and a comprehensive sequence representation.  

PubMed

Identification of DNA-binding proteins is essential in studying cellular activities as the DNA-binding proteins play a pivotal role in gene regulation. In this study, we propose newDNA-Prot, a DNA-binding protein predictor that employs support vector machine classifier and a comprehensive feature representation. The sequence representation are categorized into 6 groups: primary sequence based, evolutionary profile based, predicted secondary structure based, predicted relative solvent accessibility based, physicochemical property based and biological function based features. The mRMR, wrapper and two-stage feature selection methods are employed for removing irrelevant features and reducing redundant features. Experiments demonstrate that the two-stage method performs better than the mRMR and wrapper methods. We also perform a statistical analysis on the selected features and results show that more than 95% of the selected features are statistically significant and they cover all 6 feature groups. The newDNA-Prot method is compared with several state of the art algorithms, including iDNA-Prot, DNAbinder and DNA-Prot. The results demonstrate that newDNA-Prot method outperforms the iDNA-Prot, DNAbinder and DNA-Prot methods. More specific, newDNA-Prot improves the runner-up method, DNA-Prot for around 10% on several evaluation measures. The proposed newDNA-Prot method is available at http://sourceforge.net/projects/newdnaprot/ PMID:25240115

Zhang, Yanping; Xu, Jun; Zheng, Wei; Zhang, Chen; Qiu, Xingye; Chen, Ke; Ruan, Jishou

2014-10-01

259

Tumorigenic DNA viruses  

SciTech Connect

The eighth volume of Advances in Viral Oncology focuses on the three major DNA virus groups with a postulated or proven tumorigenic potential: papillomaviruses, animal hepatitis viruses, and the Epstein-Bar virus. In the opening chapters, the contributors analyze the evidence that papillomaviruses and animal hepatitis viruses are involved in tumorigenesis and describe the mechanisms that trigger virus-host cell interactions. A detailed section on the Epstein-Barr virus (EBV) - comprising more than half the book - examines the transcription and mRNA processing patterns of the virus genome; the mechanisms by which EBV infects lymphoid and epithelial cells; the immunological aspects of the virus; the actions of EBV in hosts with Acquired Immune Deficiency Syndrome; and the involvement of EBV in the etiology of Burkitt's lymphoma.

Klein, G.

1989-01-01

260

Size Dependent Free Solution DNA Electrophoresis in Structured Micro Fluidic Systems  

E-print Network

. The electrophoretic migration of single DNA molecules stained with the intercalator YOYO was investigated by real intercalators) labelled DNA molecules. This has been used by several groups to enlighten DNA migration of the migration of individual DNA molecules stained with the fluorescent intercalator YOYO. 4 #12;Materials

261

Parvovirus infection-induced DNA damage response  

PubMed Central

Parvoviruses are a group of small DNA viruses with ssDNA genomes flanked by two inverted terminal structures. Due to a limited genetic resource they require host cellular factors and sometimes a helper virus for efficient viral replication. Recent studies have shown that parvoviruses interact with the DNA damage machinery, which has a significant impact on the life cycle of the virus as well as the fate of infected cells. In addition, due to special DNA structures of the viral genomes, parvoviruses are useful tools for the study of the molecular mechanisms underlying viral infection-induced DNA damage response (DDR). This review aims to summarize recent advances in parvovirus-induced DDR, with a focus on the diverse DDR pathways triggered by different parvoviruses and the consequences of DDR on the viral life cycle as well as the fate of infected cells.

Luo, Yong; Qiu, Jianming

2014-01-01

262

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.

1988-05-01

263

Preparation and characterization of DNA/allophane composite hydrogels.  

PubMed

The preparation and characterization of the composite hydrogels based on double-stranded deoxyribonucleic acid (DNA) and natural allophane (AK70) were reported. To understand the propensity of the natural allophane to adsorb the DNA molecules, using zeta potential measurement, Fourier transform infrared spectroscopy (FTIR) and electrophoresis analyses assessed the adsorption characteristics. The freeze-dried DNA/AK70 hydrogels were demonstrated that the DNA bundle structure with a width of ?2?m and a length of ?15-20?m was wrapped around the clustered allophane particles as revealed by FE-SEM/EDX analysis. The incorporation of AK70 in hydrogels induced the increase in the enthalpy of the helix-coil transition of DNA duplex due to the restricted molecular motions of the DNA duplex facilitated by the interaction between the phosphate groups of DNA and the protonated (+)(OH2)Al(OH2) groups on the wall perforations of the allophane. PMID:24041573

Kawachi, Takuya; Matsuura, Yoko; Iyoda, Fumitoshi; Arakawa, Shuichi; Okamoto, Masami

2013-12-01

264

2003 NaturePublishing Group NATURE REVIEWS | MOLECULAR CELL BIOLOGY VOLUME 4 | APRIL 2003 | 261  

E-print Network

position,whereas in N2 and N3 they were located closer to the DNA ends.Some free DNA was also generated with -- the DNA,as the amount of free DNA generated was greatest with the N1 species,where the nucleosomes had© 2003 NaturePublishing Group NATURE REVIEWS | MOLECULAR CELL BIOLOGY VOLUME 4 | APRIL 2003 | 261

Kowalczykowski, Stephen C.

265

DNA bar-coding for phytoplasma identification.  

PubMed

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

2013-01-01

266

DNA demethylation by TDG.  

PubMed

DNA methylation has long been considered a very stable DNA modification in mammals that could only be removed by replication in the absence of remethylation - that is, 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. In this article, we review the recent literature highlighting the prominent role played in active DNA demethylation by base excision repair and especially by TDG. PMID:22920184

Dalton, Shannon R; Bellacosa, Alfonso

2012-08-01

267

Effect of DNA type on response of DNA biosensor for carcinogens  

NASA Astrophysics Data System (ADS)

Carcinogens are cancer causing chemicals that can bind to DNA and cause damage to the DNA. These chemicals are available everywhere including in water, air, soil and food. Therefore, a sensor that can detect the presence of these chemicals will be a very useful tool. Since carcinogens bind to DNA, DNA can be used as the biological element in a biosensor. This study has utilized different types of DNA in a biosensor for carcinogen detection. The DNAs include double stranded calf thymus DNA, single stranded calf thymus DNA and guanine rich single stranded DNA. The modified SPE was exposed to a carcinogen followed by interaction with methylene blue which acts as the electroactive indicator. The SPE was then analysed using differential pulse voltammetry (DPV). Optimization studies were conducted for MB concentration and accumulation time, DNA concentration, as well as effect of buffer concentration, buffer pH and ionic strength. The performance of the biosensor was tested on a group 1 carcinogen, formaldehyde. The results indicated that the usage of guanine rich single stranded DNA also gives higher response as carcinogens prefer to bind with guanine compared to other bases.

Sani, Nor Diyana bt. Md.; Heng, Lee Yook; Surif, Salmijah; Lazim, Azwani Mat

2013-11-01

268

Structure of DNA-Functionalized Dendrimer Nanoparticles  

E-print Network

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.

Mattaparthi Venkata Satish Kumar; Prabal K Maiti

2012-03-13

269

An assessment of whether SNPs will replace STRs in national DNA databases Joint considerations of the  

E-print Network

of the DNA working group of the European Network of Forensic Science Institutes (ENFSI) and the Scientific Working Group on DNA Analysis Methods (SWGDAM) Sir: It is unlikely that SNPs will replace STRsAn assessment of whether SNPs will replace STRs in national DNA databases ­ Joint considerations

270

Enzymatic ligation of large biomolecules to DNA.  

PubMed

The ability to synthesize, characterize, and manipulate DNA forms the foundation of a range of advanced disciplines including genomics, molecular biology, and biomolecular engineering. In particular for the latter field, DNA has proven useful as a structural or functional component in nanoscale self-assembled structures, antisense therapeutics, microarray diagnostics, and biosensors. Such applications frequently require DNA to be modified and conjugated to other macromolecules, including proteins, polymers, or fatty acids, in order to equip the system with properties required for a particular application. However, conjugation of DNA to large molecular components using classical chemistries often suffers from suboptimal yields. Here, we report the use of terminal deoxynucleotidyl transferase (TdT) for direct enzymatic ligation of native DNA to nucleotide triphosphates coupled to proteins and other large macromolecules. We demonstrate facile synthesis routes for a range of NTP-activated macromolecules and subsequent ligation to the 3' hydroxyl group of oligodeoxynucleotides using TdT. The reaction is highly specific and proceeds rapidly and essentially to completion at micromolar concentrations. As a proof of principle, parallelly labeled oligonucleotides were used to produce nanopatterned DNA origami structures, demonstrating rapid and versatile incorporation of non-DNA components into DNA nanoarchitectures. PMID:23927463

Sørensen, Rasmus Schøler; Okholm, Anders Hauge; Schaffert, David; Kodal, Anne Louise Bank; Gothelf, Kurt V; Kjems, Jørgen

2013-09-24

271

Nanomaterials Based on DNA  

PubMed Central

The combination of synthetic stable branched DNA and sticky ended cohesion has led to the development of structural DNA nanotechnology over the past 30 years. The basis of this enterprise is that it is possible to construct novel DNA-based materials by combining these features in a self-assembly protocol. Thus, simple branched molecules lead directly to the construction of polyhedra whose edges consist of double helical DNA, and whose vertices correspond to the branch points. Stiffer branched motifs can be used to produce self-assembled two-dimensional and three-dimensional periodic lattices of DNA (crystals). DNA has also been used to make a variety of nanomechanical devices, including molecules that change their shapes, and molecules that can walk along a DNA sidewalk. Devices have been incorporated into two-dimensional DNA arrangements; sequence-dependent devices are driven by increases in nucleotide pairing at each step in their machine cycles. PMID:20222824

Seeman, Nadrian C.

2012-01-01

272

Issues in DNA Fingerprinting.  

National Technical Information Service (NTIS)

The use, in court, of DNA Profiling, popularly referred to as DNA Fingerprinting, for forensic identification purposes has been questioned. A report of the National Research Council was solicited to clarify the issues and propose procedures of how and whe...

H. Chernoff

1994-01-01

273

Coffee and Your DNA  

MedlinePLUS Videos and Cool Tools

... hand corner of the player. Coffee and Your DNA HealthDay October 7, 2014 Related MedlinePlus Pages Caffeine ... Java drinking behavior may be tied to your DNA! Researchers conducted a genome-wide analysis of regular ...

274

Surreptitious DNA Testing  

MedlinePLUS

Most states do not have laws restricting surreptitious DNA testing. Those that do generally place restrictions only ... of states have laws that broadly restrict surreptitious DNA testing for both health and non-health-related ...

275

DNA Testing for VHL  

MedlinePLUS

... So Rare Commonly Occurring VHL Manifestations VHL and Cancer How Do People Get VHL? Diagnosis Challenges of Deciding about Genetic Testing DNA Testing Sources of DNA Testing Genetic Testing for ...

276

NSC DNA Computing  

E-print Network

• Start with the observation that DNA is just another way of coding information, a code that can be manipulated. • DNA sequences are strings, so computation is typically viewed as ‘string processing ’ of some form. • Computation is implemented by biological molecules and manipulation mechanisms – e.g. usual DNA reproductive mechanisms, enzymes catalyse particular joining, shortening, extension manipulations etc. • Fundamental is the notion of Crick Watson complementarity, a unique feature of the DNA molecule Department of Computer Science NSC – DNA Computing-- 2DNAC – is it for real? • Implementing DNAC requires considerable knowledge – – Of the physical properties of DNA – Of the chemical properties of DNA – Of the laboratory techniques for handling DNA – ….but this is a matter of engineering • For the most part we can assume that there are various computational primitives and assert ‘the biologists know how to implement this’.

unknown authors

277

HPV DNA test  

MedlinePLUS

The HPV DNA test is used to check for high-risk HPV infection in women. HPV infection around the genitals is ... warts spread when you have sex. The HPV-DNA test is generally not recommended for detecting low- ...

278

The Structure of DNA  

NSDL National Science Digital Library

This animation adapted from Garland Science Publishing takes a close look at the DNA double helix and its individual components, describing their chemical structures and how they function together to make the DNA molecule unique.

Foundation, Wgbh E.

2011-12-30

279

Vitamin C for DNA damage prevention.  

PubMed

The ability of vitamin C to affect genetic damage was reviewed in human studies that used molecular epidemiology methods, including analysis of DNA adducts, DNA strand breakage (using the Comet assay), oxidative damage measured as levels of 8-oxo-7,8-dihydroxy-2'-deoxyguanosine (8-oxodG), cytogenetic analysis of chromosomal aberrations and micronuclei, and the induction of DNA repair proteins. The protective effect of vitamin C was observed at plasma levels>50?mol/l. Vitamin C supplementation decreased the frequency of chromosomal aberrations in groups with insufficient dietary intake who were occupationally exposed to mutagens, and also decreased the sensitivity to mutagens as assessed using the bleomycin assay. High vitamin C levels in plasma decreased the frequency of genomic translocations in groups exposed to ionizing radiation or c-PAHs in polluted air. The frequency of micronuclei was decreased by vitamin C supplementation in smokers challenged with ?-irradiation, and higher vitamin C levels in plasma counteracted the damage induced by air pollution. The prevalence of DNA adducts inversely correlated with vitamin C levels in groups environmentally exposed to high concentrations of c-PAHs. Increased vitamin C levels decreased DNA strand breakage induced by air pollution. Oxidative damage (8-oxodG levels) was decreased by vitamin C supplementation in groups with plasma levels>50?mol/l exposed to PM2.5 and c-PAHs. Modulation of DNA repair by vitamin C supplementation was observed both in poorly nourished subjects and in groups with vitamin C plasma levels>50?mol/l exposed to higher concentrations of c-PAHs. It is possible that the impact of vitamin C on DNA damage depends both on background values of vitamin C in the individual as well as on the level of exposure to xenobiotics or oxidative stress. PMID:22178550

Sram, Radim J; Binkova, Blanka; Rossner, Pavel

2012-05-01

280

From DNA to Protein  

NSDL National Science Digital Library

This project will help you understand the relationships among DNA,genes, and protein. By moving through the different topics, you will hopefully gain greater understanding of how DNA, genes, and proteins are all related. Start by clicking on the link below and then following the directions on your handout. DNA to Protein Module The next 2 sites will continue to help you explore the structure of DNA and how ...

Buchanan, Ms.

2007-03-19

281

Group evaporation  

NASA Technical Reports Server (NTRS)

Liquid fuel combustion process is greatly affected by the rate of droplet evaporation. The heat and mass exchanges between gas and liquid couple the dynamics of both phases in all aspects: mass, momentum, and energy. Correct prediction of the evaporation rate is therefore a key issue in engineering design of liquid combustion devices. Current analytical tools for characterizing the behavior of these devices are based on results from a single isolated droplet. Numerous experimental studies have challenged the applicability of these results in a dense spray. To account for the droplets' interaction in a dense spray, a number of theories have been developed in the past decade. Herein, two tasks are examined. One was to study how to implement the existing theoretical results, and the other was to explore the possibility of experimental verifications. The current theoretical results of group evaporation are given for a monodispersed cluster subject to adiabatic conditions. The time evolution of the fluid mechanic and thermodynamic behavior in this cluster is derived. The results given are not in the form of a subscale model for CFD codes.

Shen, Hayley H.

1991-01-01

282

Onion DNA Extraction  

NSDL National Science Digital Library

This laboratory exercise is designed to show learners how DNA can easily be extracted from onion cells 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

2009-01-01

283

Wheat Germ DNA Extraction  

NSDL National Science Digital Library

This laboratory exercise is designed to show learners how DNA can easily be extracted from wheat germ 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

2009-01-01

284

Northwestern University Recombinant DNA  

E-print Network

Northwestern University Recombinant DNA Safety Program Office of Research Safety Office of the Vice deoxyribonucleic acid (DNA) shall comply with the National Institute of Health's "Guidelines for Research Involving Recombinant DNA Molecules" (NIH Guidelines) as published in the Federal Register (www

Shull, Kenneth R.

285

From Cell to DNA  

NSDL National Science Digital Library

This animation takes the students through a tour of a typical human cell, moving from larger to smaller cell structures (i.e., from nucleus to chromosomes to DNA strands and their bases). It briefly describes some of these structures and describes how DNA strands are constructed. This animation can be used as an introduction to the study of chromosomes and DNA.

Dexter Pratt (AAAS;Science Netlinks)

2008-01-01

286

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. PMID:19706433

Chow, Brian Y.; Emig, Christopher J.; Jacobson, Joseph M.

2009-01-01

287

Small Molecules, Inhibitors of DNA-PK, Targeting DNA Repair, and Beyond  

PubMed Central

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

2012-01-01

288

Molecular Cell Dynamic DNA Helicase-DNA Polymerase  

E-print Network

Molecular Cell Article Dynamic DNA Helicase-DNA Polymerase Interactions Assure Processive-associated DNA polymerases can exchange with free DNA polymerase without affecting processivity (Johnson et al DNA poly- merase and DNA helicase advance the replica- tion fork with a processivity greater than 17

289

Meta-DNA: synthetic biology via DNA nanostructures and  

E-print Network

Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions Harish Chandran1 of DNA manipulations achieved by protein enzymes be simulated via simple DNA hybridization chemistry? In this work, we develop a biochemical system which we call meta-DNA (abbreviated as mDNA), based on strands

Reif, John H.

290

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

291

DNA damage in peripheral blood leukocytes in tobacco users  

PubMed Central

Aim: To Quantify the DNA single-stranded breaks in the peripheral blood leukocytes (PBLs) of tobacco-habituated individuals with clinically normal mucosa and patients with oral carcinoma. Objectives: To evaluate DNA damage levels in PBLs of tobacco-habituated individuals with clinically normal mucosa and patients with oral carcinoma and compare with a control group of healthy volunteers. To evaluate the extent of DNA damage in PBLs using Single Cell Gel Electrophoresis (SCGE) in the above groups. Materials and Methods: Patients who were attending the outpatient department were enrolled in this study. A control group of 30 healthy volunteers included in Group I were selected from various age groups who are not tobacco users in any form. Thirty patients with tobacco habituation but with clinically normal mucosa were included in Group II, while 30 tobacco-habituated patients with oral squamous carcinoma were included in Group III. A biopsy was taken from the representative area and confirmed histologically. Intravenous blood samples were collected from all the groups for evaluation of the extent of DNA damage using ethidium bromide-stained slides under fluorescent microscope. The DNA tail length was calculated by subtracting the diameter from the total length. Twenty-five randomly selected cells per slide were analyzed and mean calculated. Results: The mean DNA damage levels in patients with tobacco habits were compared with that of the control group and the results were found to be statistically significant. The mean DNA damage level in PBLs between tobacco-habituated patients with normal mucosa and oral cancer patients was found to be statistically significant. The DNA damage in cancer patients was compared with the control group and the results were found to be statistically significant. Conclusion: DNA damage evaluation in PBLs by SCGE technique is a sensitive and reliable indicator of tobacco insult. PMID:25364170

Guttikonda, Venkateswara Rao; Patil, Rekha; Kumar, GS

2014-01-01

292

Reproductive & Cardiovascular Disease Research Group  

NSDL National Science Digital Library

The Reproductive & Cardiovascular Disease Research Group is "based in the Department of Biochemistry and Immunology at St. George's, University of London." The Group's "research interests include a number of areas concerned with reproductive and cardiovascular diseases such as trophoblast biology, nitric oxide and apoptosis, with particular emphasis on the role of these subjects in diseases of pregnancy such as pre-eclampsia." This website contains descriptions of protocols commonly utilized by the Research Group such as DNA laddering, Comet Assay, Immunoprecipitation, and Caspase Assay, to name a few. This site also contains informative sections concerning Nitric Oxide, Apoptosis, and Trophoblasts. The website includes a list of publications, and email addresses of group members as well.

Dash, Phil.

293

DNA Sequencing apparatus  

DOEpatents

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)

1992-01-01

294

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

2004-02-01

295

Dietary Berries and Ellagic Acid Prevent Oxidative DNA Damage and Modulate Expression of DNA Repair Genes  

PubMed Central

DNA damage is a pre-requisite for the initiation of cancer and agents that reduce this damage are useful in cancer prevention. In this study, we evaluated the ability of whole berries and berry phytochemical, ellagic acid to reduce endogenous oxidative DNA damage. Ellagic acid was selected based on >95% inhibition of 8-oxodeoxyguosine (8-oxodG) and other unidentified oxidative DNA adducts induced by 4-hydroxy-17ß-estradiol and CuCl2 in vitro. Inhibition of the latter occurred at lower concentrations (10 ?M) than that for 8-oxodG (100 ?M). In the in vivo study, female CD-1 mice (n=6) were fed either a control diet or diet supplemented with ellagic acid (400 ppm) and dehydrated berries (5% w/w) with varying ellagic acid contents – blueberry (low), strawberry (medium) and red raspberry (high), for 3 weeks. Blueberry and strawberry diets showed moderate reductions in endogenous DNA adducts (25%). However, both red raspberry and ellagic acid diets showed a significant reduction of 59% (p < 0.001) and 48% (p < 0.01), respectively. Both diets also resulted in a 3–8 fold over-expression of genes involved in DNA repair such as xeroderma pigmentosum group A complementing protein (XPA), DNA excision repair protein (ERCC5) and DNA ligase III (DNL3). These results suggest that red raspberry and ellagic acid reduce endogenous oxidative DNA damage by mechanisms which may involve increase in DNA repair. PMID:19325752

Aiyer, Harini S.; Vadhanam, Manicka V.; Stoyanova, Radka; Caprio, Gerard D.; Clapper, Margie L.; Gupta, Ramesh C.

2008-01-01

296

Details of T-DNA structural organization from a transgenic Petunia population exhibiting co-suppression  

Microsoft Academic Search

Analysis of Agrobacterium-transferred DNA (T-DNA) revealed strong correlations between transgene structures and floral pigmentation patterns from chalcone synthase (chs) co-suppression among 47 Petunia transformants. Presented here are the full details of T-DNA structural organization in that population. Sixteen transformants (34%) carried one T-DNA copy while 31 (66%) carried 106 complete and partial T-DNA elements in 54 linkage groups. Thirty linkage

Paul D. Cluster; Michael O'Dell; Michael Metzlaff; Richard B. Flavell

1996-01-01

297

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

G. DE BENEDICTIS; G. ROSE; G. CARRIERI; M. DE LUCA; E. FALCONE; G. PASSARINO; M. BONAFE; D. MONTI; G. BAGGIO; S. BERTOLINI; D. MARI; R. MATTACE; C. FRANCESCHI

298

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

2012-10-01

299

Optimal Placement of Origins for DNA Replication  

NASA Astrophysics Data System (ADS)

DNA replication is an essential process in biology and its timing must be robust so that cells can divide properly. Random fluctuations in the formation of replication starting points, called origins, and the subsequent activation of proteins lead to variations in the replication time. We analyze these stochastic properties of DNA and derive the positions of origins corresponding to the minimum replication time. We show that under some conditions the minimization of replication time leads to the grouping of origins, and relate this to experimental data in a number of species showing origin grouping.

Karschau, Jens; Blow, J. Julian; de Moura, Alessandro P. S.

2012-02-01

300

DNA condensing effects and sequence selectivity of DNA binding of antitumor noncovalent polynuclear platinum complexes.  

PubMed

The noncovalent analogues of antitumor polynuclear platinum complexes represent a structurally discrete class of platinum drugs. Their chemical and biological properties differ significantly from those of most platinum chemotherapeutics, which bind to DNA in a covalent manner by formation of Pt-DNA adducts. In spite of the fact that these noncovalent polynuclear platinum complexes contain no leaving groups, they have been shown to bind to DNA with high affinity. We report here on the DNA condensation properties of a series of noncovalent analogues of antitumor polynuclear platinum complexes described by biophysical and biochemical methods. The results demonstrate that these polynuclear platinum compounds are capable of inducing DNA condensation at more than 1 order of magnitude lower concentrations than conventional spermine. Atomic force microscopy studies of DNA condensation confined to a mica substrate have revealed that the DNA morphologies become more compact with increasing concentration of the platinum complexes. Moreover, we also found that the noncovalent polynuclear platinum complex [{Pt(NH3)3}2-?-{trans-Pt(NH3)2(NH2(CH2)6NH2)2}](6+) (TriplatinNC-A) binds to DNA in a sequence-dependent manner, namely, to A/T-rich sequences and A-tract regions, and that noncovalent polynuclear platinum complexes protect DNA from enzymatic cleavage by DNase I. The results suggest that mechanisms of antitumor and cytotoxic activities of these complexes may be associated with their unique ability to condense DNA along with their sequence-specific DNA binding. Owing to their high cellular accumulation, it is also reasonable to suggest that their mechanism of action is based on the competition with naturally occurring DNA condensing agents, such as polyamines spermine, spermidine, and putrescine, for intracellular binding sites, resulting in the disturbance of the correct binding of regulatory proteins initiating the onset of apoptosis. PMID:24428232

Malina, Jaroslav; Farrell, Nicholas P; Brabec, Viktor

2014-02-01

301

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

2004-01-01

302

Mitochondrial DNA (mtDNA) and schizophrenia.  

PubMed

The poorly understood aetiology of schizophrenia is known to involve a major genetic contribution even though the genetic factors remain elusive. Most genetic studies are based on Mendelian rules and focus on the nuclear genome, but current studies indicate that other genetic mechanisms are probably involved. This review focuses on mitochondrial DNA (mtDNA), a maternally inherited, 16.6-Kb molecule crucial for energy production that is implicated in numerous human traits and disorders. The aim of this review is to summarise the studies that have explored mtDNA in schizophrenia patients and those which provide evidence for its implication in this illness. Alterations in mitochondrial morphometry, brain energy metabolism, and enzymatic activity in the mitochondrial respiratory chain suggest a mitochondrial dysfunction in schizophrenia that could be related to the genetic characteristics of mtDNA. Moreover, evidence of maternal inheritance and the presence of schizophrenia symptoms in patients suffering from a mitochondrial disorder related to an mtDNA mutation suggest that mtDNA is involved in schizophrenia. The association of specific variants has been reported at the molecular level; however, additional studies are needed to determine whether the mitochondrial genome is involved in schizophrenia. PMID:20980130

Verge, B; Alonso, Y; Valero, J; Miralles, C; Vilella, E; Martorell, L

2011-01-01

303

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 PMID:10883670

Siman, S E; Povey, A C; Ward, T H; Margison, G P; Sheffield, E

2000-01-01

304

Fern spore extracts can damage DNA.  

PubMed

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. PMID:10883670

Simán, S E; Povey, A C; Ward, T H; Margison, G P; Sheffield, E

2000-07-01

305

Syndromes associated with mitochondrial DNA depletion  

PubMed Central

Mitochondrial dysfunction accounts for a large group of inherited metabolic disorders most of which are due to a dysfunctional mitochondrial respiratory chain (MRC) and, consequently, deficient energy production. MRC function depends on the coordinated expression of both nuclear (nDNA) and mitochondrial (mtDNA) genomes. Thus, mitochondrial diseases can be caused by genetic defects in either the mitochondrial or the nuclear genome, or in the cross-talk between the two. This impaired cross-talk gives rise to so-called nuclear-mitochondrial intergenomic communication disorders, which result in loss or instability of the mitochondrial genome and, in turn, impaired maintenance of qualitative and quantitative mtDNA integrity. In children, most MRC disorders are associated with nuclear gene defects rather than alterations in the mtDNA itself. The mitochondrial DNA depletion syndromes (MDSs) are a clinically heterogeneous group of disorders with an autosomal recessive pattern of transmission that have onset in infancy or early childhood and are characterized by a reduced number of copies of mtDNA in affected tissues and organs. The MDSs can be divided into least four clinical presentations: hepatocerebral, myopathic, encephalomyopathic and neurogastrointestinal. The focus of this review is to offer an overview of these syndromes, listing the clinical phenotypes, together with their relative frequency, mutational spectrum, and possible insights for improving diagnostic strategies. PMID:24708634

2014-01-01

306

Oswald Avery (c.1930), still imageSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Oswald Avery, circa 1930. In a very simple experiment, Oswald Avery's group showed that DNA was the "transforming principle." When isolated from one strain of bacteria, DNA was able to transform another strain and confer characteristics onto that second strain. DNA was carrying hereditary information. With DNA as the hereditary molecule, the stage was set for one of the most exciting periods in DNA science: understanding DNA structure and function. Now use the buttons along the top to explore some of the other sections in this module. Solve the structure of DNA!

2008-10-06

307

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

2010-03-01

308

Human mitochondrial DNA variation in Lithuania.  

PubMed

Variation in mitochondrial DNA (mt-DNA) was studied in a population sample of 154 Lithuanians after cleavage with 15 different restriction endonucleases and probing with cat mt-DNA. Polymorphic variations were found with 8 restriction endonucleases. The most frequent mt-DNA cleavage patterns (morphs) were HpaI-2 (98.7%), BamHI-1 (94.8%), HaeII-1 (91.0%), MspI-1 (99.3%), AvaII-1 (86.4%), and HincII-2 (99.4%). The morph HaeII-12 previously described in Finns was found in two Lithuanians. Altogether 16 mt-DNA types were observed in the Lithuanian population. Type 1 was the most common one (81.2%), type 6 less and type 21 more frequent than in other populations. Lithuanians have high index of homogeneity (F = 0.663) compared to other Caucasoid populations. However, there appeared to be some differences between the two main ethnic groups, Aukstaiciai (Highlanders) and Zemaiciai (Lowlanders) with respect to the distribution of mt-DNA types. Measurements of genetic distance based on mt-DNA types were small between Lithuanians and Finns and increased gradually in comparison between Lithuanians and Mediterranean populations, Asiatic Mongoloids and African Blacks, respectively. PMID:7840534

Kucinskas, V

1994-12-01

309

DNA: structure, dense phases, charges, interactions  

E-print Network

DNA: structure, dense phases, charges, interactions #12;Outline 1. DNA: structure, charges, dense phases 2. Counterion and DNA condensation 3. ES DNA-DNA interactions 4. DNA toroidal structures 5. Interactions of real DNA helices 6. DNA-DNA ES recognition 7. DNA melting in aggregates 8. Azimuthal

Potsdam, Universität

310

lambda DNA Fingerprinting Simulation  

NSDL National Science Digital Library

The purpose of this lab activity is to demonstrate (through simulation) how DNA fingerprinting (or DNA profiling) might be used to solve a crime. Learners perform restriction digests on DNA samples from four individuals, and then search for similarities between the individuals by running the restriction fragments on an electrophoresis gel. This activity does not do a true DNA fingerprint. It simulates two of the three steps of DNA fingerprinting: restriction of DNA sample and separation by electrophoresis. This activity does not make use of the third step, the radioactive probes. In order to make DNA fingerprinting affordable, lambda DNA is used instead of plasmids. This means that the instructor has to switch the labels on the samples given to the learners. What is labeled DNA is actually the different restriction enzymes and what is labeled restriction enzyme is the lambda DNA. Although there is some deception on the part of the instructor, learners are able to do a restriction digest that simulates a crime scene which adds interest for the learner.

Conley, Thomas J.

2009-01-01

311

Forensic DNA analysis.  

PubMed

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

2012-01-01

312

An overview of the structures of protein-DNA complexes  

PubMed Central

On the basis of a structural analysis of 240 protein-DNA complexes contained in the Protein Data Bank (PDB), we have classified the DNA-binding proteins involved into eight different structural/functional groups, which are further classified into 54 structural families. Here we present this classification and review the functions, structures and binding interactions of these protein-DNA complexes. PMID:11104519

Luscombe, Nicholas M; Austin, Susan E; Berman , Helen M; Thornton, Janet M

2000-01-01

313

Evaluation of DNAstable for DNA storage at ambient temperature.  

PubMed

Preserving DNA is important for validation of prospective and retrospective analyses, requiring many expensive types of equipment (e.g., freezers and back-up generators) and energy. While freezing is the most common method for storing extracted DNA evidence or well-characterized DNA samples for validation studies, DNAstable (Biomatrica), a commercially available medium for room temperature storage of DNA extracts was evaluated in this study. Two groups of samples consisting of different DNA quantities were investigated, one ranging from 20 to 400 ng (group 1) and the other one ranging from 1.4 to 20 ng (group 2). The DNA samples with and without DNAstable were stored at four different temperatures [?25 °C (room temperature), -20 °C, 37 °C or 50 °C]. DNA degradation over several months was monitored by SYBR Green-based qPCR assays and by PCR amplification of the core CODIS STR markers for group 1 and 2 DNA samples, respectively. For the time points tested in this study (up to 365 days), the findings indicate that the -20 °C controls and the DNAstable protected samples at room temperature provided similar DNA recoveries that were higher compared to the unprotected controls kept at RT, 37 °C or 50 °C. These results suggest that DNAstable can protect DNA samples with effectiveness similar to that of the traditional -20 °C freezing method. In addition, extrapolations from accelerated aging experiments conducted at high temperatures support that DNAstable is an effective technology for preserving purified DNA at room temperature with a larger protective impact on DNA samples of low quantity (<20 ng). PMID:24315605

Howlett, Susanne E; Castillo, Hilda S; Gioeni, Lora J; Robertson, James M; Donfack, Joseph

2014-01-01

314

Construction of DNA-polymer hybrids using intercalation interactions.  

PubMed

Reversible addition-fragmentation chain transfer (RAFT) polymerisation was used to produce a range of polymers terminated with an acridine group, which intercalates efficiently into dsDNA; the structure of the polymer determines the nature and strength of the interaction. Using a short 63 base pair dsDNA, discrete and well-defined DNA-polymer hybrid nanoparticles were formed, which were characterised by dynamic light scattering, small-angle X-ray scattering and atomic force microscopy. PMID:24346828

Wilks, Thomas R; Pitto-Barry, Anaïs; Kirby, Nigel; Stulz, Eugen; O'Reilly, Rachel K

2014-02-01

315

Repeated DNA sequences and species relatedness in the genus Equisetum  

Microsoft Academic Search

The kinetics with which DNA reassociates and the thermal stability of rapidly reassociating (repetitive) DNA sequences have been monitored for six species in the genusEquisetum. Using the kinetic complexity for each of two repeated DNA sequence components as the basis for comparison, species in the subgenusEquisetum (E. arvense, E. fluviatile andE. telmateia) form one group and species in the subgenusHippochaete

Arnold J. Bendich; Robert S. Anderson

1983-01-01

316

Oxidative DNA damage precedes DNA fragmentation after experimental stroke in rat brain  

PubMed Central

Experimental stroke using a focal cerebral ischemia and reperfusion (FCIR) model was induced in male Long-Evans rats by a bilateral occlusion of both common carotid arteries and the right middle cerebral artery for 30–90 min, followed by various periods of reperfusion. Oxidative DNA lesions in the ipsilateral cortex were demonstrated using Escherichia coli formamidopyrimidine DNA N-glycosylase (Fpg protein)-sensitive sites (FPGSS), as labeled in situ using digoxigenin-dUTP and detected using antibodies against digoxigenin. Because Fpg protein removes 8-hydroxy-2?-deoxyguanine (oh8dG) and other lesions in DNA, FPGSS measure oxidative DNA damage. The number of FPGSS-positive cells in the cortex from the sham-operated control group was 3 ± 3 (mean ± SD per mm2). In animals that received 90 min occlusion and 15 min of reperfusion (FCIR 90/15), FPGSS-positive cells were significantly increased by 200-fold. Oxidative DNA damage was confirmed by using monoclonal antibodies against 8-hydroxy-guanosine (oh8G) and oh8dG. A pretreatment of RNase A (100 ?g/ml) to the tissue reduced, but did not abolish, the oh8dG signal. The number of animals with positive FPGSS or oh8dG was significantly (P<0.01) higher in the FCIR group than in the sham-operated control group. We detected few FPGSS of oh8dG-positive cells in the animals treated with FCIR of 90/60. No terminal UTP nicked-end labeling (TUNEL)-positive cells, as a detection of cell death, were detected at this early reperfusion time. Our data suggest that early oxidative DNA lesions elicited by experimental stroke could be repaired. Therefore, the oxidative DNA lesions observed in the nuclear and mitochondrial DNA of the brain are different from the DNA fragmentation detected using TUNEL. PMID:10783150

CUI, JIANKUN; HOLMES, ERIC H.; GREENE, THOMAS G.; LIU, PHILIP K.

2009-01-01

317

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

DOEpatents

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 DNA mutation binding proteins such at TthMutS to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by binding which gives an increase in signal. Unlabeled DNA is utilized with labeled chimeras to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by nuclease activity of the chimera which gives a decrease in signal.

McCutchen-Maloney, Sandra L. (Pleasanton, CA)

2002-01-01

318

Gene duplications in evolution of archaeal family B DNA polymerases.  

PubMed Central

All archaeal DNA-dependent DNA polymerases sequenced to date are homologous to family B DNA polymerases from eukaryotes and eubacteria. Presently, representatives of the euryarchaeote division of archaea appear to have a single family B DNA polymerase, whereas two crenarchaeotes, Pyrodictium occultum and Sulfolobus solfataricus, each possess two family B DNA polymerases. We have found the gene for yet a third family B DNA polymerase, designated B3, in the crenarchaeote S. solfataricus P2. The encoded protein is highly divergent at the amino acid level from the previously characterized family B polymerases in S. solfataricus P2 and contains a number of nonconserved amino acid substitutions in catalytic domains. We have cloned and sequenced the ortholog of this gene from the closely related Sulfolobus shibatae. It is also highly divergent from other archaeal family B DNA polymerases and, surprisingly, from the S. solfataricus B3 ortholog. Phylogenetic analysis using all available archaeal family B DNA polymerases suggests that the S. solfataricus P2 B3 and S. shibatae B3 paralogs are related to one of the two DNA polymerases of P. occultum. These sequences are members of a group which includes all euryarchaeote family B homologs, while the remaining crenarchaeote sequences form another distinct group. Archaeal family B DNA polymerases together constitute a monophyletic subfamily whose evolution has been characterized by a number of gene duplication events. PMID:9098062

Edgell, D R; Klenk, H P; Doolittle, W F

1997-01-01

319

DNA-Based Machines.  

PubMed

The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H(+)/OH(-)), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications. PMID:24647836

Wang, Fuan; Willner, Bilha; Willner, Itamar

2014-01-01

320

DNA Isolation from Onion  

NSDL National Science Digital Library

Many students find studying DNA difficult because it is so small that the concepts are quite abstract. This lab enables students to work with DNA concretely by easily isolating chromosomal DNA using the same basic tools and methods that scientists use. The lab is a good introduction to using pipets and to using the metric system. If the chemistry of the solutions is taught it is also a great practical application.

Kate Dollard (Cambridge Rindge and Latin REV)

1994-07-30

321

DNA Extraction Virtual Lab  

NSDL National Science Digital Library

This virtual lab from the Genetic Science Learning Center at the University of Utah provides a simple overview of DNA extraction, including what it's used for, illustrations, and an activity using cheek cells and laboratory equipment to isolate DNA. The lab is followed by a classroom activity that allows students and teachers to Extract DNA from Anything Living, using household items like spinach but not little sister's big toe.

2006-01-01

322

Thymus DNA Extractions  

NSDL National Science Digital Library

This laboratory exercise is designed to show learners how DNA can be extracted from a chunk of thymus (sweetbread) or liver. This experiment requires the use of a centrifuge (not included in cost of 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

2009-01-01

323

Design and synthesis of boronic-acid-labeled thymidine triphosphate for incorporation into DNA  

PubMed Central

The boronic acid moiety is a versatile functional group useful in carbohydrate recognition, glycoprotein pull-down, inhibition of hydrolytic enzymes and boron neutron capture therapy. The incorporation of the boronic-acid group into DNA could lead to molecules of various biological functions. We have successfully synthesized a boronic acid-labeled thymidine triphosphate (B-TTP) linked through a 14-atom tether and effectively incorporated it into DNA by enzymatic polymerization. The synthesis was achieved using the Huisgen cycloaddition as the key reaction. We have demonstrated that DNA polymerase can effectively recognize the boronic acid-labeled DNA as the template for DNA polymerization, that allows PCR amplification of boronic acid-labeled DNA. DNA polymerase recognitions of the B-TTP as a substrate and the boronic acid-labeled DNA as a template are critical issues for the development of DNA-based lectin mimics via in vitro selection. PMID:17267413

Lin, Na; Yan, Jun; Huang, Zhen; Altier, Craig; Li, Minyong; Carrasco, Nicolas; Suyemoto, Mitsu; Johnston, Lynette; Wang, Siming; Wang, Qian; Fang, Hao; Caton-Williams, Julianne; Wang, Binghe

2007-01-01

324

Design and synthesis of boronic-acid-labeled thymidine triphosphate for incorporation into DNA.  

PubMed

The boronic acid moiety is a versatile functional group useful in carbohydrate recognition, glycoprotein pull-down, inhibition of hydrolytic enzymes and boron neutron capture therapy. The incorporation of the boronic-acid group into DNA could lead to molecules of various biological functions. We have successfully synthesized a boronic acid-labeled thymidine triphosphate (B-TTP) linked through a 14-atom tether and effectively incorporated it into DNA by enzymatic polymerization. The synthesis was achieved using the Huisgen cycloaddition as the key reaction. We have demonstrated that DNA polymerase can effectively recognize the boronic acid-labeled DNA as the template for DNA polymerization, that allows PCR amplification of boronic acid-labeled DNA. DNA polymerase recognitions of the B-TTP as a substrate and the boronic acid-labeled DNA as a template are critical issues for the development of DNA-based lectin mimics via in vitro selection. PMID:17267413

Lin, Na; Yan, Jun; Huang, Zhen; Altier, Craig; Li, Minyong; Carrasco, Nicolas; Suyemoto, Mitsu; Johnston, Lynette; Wang, Siming; Wang, Qian; Fang, Hao; Caton-Williams, Julianne; Wang, Binghe

2007-01-01

325

Low-Dose Formaldehyde Delays DNA Damage Recognition and DNA Excision Repair in Human Cells  

PubMed Central

Objective Formaldehyde is still widely employed as a universal crosslinking agent, preservative and disinfectant, despite its proven carcinogenicity in occupationally exposed workers. Therefore, it is of paramount importance to understand the possible impact of low-dose formaldehyde exposures in the general population. Due to the concomitant occurrence of multiple indoor and outdoor toxicants, we tested how formaldehyde, at micromolar concentrations, interferes with general DNA damage recognition and excision processes that remove some of the most frequently inflicted DNA lesions. Methodology/Principal Findings The overall mobility of the DNA damage sensors UV-DDB (ultraviolet-damaged DNA-binding) and XPC (xeroderma pigmentosum group C) was analyzed by assessing real-time protein dynamics in the nucleus of cultured human cells exposed to non-cytotoxic (<100 ?M) formaldehyde concentrations. The DNA lesion-specific recruitment of these damage sensors was tested by monitoring their accumulation at local irradiation spots. DNA repair activity was determined in host-cell reactivation assays and, more directly, by measuring the excision of DNA lesions from chromosomes. Taken together, these assays demonstrated that formaldehyde obstructs the rapid nuclear trafficking of DNA damage sensors and, consequently, slows down their relocation to DNA damage sites thus delaying the excision repair of target lesions. A concentration-dependent effect relationship established a threshold concentration of as low as 25 micromolar for the inhibition of DNA excision repair. Conclusions/Significance A main implication of the retarded repair activity is that low-dose formaldehyde may exert an adjuvant role in carcinogenesis by impeding the excision of multiple mutagenic base lesions. In view of this generally disruptive effect on DNA repair, we propose that formaldehyde exposures in the general population should be further decreased to help reducing cancer risks. PMID:24722772

Luch, Andreas; Frey, Flurina C. Clement; Meier, Regula; Fei, Jia; Naegeli, Hanspeter

2014-01-01

326

Electrochemical DNA Hybridization Detection Using DNA Dohyoung Kwon,a  

E-print Network

Full Paper Electrochemical DNA Hybridization Detection Using DNA Cleavage Dohyoung Kwon,a Kyuwon method for detection of DNA hybridization using enzymatic cleavage. The strategy is based on that S1 nuclease is able to specifically cleave only single strand DNA, but not double strand DNA. The capture

Kwak, Juhyoun

327

Novobiocin and Coumermycin Inhibit DNA Supercoiling Catalyzed by DNA Gyrase  

Microsoft Academic Search

Novobiocin and coumermycin are known to inhibit the replication of DNA in Escherichia coli. We show that these drugs inhibit the supercoiling of DNA catalyzed by E. coli DNA gyrase, a recently discovered enzyme that introduces negative superhelical turns into covalently circular DNA. The activity of DNA gyrase purified from a coumermycin-resistant mutant strain is resistant to both drugs. The

Martin Gellert; Mary H. O'Dea; Tateo Itoh; Jun-Ichi Tomizawa

1976-01-01

328

Multiprotein DNA looping  

E-print Network

DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switch-like transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.

Jose M. G. Vilar; Leonor Saiz

2006-03-17

329

Imaging DNA Structure  

NSDL National Science Digital Library

Students are introduced to the latest imaging methods used to visualize molecular structures and the method of electrophoresis that is used to identify and compare genetic code (DNA). Students should already have basic knowledge of genetics, DNA (DNA structure, nucleotide bases), proteins and enzymes. The lesson begins with a discussion to motivate the need for imaging techniques and DNA analysis, which prepares students to participate in the associated two-part activity: 1) students each choose an imaging method to research (from a provided list of molecular imaging methods), 2) they research basic information about electrophoresis.

University Of Houston

330

DNA Damage Response  

PubMed Central

Structural changes to DNA severely affect its functions, such as replication and transcription, and play a major role in age-related diseases and cancer. A complicated and entangled network of DNA damage response (DDR) mechanisms, including multiple DNA repair pathways, damage tolerance processes, and cell-cycle checkpoints safeguard genomic integrity. Like transcription and replication, DDR is a chromatin-associated process that is generally tightly controlled in time and space. As DNA damage can occur at any time on any genomic location, a specialized spatio-temporal orchestration of this defense apparatus is required. PMID:20980439

Giglia-Mari, Giuseppina; Zotter, Angelika; Vermeulen, Wim

2011-01-01

331

Bisulfite Sequencing of DNA  

PubMed Central

Exact positions of 5-methylcytosine (m5C) on a single strand of DNA can be determined by bisulfite genomic sequencing (BGS). Treatment with bisulfite ion preferentially deaminates unmethylated cytosines, which then convert to uracil upon desulfonation. Amplifying regions of interest from deaminated DNA and sequencing products cloned from amplicons permits determination of methylation at single nucleotide resolution along single DNA molecules, which is not possible with other methylation analysis techniques. This unit describes a BGS technique suitable for most DNA sources, including formaldehyde-fixed tissue. Considerations for experimental design and common sources of error are discussed. PMID:20583099

Darst, Russell P.; Pardo, Carolina E.; Ai, Lingbao; Brown, Kevin D.; Kladde, Michael P.

2010-01-01

332

DNA Overview Learning Module  

NSDL National Science Digital Library

The Southwest Center for Microsystems Education is a Regional Advanced Technology Education Center funded in part by the National Science Foundation. These resources provide an overview on the topic of DNA. Users will learn the role of DNA as genetic material, the molecular components of DNA and the structure and replication of DNA. A comprehensive PowerPoint presentation is included along with instructor and participant guides. Visitors are encouraged to create an account and log in in order to access the full set of resources.

2010-03-02

333

Multiprotein DNA Looping  

NASA Astrophysics Data System (ADS)

DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switchlike transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.

Vilar, Jose M. G.; Saiz, Leonor

2006-06-01

334

Phytoplasma plasmid DNA extraction.  

PubMed

Phytoplasma plasmids have generally been detected from DNA extracted from plants and insects using methods designed for the purification of total phytoplasma DNA. Methods include extraction from tissues that are high in phytoplasma titre, such as the phloem of plants, with the use of CsCl-bisbenzimide gradients that exploit the low G+C content of phytoplasma DNA. Many of the methods employed for phytoplasma purification have been described elsewhere in this book. Here we describe in detail two methods that are specifically aimed at isolating plasmid DNA. PMID:22987431

Andersen, Mark T; Liefting, Lia W

2013-01-01

335

DNA Jewelry Models  

NSDL National Science Digital Library

Making DNA Jewelry Models is a portion of a unit on molecular genetics. Using the directions for this hands-on activity/lab helps students construct a model of DNA to learn DNA structure and decode it to better understand protein synthesis. They also have an actual badge of their DNA literacy to wear or use. Whether a key ring, earrings, bracelet, or necklace, students from fourth grade through adult can do and enjoy this activity. (Even visually impaired students made a model using larger beads.)

BEGIN:VCARD VERSION:2.1 FN:Catherine Sheils Ross N:Sheils Ross;Catherine ORG:Berkley High School (retired-6/98) REV:2005-04-09 END:VCARD

1995-06-30

336

[Mitochondrial DNA variation in Asian guardian dogs].  

PubMed

The hypervariable site of the mitochondrial DNA (mtDNA) control region has been studied in several sheepdog breeds. The genetic diversity is high in the Central Asian guardian dog and the Northern Caucasian wolf dog (an aboriginal group of breeds) and low in the Caucasian guardian dog. Haplotypes of groups A, B, C, and E/W have been found in Central Asian guardian dogs; haplotypes of groups A and B, in Caucasian guardian dogs. There is evidence suggesting a gene flow from Scandinavian dog populations to the Northern Caucasus. The results of the analysis allow the Caucasian guardian dog, Northern Caucasian wolf dog, Central Asian guardian dog, and the Turkish breeds akbash and kangal to be combined into a single group with an extremely low degree of differentiation. PMID:16915922

Riabinina, O M

2006-07-01

337

The interplay of primer-template DNA phosphorylation status and single-stranded DNA binding proteins in directing clamp loaders to the appropriate polarity of DNA  

PubMed Central

Sliding clamps are loaded onto DNA by clamp loaders to serve the critical role of coordinating various enzymes on DNA. Clamp loaders must quickly and efficiently load clamps at primer/template (p/t) junctions containing a duplex region with a free 3?OH (3?DNA), but it is unclear how clamp loaders target these sites. To measure the Escherichia coli and Saccharomyces cerevisiae clamp loader specificity toward 3?DNA, fluorescent ? and PCNA clamps were used to measure clamp closing triggered by DNA substrates of differing polarity, testing the role of both the 5?phosphate (5?P) and the presence of single-stranded binding proteins (SSBs). SSBs inhibit clamp loading by both clamp loaders on the incorrect polarity of DNA (5?DNA). The 5?P groups contribute selectivity to differing degrees for the two clamp loaders, suggesting variations in the mechanism by which clamp loaders target 3?DNA. Interestingly, the ? subunit of the E. coli clamp loader is not required for SSB to inhibit clamp loading on phosphorylated 5?DNA, showing that ?·SSB interactions are dispensable. These studies highlight a common role for SSBs in directing clamp loaders to 3?DNA, as well as uncover nuances in the mechanisms by which SSBs perform this vital role. PMID:25159615

Hayner, Jaclyn N.; Douma, Lauren G.; Bloom, Linda B.

2014-01-01

338

The interplay of primer-template DNA phosphorylation status and single-stranded DNA binding proteins in directing clamp loaders to the appropriate polarity of DNA.  

PubMed

Sliding clamps are loaded onto DNA by clamp loaders to serve the critical role of coordinating various enzymes on DNA. Clamp loaders must quickly and efficiently load clamps at primer/template (p/t) junctions containing a duplex region with a free 3'OH (3'DNA), but it is unclear how clamp loaders target these sites. To measure the Escherichia coli and Saccharomyces cerevisiae clamp loader specificity toward 3'DNA, fluorescent ? and PCNA clamps were used to measure clamp closing triggered by DNA substrates of differing polarity, testing the role of both the 5'phosphate (5'P) and the presence of single-stranded binding proteins (SSBs). SSBs inhibit clamp loading by both clamp loaders on the incorrect polarity of DNA (5'DNA). The 5'P groups contribute selectivity to differing degrees for the two clamp loaders, suggesting variations in the mechanism by which clamp loaders target 3'DNA. Interestingly, the ? subunit of the E. coli clamp loader is not required for SSB to inhibit clamp loading on phosphorylated 5'DNA, showing that ?·SSB interactions are dispensable. These studies highlight a common role for SSBs in directing clamp loaders to 3'DNA, as well as uncover nuances in the mechanisms by which SSBs perform this vital role. PMID:25159615

Hayner, Jaclyn N; Douma, Lauren G; Bloom, Linda B

2014-12-01

339

Low integrated DNA repair score and lung cancer risk.  

PubMed

DNA repair is a prime mechanism for preventing DNA damage, mutation, and cancers. Adopting a functional approach, we examined the association with lung cancer risk of an integrated DNA repair score, measured by a panel of three enzymatic DNA repair activities in peripheral blood mononuclear cells. The panel included assays for AP endonuclease 1 (APE1), 8-oxoguanine DNA glycosylase (OGG1), and methylpurine DNA glycosylase (MPG), all of which repair oxidative DNA damage as part of the base excision repair pathways. A blinded population-based case-control study was conducted with 96 patients with lung cancer and 96 control subjects matched by gender, age (±1 year), place of residence, and ethnic group (Jews/non-Jews). The three DNA repair activities were measured, and an integrated DNA repair OMA (OGG1, MPG, and APE1) score was calculated for each individual. Conditional logistic regression analysis revealed that individuals in the lowest tertile of the integrated DNA repair OMA score had an increased risk of lung cancer compared with the highest tertile, with OR = 9.7; 95% confidence interval (CI), 3.1-29.8; P < 0.001, or OR = 5.6; 95% CI, 2.1-15.1; P < 0.001 after cross-validation. These results suggest that pending validation, this DNA repair panel of risk factors may be useful for lung cancer risk assessment, assisting prevention and referral to early detection by technologies such as low-dose computed tomography scanning. PMID:24356339

Sevilya, Ziv; Leitner-Dagan, Yael; Pinchev, Mila; Kremer, Ran; Elinger, Dalia; Rennert, Hedy S; Schechtman, Edna; Freedman, Laurence S; Rennert, Gad; Paz-Elizur, Tamar; Livneh, Zvi

2014-04-01

340

Photosensitive interaction of RSU 1069 with DNA.  

PubMed

RSU 1069 is a 2-nitroimidazole radiosensitizer with an aziridine-containing side chain. In light (360 nm) the absorbance maximum of the nitro group at 325 nm disappears, which is accompanied by expulsion of the nitro group as the nitrite ion. We suggest an intramolecular cyclization of the aziridine side chain and the C2 of the imidazole ring as a possible explanation. This photosensitive effect was used to determine separately the damage to DNA induced by the reduced nitro group and the alkylating property of the aziridine. The aziridine-induced DNA damage is maximized in the dark when the nitro group is either absent (electrolytically reduced prior to the addition of DNA) or non functional (unreduced). In the light, damage is reduced. Typical DNA damage includes helix disruption leading to single strand breaks and the release of thymidine. Alkaline filter elution studies show evidence only for strand breakage and none for cross-linking indicating the drug is capable of mono-functional alkylation only. PMID:6547937

Edwards, D I; Knox, R J; Skolimowski, I M; Zahoor, A; Knight, R C

1984-08-01

341

Many Ways to Loop DNA  

PubMed Central

In the 1960s, I developed methods for directly visualizing DNA and DNA-protein complexes using an electron microscope. This made it possible to examine the shape of DNA and to visualize proteins as they fold and loop DNA. Early applications included the first visualization of true nucleosomes and linkers and the demonstration that repeating tracts of adenines can cause a curvature in DNA. The binding of DNA repair proteins, including p53 and BRCA2, has been visualized at three- and four-way junctions in DNA. The trombone model of DNA replication was directly verified, and the looping of DNA at telomeres was discovered. PMID:24005675

Griffith, Jack D.

2013-01-01

342

Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules  

PubMed Central

DNA lesions produced by aromatic isocyanates have an extra bulky group on the nucleotide bases, with the capability of forming stacking interaction within a DNA helix. In this work, we investigated the conformation of the 2?-deoxyadenosine and 2?-deoxycytidine derivatives tethering a phenyl or naphthyl group, introduced in a DNA duplex. The chemical modification experiments using KMnO4 and 1-cyclohexyl-3 -(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate have shown that the 2?-deoxycytidine lesions form the base pair with guanine while the 2?-deoxyadenosine lesions have less ability of forming the base pair with thymine in solution. Nevertheless, the kinetic analysis shows that these DNA lesions are compatible with DNA ligase and DNA polymerase reactions, as much as natural DNA bases. We suggest that the adduct lesions have a capability of adopting dual conformations, depending on the difference in their interaction energies between stacking of the attached aromatic group and base pairing through hydrogen bonds. It is also presented that the attached aromatic groups change their orientation by interacting with the minor groove binding netropsin, distamycin and synthetic polyamide. The nucleotide derivatives would be useful for enhancing the phenotypic diversity of DNA molecules and for exploring new non-natural nucleotides. PMID:23873956

Nakano, Shu-ichi; Uotani, Yuuki; Sato, Yuichi; Oka, Hirohito; Fujii, Masayuki; Sugimoto, Naoki

2013-01-01

343

Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules.  

PubMed

DNA lesions produced by aromatic isocyanates have an extra bulky group on the nucleotide bases, with the capability of forming stacking interaction within a DNA helix. In this work, we investigated the conformation of the 2'-deoxyadenosine and 2'-deoxycytidine derivatives tethering a phenyl or naphthyl group, introduced in a DNA duplex. The chemical modification experiments using KMnO4 and 1-cyclohexyl-3 -(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate have shown that the 2'-deoxycytidine lesions form the base pair with guanine while the 2'-deoxyadenosine lesions have less ability of forming the base pair with thymine in solution. Nevertheless, the kinetic analysis shows that these DNA lesions are compatible with DNA ligase and DNA polymerase reactions, as much as natural DNA bases. We suggest that the adduct lesions have a capability of adopting dual conformations, depending on the difference in their interaction energies between stacking of the attached aromatic group and base pairing through hydrogen bonds. It is also presented that the attached aromatic groups change their orientation by interacting with the minor groove binding netropsin, distamycin and synthetic polyamide. The nucleotide derivatives would be useful for enhancing the phenotypic diversity of DNA molecules and for exploring new non-natural nucleotides. PMID:23873956

Nakano, Shu-ichi; Uotani, Yuuki; Sato, Yuichi; Oka, Hirohito; Fujii, Masayuki; Sugimoto, Naoki

2013-10-01

344

Replicative DNA polymerases.  

PubMed

In 1959, Arthur Kornberg was awarded the Nobel Prize for his work on the principles by which DNA is duplicated by DNA polymerases. Since then, it has been confirmed in all branches of life that replicative DNA polymerases require a single-stranded template to build a complementary strand, but they cannot start a new DNA strand de novo. Thus, they also depend on a primase, which generally assembles a short RNA primer to provide a 3'-OH that can be extended by the replicative DNA polymerase. The general principles that (1) a helicase unwinds the double-stranded DNA, (2) single-stranded DNA-binding proteins stabilize the single-stranded DNA, (3) a primase builds a short RNA primer, and (4) a clamp loader loads a clamp to (5) facilitate the loading and processivity of the replicative polymerase, are well conserved among all species. Replication of the genome is remarkably robust and is performed with high fidelity even in extreme environments. Work over the last decade or so has confirmed (6) that a common two-metal ion-promoted mechanism exists for the nucleotidyltransferase reaction that builds DNA strands, and (7) that the replicative DNA polymerases always act as a key component of larger multiprotein assemblies, termed replisomes. Furthermore (8), the integrity of replisomes is maintained by multiple protein-protein and protein-DNA interactions, many of which are inherently weak. This enables large conformational changes to occur without dissociation of replisome components, and also means that in general replisomes cannot be isolated intact. PMID:23732474

Johansson, Erik; Dixon, Nicholas

2013-06-01

345

Attenuated Expression of Xeroderma Pigmentosum Group C Is Associated with Critical Events in Human Bladder Cancer Carcinogenesis and Progression  

Microsoft Academic Search

Xeroderma pigmentosum group C (XPC) is an important DNA damage recognition protein that binds to damaged DNA at a very early stage during DNA repair. The XPC protein is also involved in DNA damage-induced cell cycle checkpoint regulation and apoptosis. XPC defects are associated with many types of solid tumors. The mechanism of the XPC protein in cancer progression, however,

Zhiwen Chen; Jin Yang; Gan Wang; Zhigang Xu

346

Restriction Enzymes and DNA Fingerprinting  

NSDL National Science Digital Library

The discovery of restriction enzymes and their applications in DNA analysis has proven to be essential for biologists and chemists. This lesson focuses on restriction enzymes and their applications to DNA analysis and DNA fingerprinting. Use this lesson and its associated activity in conjunction with biology lessons on DNA analysis and DNA replication.

National Science Foundation GK-12 and Research Experience for Teachers (RET) Programs,

347

(2) DNA O(n^5) Quorum-Sensing Lux  

E-print Network

- 1 - ( ) ( ) DNA RNA DNA RNA DNA DNA 2 DNA #12;- 2 - 17 6 (1) (2) DNA O(n^5) (3) Quorum-Sensing Lux (4) (5) LMNtal ambient LMNtal (1) (2) DNA (3) DNA (4) DNA (5) DNA (1) DNA ANP-96 (Precision System Science ) (2) RTRACS DNA RTRACS (3) in vivo in vivo (4) DNA trans cis 1/10 (5) DNA-PNA DNA DNA DNA DNA DNA

Hagiya, Masami

348

Defective DNA-dependent protein kinase activity is linked to V(D)J recombination and DNA repair defects associated with the murine scid mutation  

Microsoft Academic Search

Murine cells homozygous for the severe combined immune deficiency mutation (scid) and V3 mutant hamster cells fall into the same complementation group and show similar defects in V(D)J recombination and DNA double-stranded break repair. Here we show that both cell types lack DNA-dependent protein kinase (DNA-PK) activity owing to defects in DNA-PKcs, the catalytic subunit of this enzyme. Furthermore, we

Tracy Blunt; Nicholas J Finnie; Guillermo E Taccioli; Graeme C. M Smith; Jocelyne Demengeot; Tanya M Gottlieb; Ryushin Mizuta; A. J Varghese; Frederick W Alt; Penny A Jeggo; Stephen P Jackson

1995-01-01

349

DNA sequencing: Clinical applications of new DNA sequencing technologies  

E-print Network

DNA sequencing: Clinical applications of new DNA sequencing technologies Frederick E. Dewey, MD1, Stanford, CA 2Department of Bioengineering, Stanford University, Stanford, CA Keywords DNA polymorphism complete sequencing of human genomes. These technological advances have facilitated a precipitous drop

Quake, Stephen R.

350

Original Article Using DNA to Test the Utility of  

E-print Network

-tailed deer (Odocoileus hemionus sitkensis) during a 3-year study (2006­2008) in 3 watersheds in southeast The Wildlife Society. KEY WORDS Alaska, DNA, fecal pellets, Odocoileus hemionus sitkensis, pellet-group counts

Ickert-Bond, Steffi

351

Complete sequence of Euglena gracilis chloroplast DNA.  

PubMed Central

We report the complete DNA sequence of the Euglena gracilis, Pringsheim strain Z chloroplast genome. This circular DNA is 143,170 bp, counting only one copy of a 54 bp tandem repeat sequence that is present in variable copy number within a single culture. The overall organization of the genome involves a tandem array of three complete and one partial ribosomal RNA operons, and a large single copy region. There are genes for the 16S, 5S, and 23S rRNAs of the 70S chloroplast ribosomes, 27 different tRNA species, 21 ribosomal proteins plus the gene for elongation factor EF-Tu, three RNA polymerase subunits, and 27 known photosynthesis-related polypeptides. Several putative genes of unknown function have also been identified, including five within large introns, and five with amino acid sequence similarity to genes in other organisms. This genome contains at least 149 introns. There are 72 individual group II introns, 46 individual group III introns, 10 group II introns and 18 group III introns that are components of twintrons (introns-within-introns), and three additional introns suspected to be twintrons composed of multiple group II and/or group III introns, but not yet characterized. At least 54,804 bp, or 38.3% of the total DNA content is represented by introns. PMID:8346031

Hallick, R B; Hong, L; Drager, R G; Favreau, M R; Monfort, A; Orsat, B; Spielmann, A; Stutz, E

1993-01-01

352

DNA Microarray Fabrication  

NSDL National Science Digital Library

In this YouTube video, created by Southwest Center for Microsystems Education (SCME), viewers are introduced to the concept of DNA microarray fabrication. Specific topics include: non-contact printing process, photolithography process and maskless photolithography process. This is the third in a series of presentations on DNA microarrays. Supporting materials can be downloaded from the SCME website.

2014-07-03

353

MICROWAVE RESONANCES IN DNA  

EPA Science Inventory

This report describes spectroscopic studies of DNA which were undertaken to better understand a physical basis for microwave absorption by this molecule. hree types of studies are described. ) The low frequency scattered light spectrum of DNA was studied by two methods. irst, Ram...

354

Exploring Structures: DNA  

NSDL National Science Digital Library

In this activity, learners create a necklace of wheat germ DNA. Learners add alcohol to wheat germ so that the DNA clumps together. Use this activity to talk about how self-assembly is a process by which molecules and cells form themselves into functional structures. Safety note: do not allow learners to ingest any of the materials!

Network, Nanoscale I.; Sciencenter

2011-01-01

355

Human Mitochondrial DNA Replication  

PubMed Central

Elucidation of the process of DNA replication in mitochondria is in its infancy. For many years, maintenance of the mitochondrial genome was regarded as greatly simplified compared to the nucleus. Mammalian mitochondria were reported to lack all DNA repair systems, to eschew DNA recombination, and to possess but a single DNA polymerase, polymerase ?. Pol? was said to replicate mitochondrial DNA exclusively via one mechanism, involving only two priming events and a handful of proteins. In this “strand-displacement model,” leading strand DNA synthesis begins at a specific site and advances approximately two-thirds of the way around the molecule before DNA synthesis is initiated on the “lagging” strand. Although the displaced strand was long-held to be coated with protein, RNA has more recently been proposed in its place. Furthermore, mitochondrial DNA molecules with all the features of products of conventional bidirectional replication have been documented, suggesting that the process and regulation of replication in mitochondria is complex, as befits a genome that is a core factor in human health and longevity. PMID:23143808

Holt, Ian J.; Reyes, Aurelio

2012-01-01

356

Translesion DNA synthesis  

PubMed Central

All living organisms are continually exposed to agents that damage their DNA, which threatens the integrity of their genome. As a consequence, cells are equipped with a plethora of DNA repair enzymes to remove the damaged DNA. Unfortunately, situations nevertheless arise where lesions persist, and these lesions block the progression of the cell’s replicase. Under these situations, cells are forced to choose between recombination-mediated “damage avoidance” pathways, or use a specialized DNA polymerase (pol) to traverse the blocking lesion. The latter process is referred to as Translesion DNA Synthesis (TLS). As inferred by its name, TLS not only results in bases being (mis)incorporated opposite DNA lesions, but also downstream of the replicase-blocking lesion, so as to ensure continued genome duplication and cell survival. Escherichia coli and Salmonella typhimurium possess five DNA polymerases, and while all have been shown to facilitate TLS under certain experimental conditions, it is clear that the LexA-regulated and damage-inducible pols II, IV and V perform the vast majority of TLS under physiological conditions. Pol V can traverse a wide range of DNA lesions and performs the bulk of mutagenic TLS, whereas pol II and pol IV appear to be more specialized TLS polymerases. PMID:25401115

Vaisman, Alexandra; McDonald, John P.; Woodgate, Roger

2014-01-01

357

Recombinant DNA for Teachers.  

ERIC Educational Resources Information Center

A science teacher describes his experience at a workshop to learn to teach the Cold Spring Harbor DNA Science Laboratory Protocols. These protocols lead students through processes for taking E. coli cells and transforming them into a new antibiotic resistant strain. The workshop featured discussions of the role of DNA recombinant technology in…

Duvall, James G., III

1992-01-01

358

Amplification of Mitochondrial DNA  

NSDL National Science Digital Library

This laboratory activity, by the Biotechnology Education and Training Sequence Investment (BETSI) project at Southwestern College, walks students and educators through the procedure of amplifying mitochondrial DNA. The first section of the activity details the actual amplifying; the second section shows the procedure for DNA analysis by gel electrophoresis once amplification is complete.

2008-08-18

359

Electrochemical DNA sensors  

Microsoft Academic Search

Electrochemistry-based sensors offer sensitivity, selectivity and low cost for the detection of selected DNA sequences or mutated genes associated with human disease. DNA-based electrochemical sensors exploit a range of different chemistries, but all take advantage of nanoscale interactions between the target in solution, the recognition layer and a solid electrode surface. Numerous approaches to electrochemical detection have been developed, including

T Gregory Drummond; Michael G Hill; Jacqueline K Barton

2003-01-01

360

The DNA methylome  

Microsoft Academic Search

Methylation of cytosines is a pervasive feature of eukaryotic genomes and an important epigenetic layer that is fundamental for cellular differentiation processes and control of transcriptional potential. DNA methylation patterns can be inherited and influenced by the environment, diet and aging, and disrupted in diseases.Complete DNA methylomes for several organisms are now available, helping clarify the evolutionary story of this

Mattia Pelizzola; Joseph R. Ecker

2011-01-01

361

Characterization of muntjac DNA  

SciTech Connect

Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange.

Davis, R.C.

1981-05-27

362

Forensic DNA databases  

Microsoft Academic Search

Genetic databases have been created in several countries: the United Kingdom was the first European country to have, in 1995, a DNA database. Subsequently, the Netherlands and Austria (1997), Germany (1998), Finland and Norway (1999) and many others have introduced or are preparing databases.Different national legal systems have conditioned the DNA databases and so there is a great heterogeneity between

Francisco Corte-Real

2004-01-01

363

Modeling DNA Replication Intermediates  

SciTech Connect

While there is now available a great deal of information on double stranded DNA from X-ray crystallography, high resolution NMR and computer modeling, very little is known about structures that are representative of the DNA core of replication intermediates. DNA replication occurs at a single strand/double strand junction and bulged out intermediates near the junction can lead to frameshift mutations. The single stranded domains are particularly challenging. Our interest is focused on strategies for modeling the DNA of these types of replication intermediates. Modeling such structures presents special problems in addressing the multiple minimum problem and in treating the electrostatic component of the force field. We are testing a number of search strategies for locating low energy structures of these types and we are also investigating two different distance dependent dielectric functions in the coulombic term of the force field. We are studying both unmodified DNA and DNA damaged by aromatic amines, carcinogens present in the environment in tobacco smoke, barbecued meats and automobile exhaust. The nature of the structure adopted by the carcinogen modified DNA at the replication fork plays a key role in determining whether the carcinogen will cause a mutation during replication that can initiate the carcinogenic process. In the present work results are presented for unmodified DNA.

Broyde, S.; Roy, D.; Shapiro, R.

1997-06-01

364

Total dissociative electron attachment cross sections for molecular constituents of DNA  

E-print Network

groups, tetrahydrofuran, 3-hydroxytetrahydrofuran, and trimethylphosphate, respectively. Cross section in DNA, and two molecules commonly used to model the deoxyribose ring, namely, tetrahydrofuran THF and 3

Simons, Jack

365

DNA Replicating Itself  

NSDL National Science Digital Library

A simplified representation of a DNA molecule separating to form two new molecules.   To reproduce, a cell must copy and transmit its genetic information (DNA) to all of its progeny. To do so, DNA replicates, following the process of semiconservative replication. Each strand of the original molecule acts as a template for the synthesis of a new complementary DNA molecule. The two strands of the double helix are first separated by enzymes. With the assistance of other enzymes, spare parts available inside the cell are bound to the individual strands following the rules of complementary base pairing: adenine (A) to thymine (T) and guanine (G) to cytosine (C). Two strands of DNA are obtained from one, having produced two daughter molecules which are identical to one another and to the parent molecule.

Excellence, Access

2005-03-12

366

Oxidative damage to 5-methylcytosine in DNA.  

PubMed Central

Exposure of pyrimidines of DNA to ionizing radiation under aerobic conditions or oxidizing agents results in attack on the 5,6 double bond of the pyrimidine ring or on the exocyclic 5-methyl group. The primary product of oxidation of the 5,6 double bond of thymine is thymine glycol, while oxidation of the 5-methyl group yields 5-hydroxymethyluracil. Oxidation of the 5,6 double bond of cytosine yields cytosine glycol, which decomposes to 5-hydroxycytosine, 5-hydroxyuracil and uracil glycol, all of which are repaired in DNA by Escherichia coli endonuclease III. We now describe the products of oxidation of 5-methylcytosine in DNA. Poly(dG-[3H]dmC) was gamma-irradiated or oxidized with hydrogen peroxide in the presence of Fe3+ and ascorbic acid. The oxidized co-polymer was incubated with endonuclease III or 5-hydroxymethyluracil-DNA glycosylase, to determine whether repairable products were formed, or digested to 2'-deoxyribonucleosides, to determine the total complement of oxidative products. Oxidative attack on 5-methylcytosine resulted primarily in formation of thymine glycol. The radiogenic yield of thymine glycol in poly(dG-dmC) was the same as that in poly(dA-dT), demonstrating that 5-methylcytosine residues in DNA were equally susceptible to radiation-induced oxidation as were thymine residues. PMID:7667100

Zuo, S; Boorstein, R J; Teebor, G W

1995-01-01

367

Structure of DNA-Functionalized Dendrimer Nanoparticles  

E-print Network

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 molecul...

Kumar, Mattaparthi Venkata Satish; 10.1039/c1sm06317k

2012-01-01

368

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

1994-01-01

369

Studying DNA in the Classroom.  

ERIC Educational Resources Information Center

Outlines a workshop for teachers that illustrates a method of extracting DNA and provides instructions on how to do some simple work with DNA without sophisticated and expensive equipment. Provides details on viscosity studies and breaking DNA molecules. (DDR)

Zarins, Silja

1993-01-01

370

Visualizing DNA What is it?  

E-print Network

Visualizing DNA #12;What is it? Gel electrophoresis is one of the techniques scientists use to look at the DNA they have. This technique separates DNA by size. #12;How does it work? First a gel is prepared. Gels

Rose, Michael R.

371

A Simply Fruity DNA Extraction  

NSDL National Science Digital Library

In this activity, learners extract DNA from a strawberry and discover that DNA is in the food they eat. Learners use simple materials to break open the cells of a strawberry and see DNA with their very own eyes.

Workshop, Mission S.

2012-01-01

372

Simple & Safe Genomic DNA Isolation.  

ERIC Educational Resources Information Center

A procedure for purifying DNA using either bacteria or rat liver is presented. Directions for doing a qualitative DNA assay using diphenylamine and a quantitative DNA assay using spectroscopy are included. (KR)

Moss, Robert; Solomon, Sondra

1991-01-01

373

DNA: Building Blocks of Nanotechnology  

E-print Network

robot- in this case termed “ DNA spiders” which can walk across a flat sheet of DNADNA walkersrobot which moves forward and turns based on preprogrammed instructions - except about 109 times smaller. The walker

Powers, Alexander

2014-01-01

374

Microsystems and Nanotechnology Group  

E-print Network

Microsystems and Nanotechnology Group Microsystems and Nanotechnology Group 1 Microsystems and Nanotechnology Research Group The University of British Columbia Microsystems and Nanotechnology Research Group The University of British Columbia Annual Report ­ 2007 Microsystems and Nanotechnology Research Group 1 About

Pulfrey, David L.

375

Molecular structure of r/GCG/d/TATACGC/ - A DNA-RNA hybrid helix joined to double helical DNA  

NASA Technical Reports Server (NTRS)

The molecule r(GCG)d(TATACGC) is self-complementary and forms two DNA-RNA hybrid segments surrounding a central region of double helical DNA; its molecular structure has been solved by X-ray analysis. All three parts of the molecule adopt a conformation which is close to that seen in the 11-fold RNA double helix. The conformation of the ribonucleotides is partly determined by water molecules bridging between the ribose O2' hydroxyl group and cytosine O2. The hybrid-DNA duplex junction contains no structural discontinuities. However, the central DNA TATA sequence has some structural irregularities.

Wang, A. H.-J.; Fujii, S.; Rich, A.; Van Boom, J. H.; Van Der Marel, G. A.; Van Boeckel, S. A. A.

1982-01-01

376

Distinct evolutionary histories of the DNA-A and DNA-B components of bipartite begomoviruses  

PubMed Central

Background Viruses of the genus Begomovirus (family Geminiviridae) have genomes consisting of either one or two genomic components. The component of bipartite begomoviruses known as DNA-A is homologous to the genomes of all geminiviruses and encodes proteins required for replication, control of gene expression, overcoming host defenses, encapsidation and insect transmission. The second component, referred to as DNA-B, encodes two proteins with functions in intra- and intercellular movement in host plants. The origin of the DNA-B component remains unclear. The study described here was initiated to investigate the relationship between the DNA-A and DNA-B components of bipartite begomoviruses with a view to unraveling their evolutionary histories and providing information on the possible origin of the DNA-B component. Results Comparative phylogenetic and exhaustive pairwise sequence comparison of all DNA-A and DNA-B components of begomoviruses demonstrates that the two molecules have very distinct molecular evolutionary histories and likely are under very different evolutionary pressures. The analysis highlights that component exchange has played a far greater role in diversification of begomoviruses than previously suspected, although there are distinct differences in the apparent ability of different groups of viruses to utilize this "sexual" mechanism of genetic exchange. Additionally we explore the hypothesis that DNA-B originated as a satellite that was captured by the monopartite progenitor of all extant bipartite begomoviruses and subsequently evolved to become the integral (essential) genome component that we recognize today. The situation with present-day satellites associated with begomoviruses provides some clues to the processes and selection pressures that may have led to the "domestication" of a wild progenitor of the DNA-B component. Conclusions The analysis has highlighted the greater genetic variation of DNA-B components, in comparison to the DNA-A components, and that component exchange is more widespread than previously demonstrated and confined to viruses from the Old World. Although the vast majority of New World and some Old World begomoviruses show near perfect co-evolution of the DNA-A and DNA-B components, this is not the case for the majority of Old World viruses. Genetic differences between Old and New World begomoviruses and the cultivation of exotic crops in the Old World are likely factors that have led to this dichotomy. PMID:20377896

2010-01-01

377

Repair of 06-Alkylguanine during DNA Synthesis in Murine Bone Marrow Hematopoietic Precursors1  

Microsoft Academic Search

O'-AIkylguanine, a DNA adduci formed by nitrosoureas, becomes the site of a point mutation during DNA synthesis by preferentially base mispairing with thymine rather than correctly base pairing with cytosine. To repair this adduct, cells contain a limited amount of 06-alkylguanine- DNA alkyltransferase (alkyltransferase), a protein which removes the alkyl group in a stoichiometric reaction. To prevent mutations, repair must

Stanton L. Gerson; Joan E. Trey; Kathleen Miller; Evan Benjamin

378

DNA as a Binary Code: How the Physical Structure of Nucleotide Bases Carries Information  

ERIC Educational Resources Information Center

The DNA triplet code also functions as a binary code. Because double-ring compounds cannot bind to double-ring compounds in the DNA code, the sequence of bases classified simply as purines or pyrimidines can encode for smaller groups of possible amino acids. This is an intuitive approach to teaching the DNA code. (Contains 6 figures.)

McCallister, Gary

2005-01-01

379

Theoretical and Experimental Investigations of DNA Open States  

E-print Network

This research is a review and assay of literature data on the properties of DNA open states. The states result from large fluctuations of a duplex and have a great influence on a wide range of biochemical processes, including electric charge transfer in DNA. A comparative analysis of kinetic and thermodynamic experimental data on DNA open states has been performed for a wide temperature range. Apparent contradictions between the data of different experiments have been explained. Based on differences in thermodynamic properties and other characteristics three different types of DNA open states have been identified; a modern definition of the term "open state" has been given. A brief review of simple mathematical models of DNA has been presented; in most of the models the state of every base pair is defined by one or two variables. The central problems of investigation of heterogeneous DNA within the approaches of the level considered are examined. The roles of every model group in experimental data interpretat...

Shigaev, A S; Lakhno, V D

2014-01-01

380

Chimeric proteins for detection and quantitation of DNA mutations, DNA sequence variations, DNA damage and DNA mismatches  

DOEpatents

Chimeric proteins having both DNA mutation binding activity and nuclease activity are synthesized by recombinant technology. The proteins are of the general formula A-L-B and B-L-A where A is a peptide having DNA mutation binding activity, L is a linker and B is a peptide having nuclease activity. The chimeric proteins are useful for detection and identification of DNA sequence variations including DNA mutations (including DNA damage and mismatches) by binding to the DNA mutation and cutting the DNA once the DNA mutation is detected.

McCutchen-Maloney, Sandra L. (Pleasanton, CA)

2002-01-01

381

What Controls DNA Looping?  

PubMed Central

The looping of DNA provides a means of communication between sequentially distant genomic sites that operate in tandem to express, copy, and repair the information encoded in the DNA base sequence. The short loops implicated in the expression of bacterial genes suggest that molecular factors other than the naturally stiff double helix are involved in bringing the interacting sites into close spatial proximity. New computational techniques that take direct account of the three-dimensional structures and fluctuations of protein and DNA allow us to examine the likely means of enhancing such communication. Here, we describe the application of these approaches to the looping of a 92 base-pair DNA segment between the headpieces of the tetrameric Escherichia coli Lac repressor protein. The distortions of the double helix induced by a second protein—the nonspecific nucleoid protein HU—increase the computed likelihood of looping by several orders of magnitude over that of DNA alone. Large-scale deformations of the repressor, sequence-dependent features in the DNA loop, and deformability of the DNA operators also enhance looping, although to lesser degrees. The correspondence between the predicted looping propensities and the ease of looping derived from gene-expression and single-molecule measurements lends credence to the derived structural picture. PMID:25167135

Perez, Pamela J.; Clauvelin, Nicolas; Grosner, Michael A.; Colasanti, Andrew V.; Olson, Wilma K.

2014-01-01

382

Structural effects of cobalt-amine compounds on DNA condensation.  

PubMed

Light scattering and electron microscopy have been used to investigate the structural effects of the trivalent complexes hexaammine cobalt (III) chloride (Cohex), tris(ethylenediamine) cobalt(III) chloride (Coen), and cobalt(III) sepulchrate chloride (Cosep) on DNA condensation. These cobalt-amine compounds have similar ligand coordination geometries but differ slightly in size. Their hydrophobicity is in the order Cosep > Coen > Cohex, according to the numbers of methylene groups in these ligands. All of these compounds effectively precipitate DNA at high concentrations; but despite a lower surface charge density, Cosep condenses DNA twice as effectively as Coen or Cohex. UV and CD measurements of the supernatants of cobalt-amine/DNA solutions reveal a preferential binding of Delta-Coen over Lambda-Coen to the precipitated DNA, but there is no chiral selectivity for Cosep. Competition experiments show that the binding strengths of these three cobalt-amine compounds to aggregated DNA are comparable. A charge neutralization of 88-90% is required for DNA condensation. Our data indicate that 1) electrostatic interaction is the main driving force for binding of multivalent cations to DNA; 2) DNA condensation is dependent on the structure of the condensing agent; and 3) the hydration pattern or polarization of water molecules on the surface of condensing agents plays an important role in DNA condensation and chiral recognition. PMID:10465766

Deng, H; Bloomfield, V A

1999-09-01

383

Comparison of genetic and physical maps of group 7 chromosomes from Triticum aestivum L  

Microsoft Academic Search

We present a high density physical map of homoeologous group 7 chromosomes from Triticum aestivum L. using a series of 54 deletion lines, 6 random amplified polymorphic DNA (RAPD) markers and 91 cDNA or genomic DNA clones from wheat, barley and oat. So far, 51 chromosome segments have been distinguished by molecular markers, and 54 homoeoloci have been allocated among

Uwe Hohmann; Takashi R. Endo; Kulvinder S. Gill; Bikram S. Gill

1994-01-01

384

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

2006-12-07

385

Studies of interaction between Safranine T and double helix DNA by spectral methods  

NASA Astrophysics Data System (ADS)

In this paper, the DNA affinity properties of Safranine T (ST), which features a phenazinyl group, were studied. The studies indicated that ST could intercalate into the stack base pairs of DNA. Intrinsic binding constants obtained by different spectral methods were consistent within experimental errors. They were of the order of 10 4 M -1 in DNA base pairs, and the binding site size was about 7 in DNA base pairs. Studies of fluorescence quenching by anionic quenchers and melting temperature of DNA all supported the intercalative binding of ST with DNA. The experiments also showed that electrostatic binding played an important role in the interaction of ST with DNA. This research offers a new intercalation functional group to DNA-targeted drug design.

Cao, Ying; He, Xi-wen

1998-06-01

386

A compendium of human mitochondrial DNA control region: development of an international standard forensic database.  

PubMed

A compendium of human mitochondrial DNA (mtDNA) control region types has been constructed. This updated compilation indexes over 10,000 population-specific mtDNA nucleotide sequences in a standardized format. The sequences represent mtDNA types from the Scientific Working Group on DNA Analysis Methods (SWGDAM) mtDNA database and from the public literature. The SWGDAM data are considered to be of higher quality than the public data, particularly for counting the number of times a particular haplotype has been observed. PMID:11387646

Miller, K W; Budowle, B

2001-06-01

387

Peripheral blood mitochondrial DNA/nuclear DNA (mtDNA/nDNA) ratio as a marker of mitochondrial toxicities of stavudine containing antiretroviral therapy in HIV-infected Malawian patients.  

PubMed

Mitochondrial toxicity is a major concern related to nucleoside reverse transcriptase inhibitors. Common manifestations are peripheral neuropathy and lipodystrophy. Depletion of mitochondria has been associated with mitochondrial dysfunction. We investigated whether mitochondria DNA (mtDNA) levels in peripheral blood can be used as biomarker of stavudine-associated mitochondrial toxicities. We enrolled 203 HIV-infected Malawian adult patients on stavudine-containing ART and 64 healthy controls of Bantu origin in a cross-sectional study. Total DNA was extracted from whole blood.The glyceraldehyde-3-phosphate dehydrogenase gene was used to estimate nuclear DNA (nDNA) levels and the ATP synthase-8 mitochondrial DNA gene to estimate mtDNA levels, from which mtDNA/nDNA ratios were determined. MtDNA subhaplogroups were established by sequencing. Among patients, peripheral neuropathy was present in 21% (43/203), lipodystrophy in 18% (20/112), elevated lactate level (>2.5 mmol/L) in 17% (19/113). Healthy controls had a higher median mtDNA/nDNA ratio when compared to HIV/AIDS patients (6.64 vs. 5.08; p=0.05), patients presenting with peripheral neuropathy (6.64 vs. 3.40, p=0.039), and patients with high lactate levels (6.64 vs. 0.68, p=0.024), respectively. Significant differences in median mtDNA/nDNA ratios were observed between patients with high and normal lactate levels (5.88 vs. 0.68, p=0.018). The median mtDNA/nDNA ratio of patients in subhaplogroup L0a2 was much lower (0.62 vs. 8.50, p=0.01) than that of those in subhaplogroup L2a. Our data indicate that peripheral blood mtDNA/nDNA ratio is a marker of mitochondrial toxicities of stavudine and is associated with elevated lactate levels and mtDNA subhaplogroups. This could open the prospect to select a substantial group of patients who will not have problematic side effects from stavudine, an affordable and effective antiretroviral drug that is being phased out in Africa due to its toxicity. PMID:24816082

Kampira, Elizabeth; Dzobo, Kevin; Kumwenda, Johnstone; van Oosterhout, Joep J; Parker, M Iqbal; Dandara, Collet

2014-07-01

388

Hibbett lab protocols for DNA isolation, PCR, and DNA sequencing.  

E-print Network

precipitate forms, spin down immediately, 5-10 min. If no DNA is seen, put at ­20 for 15+ min and then spinHibbett lab protocols for DNA isolation, PCR, and DNA sequencing. Last update June, 2003. Manfred the workflow and to streamline the sequencing process are made. Please also read the document "ABI 377 DNA

Hibbett, David S.

389

DNA chips --Integrated Chemical Circuits for DNADiagnosis and DNA computers  

E-print Network

DNA chips -- Integrated Chemical Circuits for DNADiagnosis and DNA computers Akira Suyama, Associate Professor Institute of Physics, Graduate School of Arts and Sciences, The University of Tokyo DNA chips are si l i con­ or glass­based smal l surfaces on which many DNA ol i gonuc l eotides are i

Hagiya, Masami

390

A dna-fuelled molecular machine made of dna  

Microsoft Academic Search

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 semi-conductor nanocrystals, and metal wires,. As a structural material in its own right, DNA can be used to make ordered static arrays of tiles,,

B. Yurke; A. Turberfield; A. Mills; F. Simmel; J. Neumann

2000-01-01

391

DNA Display I. Sequence-Encoded Routing of DNA Populations  

Microsoft Academic Search

Recently reported technologies for DNA-directed organic synthesis and for DNA computing rely on routing DNA populations through complex networks. The reduction of these ideas to practice has been limited by a lack of practical experimental tools. Here we describe a modular design for DNA routing genes, and routing machinery made from oligonucleotides and commercially available chromatography resins. The routing machinery

David R. Halpin; Pehr B. Harbury

2004-01-01

392

Raman spectroscopy of topotecan, an inhibitor of DNA topoisomerase I  

NASA Astrophysics Data System (ADS)

Topotecan (TPT), a water-soluble derivative of camptothecin (inhibitor of human DNA topoiomerase I), has found wide application in cancer chemotherapy. The central problem in using topotecan is the presence of lactone rings in its molecules, which undergo hydrolysis at a physiological pH yielding an inactive and even toxic form of the drug. The analysis of Raman spectra of TPT in H2O and D2O solutions made it possible to assign the spectral bands to the vibrations of particular molecular groups. Spectral features indicative of the opening of the lactone rings of the TPT molecules, deprotonation of the hydroxyl groups in their quinoline fragments, and of possible participation of the hydroxyl and carbonyl groups in H bonding are found. The data obtained are necessary to study the molecular mechanisms of TPT-DNA interaction and the formation of ternary complexes between TPT, DNA, and DNA topoisomerase I.

Mochalov, K. E.; Ustinova, O. A.; Strel'Tsov, S. A.; Grokhovskii, S. L.; Zhuze, A. L.; Nabiev, I. R.; Sukhanova, A. V.; Oleinikov, V. A.

2002-10-01

393

Group typicality, group loyalty and cognitive development.  

PubMed

Over the course of childhood, children's thinking about social groups changes in a variety of ways. Developmental Subjective Group Dynamics (DSGD) theory emphasizes children's understanding of the importance of conforming to group norms. Abrams et al.'s study, which uses DSGD theory as a framework, demonstrates the social cognitive skills underlying young elementary school children's thinking about group norms. Future research on children's thinking about groups and group norms should explore additional elements of this topic, including aspects of typicality beyond loyalty. PMID:24935627

Patterson, Meagan M

2014-09-01

394

Sparse Group Selection on Fused Lasso Components for Identifying Group-specific DNA Copy Number Variations  

E-print Network

and bladder cancer datasets, SGS-FL detected CNV regions that are more relevant to cancer, and provided latent gene in the double- stranded DNAs of human genome. Alterations of the DNAs can lead to a different

Kuang, Rui

395

Radiation of human mitochondria DNA types analyzed by restriction endonuclease cleavage patterns  

Microsoft Academic Search

Summary Human mitochondrial DNA (mtDNA) restriction endonuclease fragment patterns were analyzed using total blood cell DNA isolated from 200 individuals representing five different populations. Thirty-two fragment patterns (morphs) were observed with the enzymes Hpa I, Bam HI, Hae II, Msp I and Ava II yielding thirty-five different combinations of fragment patterns (mt DNA types). The major ethnic groups exhibit quantitative

M. J. Johnson; D. C. Wallace; S. D. Ferris; M. C. Rattazzi; L. L. Cavalli-Sforza

1983-01-01

396

Comprehensive analysis of DNA polymerase III ? subunits and their homologs in bacterial genomes  

PubMed Central

The analysis of ?2000 bacterial genomes revealed that they all, without a single exception, encode one or more DNA polymerase III ?-subunit (PolIII?) homologs. Classified into C-family of DNA polymerases they come in two major forms, PolC and DnaE, related by ancient duplication. While PolC represents an evolutionary compact group, DnaE can be further subdivided into at least three groups (DnaE1-3). We performed an extensive analysis of various sequence, structure and surface properties of all four polymerase groups. Our analysis suggests a specific evolutionary pathway leading to PolC and DnaE from the last common ancestor and reveals important differences between extant polymerase groups. Among them, DnaE1 and PolC show the highest conservation of the analyzed properties. DnaE3 polymerases apparently represent an ‘impaired’ version of DnaE1. Nonessential DnaE2 polymerases, typical for oxygen-using bacteria with large GC-rich genomes, have a number of features in common with DnaE3 polymerases. The analysis of polymerase distribution in genomes revealed three major combinations: DnaE1 either alone or accompanied by one or more DnaE2s, PolC + DnaE3 and PolC + DnaE1. The first two combinations are present in Escherichia coli and Bacillus subtilis, respectively. The third one (PolC + DnaE1), found in Clostridia, represents a novel, so far experimentally uncharacterized, set. PMID:24106089

Timinskas, K?stutis; Balvo?i?t?, Monika; Timinskas, Albertas; Venclovas, ?eslovas

2014-01-01

397

Close encounters with DNA.  

PubMed

Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field. PMID:25238560

Maffeo, C; Yoo, J; Comer, J; Wells, D B; Luan, B; Aksimentiev, A

2014-10-15

398

DNA replication and chromatin  

Microsoft Academic Search

The study of DNA replication in eukaryotic chromosomes has revealed a multitude of different regulatory levels. Nuclear and chromosomal location as well as chromatin structure may affect the activity of replication origins and their modulation during development.

Susan A Gerbi; Anja-Katrin Bielinsky

2002-01-01

399

FBI's DNA analysis program  

NASA Astrophysics Data System (ADS)

Forensic DNA profiling technology is a significant law enforcement tool due to its superior discriminating power. Applying the principles of population genetics to the DNA profile obtained in violent crime investigations results in low frequency of occurrence estimates for the DNA profile. These estimates often range from a frequency of occurrence of 1 in 50 unrelated individuals to 1 in a million unrelated individuals or even smaller. It is this power to discriminate among individuals in the population that has propelled forensic DNA technology to the forefront of forensic testing in violent crime cases. Not only is the technology extremely powerful in including or excluding a criminal suspect as the perpetrator, but it also gives rise to the potential of identifying criminal suspects in cases where the investigators of unknown suspect cases have exhausted all other available leads.

Brown, John R.

1994-03-01

400

Making DNA Fingerprints.  

ERIC Educational Resources Information Center

Presents an activity to simulate electrophoresis using everyday items. Uses adding machine paper to construct a set of DNA fingerprints that can be used to solve crime cases designed by students in any biology class. (JRH)

Nunley, Kathie F.

1996-01-01

401

Advance the DNA computing  

E-print Network

algorithms can significantly speed up computation and therefore achieve a consistently better time performance. With the given resource, these algorithms can also solve problems of a much greater size, especially as compared to existing DNA computation...

Qiu, Zhiquan Frank

2004-09-30

402

Close encounters with DNA  

NASA Astrophysics Data System (ADS)

Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.

Maffeo, C.; Yoo, J.; Comer, J.; Wells, D. B.; Luan, B.; Aksimentiev, A.

2014-10-01

403

Automating DNA processing  

E-print Network

and resources must be spent in laboratory research to determine the genetic structure of the relevant organisms. DNA processing is riddled with time intensive laboratory techniques that must be improved or replaced if genotyping large numbers of samples...

Wienen, Michael Jan

2012-06-07

404

Shear Unzipping of DNA  

E-print Network

We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder model of shear unzipping proposed earlier by deGennes [deGennes P. G. C. R. Acad. Sci., Ser. IV; Phys., Astrophys. 2001, 1505]. Using this model and a combination of analytical and numerical methods, we study the DNA "unzipping" transition when the shearing force exceeds a critical threshold at zero temperature. We also explore the effects of sequence heterogeneity and finite temperature and discuss possible applications to determine the strength of colloidal nanoparticle assemblies functionalized by DNA.

Buddhapriya Chakrabarti; David R. Nelson

2009-04-09

405

Ratchet Nanofiltration of DNA  

PubMed Central

The DNA nanofilter is a microfabricated electrophoretic separation device consisting of a periodic array of thin slits (circa 60 nm) separated by deeper wells (circa 320 nm). We demonstrate that this device can act as a tuneable, clog-free filter when operating in a low frequency, asymmetric field inversion mode. This filtration occurs by using the asymmetric field inversion to achieve bi-directional migration of short (less than 1000 bp) DNA. Moreover, similar ratchet-type operation can improve separations when compared to a constant field separation in the same device. These modes of operation enhance the utility of the DNA nanofilter as a component of integrated lab-on-a-chip devices. The experimental data confirm theoretical predictions for the bidirectional transport of DNA in entropy-based separations. PMID:23896739

Thomas, Joel D. P.; Joswiak, Mark N.; Olson, Daniel W.; Park, Sung-Gyu

2013-01-01

406

DNA vaccines and intradermal vaccination by DNA tattooing.  

PubMed

Over the past two decades, DNA vaccination has been developed as a method for the induction of immune responses. However, in spite of high expectations based on their efficacy in preclinical models, immunogenicity of first generation DNA vaccines in clinical trials was shown to be poor, and no DNA vaccines have yet been licensed for human use. In recent years significant progress has been made in the development of second generation DNA vaccines and DNA vaccine delivery methods. Here we review the key characteristics of DNA vaccines as compared to other vaccine platforms, and recent insights into the prerequisites for induction of immune responses by DNA vaccines will be discussed. We illustrate the development of second generation DNA vaccines with the description of DNA tattooing as a novel DNA delivery method. This technique has shown great promise both in a small animal model and in non-human primates and is currently under clinical evaluation. PMID:21107792

Oosterhuis, K; van den Berg, J H; Schumacher, T N; Haanen, J B A G

2012-01-01

407

Sperm DNA fragmentation in couples with unexplained recurrent spontaneous abortions.  

PubMed

The aim of the present study was to evaluate the degree of sperm DNA fragmentation in couples with idiopathic recurrent spontaneous abortion (RSA) and in those with no history of infertility or abortion. In this cohort study, 30 couples with RSA and 30 fertile couples as control group completed the demographic data questionnaires, and their semen samples were analysed according to World Health Organization (WHO) standards (September 2009-March 2010) for evaluation of sperm DNA fragmentation, using sperm chromatin dispersion (SCD) technique. The percentage of morphologically normal sperm was significantly lower in RSA patients compared with control group (51.50 ± 11.60 versus 58.00 ± 9.05, P = 0.019), but not in other parameters. Additionally, the level of abnormal DNA fragmentation in the RSA group was significantly higher than in the control group (43.3% versus 16.7%, P = 0.024). Our results indicated a negative correlation between the number of sperm with progressive motility and DNA fragmentation (r = -0.613; P < 0.001). The sperm from men with a history of RSA had a higher incidence of DNA fragmentation and poor motility than those of the control group, indicating a possible relationship between idiopathic RSA and DNA fragmentation. PMID:23278374

Khadem, N; Poorhoseyni, A; Jalali, M; Akbary, A; Heydari, S T

2014-03-01

408

Das DNA-Puzzle  

NASA Astrophysics Data System (ADS)

Im Jahre 1953 wurde von James Watson und Francis Crick erstmalig der strukturelle Aufbau der sogenannten DNA (Desoxyribonukleinsäure) beschrieben, welche das Erbgut jedes Lebewesens enthält. Der wesentliche Teil des Erbguts wird dabei durch eine sehr lange Folge der vier Basen Adenin (A), Cytosin (C), Guanin (G) und Thymin (T) codiert. Seit einigen Jahren ist es möglich, die Folge der vier Basen zu einer gegebenen DNA zu bestimmen. Biologen bezeichnen diesen Vorgang als Sequenzierung.

Kirchner, Stefan

409

Microfluidic DNA hybridization assays  

Microsoft Academic Search

DNA hybridization is one of the most powerful techniques applied in diagnostic assays. Microfluidics provides a promising\\u000a means to analyse small sample volumes, reduce reagent consumption and cost, shorten processing time as well as develop fast,\\u000a sensitive and portable diagnostic tools. By coupling with the microfluidic technology, DNA hybridization assay can achieve\\u000a high sensitivity, enhance hybridization kinetics and decrease the

Xuan WengHai; Hai Jiang; Dongqing Li

410

Elastic Correlations in Nucleosomal DNA Structure  

E-print Network

The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J. Richmond and C.A. Davey, Nature {\\bf 423}, 145 (2003)], it is shown that elastic correlations exist between twist, roll, tilt, and stretching of DNA, as well as the distance between phosphate groups. The twist-bend coupling term is shown to be able to capture these correlations to a large extent, and a fit to the experimental data yields a new estimate of G=25 nm for the value of the twist-bend coupling constant.

Farshid Mohammad-Rafiee; Ramin Golestanian

2007-01-09

411

[Staphylococcal DNA as a basis for classification].  

PubMed

The genome characterization of the typing strains for all 13 species of the genus Staphylococcus, included into the Approval List of the Names of Bacterial (1980), is presented. The nucleotide composition of DNA (28-33% of GC) did not permit the differentiation between staphylococcal species, but some of the groups of these species could be differentiated by the size of their genome (0.6-1.6 X 10(9) daltons). Differences in the degree of similarity between the nucleotide sequences of the DNA of all species (5-6% of DNA homology) made it possible to suggest raising the genus Staphylococcus to the rank of the family Staphylococcaceae fam. nov. The hypothetical classification scheme of this family is presented for discussion. PMID:3245368

Akatov, A K; Levanova, G F; Degteva, G K; Badin, V A

1988-12-01

412

Independent versus cooperative binding in polyethylenimine-DNA and Poly(L-lysine)-DNA polyplexes.  

PubMed

The mechanism of polyethylenimine-DNA and poly(L-lysine)-DNA complex formation at pH 5.2 and 7.4 was studied by a time-resolved spectroscopic method. The formation of a polyplex core was observed to be complete at approximately N/P = 2, at which point nearly all DNA phosphate groups were bound by polymer amine groups. The data were analyzed further both by an independent binding model and by a cooperative model for multivalent ligand binding to multisubunit substrate. At pH 5.2, the polyplex formation was cooperative at all N/P ratios, whereas for pH 7.4 at N/P < 0.6 the polyplex formation followed independent binding changing to cooperative binding at higher N/Ps. PMID:23941196

Ketola, Tiia-Maaria; Hanzlíková, Martina; Leppänen, Linda; Raviña, Manuela; Bishop, Corey J; Green, Jordan J; Urtti, Arto; Lemmetyinen, Helge; Yliperttula, Marjo; Vuorimaa-Laukkanen, Elina

2013-09-12

413

Independent versus Cooperative Binding in Polyethylenimine-DNA and Poly(L-lysine)-DNA Polyplexes  

PubMed Central

The mechanism of polyethylenimine–DNA and poly(L-lysine)–DNA complex formation at pH 5.2 and 7.4 was studied by a time-resolved spectroscopic method. The formation of a polyplex core was observed to be complete at approximately N/P = 2, at which point nearly all DNA phosphate groups were bound by polymer amine groups. The data were analyzed further both by an independent binding model and by a cooperative model for multivalent ligand binding to multisubunit substrate. At pH 5.2, the polyplex formation was cooperative at all N/P ratios, whereas for pH 7.4 at N/P < 0.6 the polyplex formation followed independent binding changing to cooperative binding at higher N/Ps. PMID:23941196

Ketola, Tiia-Maaria; Hanzlikova, Martina; Leppanen, Linda; Ravina, Manuela; Bishop, Corey J.; Green, Jordan J.; Urtti, Arto; Lemmetyinen, Helge; Yliperttula, Marjo; Vuorimaa-Laukkanen, Elina

2013-01-01

414

DNA biosensors that reason.  

PubMed

Despite the many designs of devices operating with the DNA strand displacement, surprisingly none is explicitly devoted to the implementation of logical deductions. The present article introduces a new model of biosensor device that uses nucleic acid strands to encode simple rules such as "IF DNA_strand(1) is present THEN disease(A)" or "IF DNA_strand(1) AND DNA_strand(2) are present THEN disease(B)". Taking advantage of the strand displacement operation, our model makes these simple rules interact with input signals (either DNA or any type of RNA) to generate an output signal (in the form of nucleotide strands). This output signal represents a diagnosis, which either can be measured using FRET techniques, cascaded as the input of another logical deduction with different rules, or even be a drug that is administered in response to a set of symptoms. The encoding introduces an implicit error cancellation mechanism, which increases the system scalability enabling longer inference cascades with a bounded and controllable signal-noise relation. It also allows the same rule to be used in forward inference or backward inference, providing the option of validly outputting negated propositions (e.g. "diagnosis A excluded"). The models presented in this paper can be used to implement smart logical DNA devices that perform genetic diagnosis in vitro. PMID:22406690

Sainz de Murieta, Iñaki; Rodríguez-Patón, Alfonso

2012-08-01

415

DNA methylation and differentiation.  

PubMed Central

The methylation of specific cytosine residues in DNA has been implicated in regulating gene expression and facilitating functional specialization of cellular phenotypes. Generally, the demethylation of certain CpG sites correlates with transcriptional activation of genes. 5-Azacytidine is an inhibitor of DNA methylation and has been widely used as a potent activator of suppressed genetic information. Treatment of cells with 5-azacytidine results in profound phenotypic alterations. The drug-induced hypomethylation of DNA apparently perturbs DNA-protein interactions that may consequently alter transcriptional activity and cell determination. The inhibitory effect of cytosine methylation may be exerted via altered DNA-protein interactions specifically or may be transduced by a change in the conformation of chromatin. Recent studies have demonstrated that cytosine methylation also plays a central role in parental imprinting, which in turn determines the differential expression of maternal and paternal genomes during embryogenesis. In other words, methylation is the mechanism whereby the embryo retains memory of the gametic origin of each component of genetic information. A memory of this type would probably persist during DNA replication and cell division as methylation patterns are stable and heritable. PMID:2466640

Michalowsky, L A; Jones, P A

1989-01-01

416

Toward larger DNA origami.  

PubMed

Structural DNA nanotechnology, and specifically scaffolded DNA origami, is rapidly developing as a versatile method for bottom-up fabrication of novel nanometer-scale materials and devices. However, lengths of conventional single-stranded scaffolds, for example, 7,249-nucleotide circular genomic DNA from the M13mp18 phage, limit the scales of these uniquely addressable structures. Additionally, increasing DNA origami size generates the cost burden of increased staple-strand synthesis. We addressed this 2-fold problem by developing the following methods: (1) production of the largest to-date biologically derived single-stranded scaffold using a ?/M13 hybrid virus to produce a 51?466-nucleotide DNA in a circular, single-stranded form and (2) inexpensive DNA synthesis via an inkjet-printing process on a chip embossed with functionalized micropillars made from cyclic olefin copolymer. We have experimentally demonstrated very efficient assembly of a 51-kilobasepair origami from the ?/M13 hybrid scaffold folded by chip-derived staple strands. In addition, we have demonstrated two-dimensional, asymmetric origami sheets with controlled global curvature such that they land on a substrate in predictable orientations that have been verified by atomic force microscopy. PMID:25179827

Marchi, Alexandria N; Saaem, Ishtiaq; Vogen, Briana N; Brown, Stanley; LaBean, Thomas H

2014-10-01

417

DNA Microarrays An R Tutorial  

E-print Network

DNA Microarrays An R Tutorial Gene Expression Analysis & R Tutorial Weigang Qiu Department Expression Analysis & R Tutorial #12;DNA Microarrays An R Tutorial Outline 1 DNA Microarrays 2 An R Tutorial Weigang Qiu Gene Expression Analysis & R Tutorial #12;DNA Microarrays An R Tutorial Functional Genomics

Qiu, Weigang

418

-DNA 1217 BK21-IT,  

E-print Network

- DNA 1217 BK21-IT, (MEC) (NRL) . . : : : : syshin@bi.snu.ac.kr ihlee@bi.snu.ac.kr btzhang@bi.snu.ac.kr 2004 9 16 2005 10 14 - DNA (DNA Sequence Design using -Multiobjective Evolutionary Algorithm) (Soo-Yong Shin) (In-Hee Lee) (Byoung-Tak Zhang) DNA

419

Recombinational DNA Repair in Bacteria  

E-print Network

Recombinational DNA Repair in Bacteria: Postreplication Kevin P Rice,University of Wisconsin Recombinational DNA repair represents the primary function for homologous DNA recombination in bacteria. Most of this repair occurs at replication forks that are stalled at sites of DNA damage. Introduction Deoxyribonucleic

Cox, Michael M.

420

DNA amplification fingerprinting of bacteria  

Microsoft Academic Search

We have amplified short arbitrary stretches of total bacterial DNA to produce highly characteristic and complex DNA fingerprints. This DNA amplification fingerprinting (DAF) strategy involves enzymatic amplification of DNA directed by a single arbitrary oligonucleotide primer. Amplification produces a characteristic spectrum of products that is adequately resolved by polyacrylamide gel electrophoresis and visualized by silver staining. Although DAF is simple

Brant J. Bassam; Gustavo Caetano-Anollés; Peter M. Gresshoff

1992-01-01

421

Functions of eukaryotic DNA polymerases.  

PubMed

A major function of DNA polymerases is to accurately replicate the six billion nucleotides that constitute the human genome. This task is complicated by the fact that the genome is constantly challenged by a variety of endogenous and exogenous DNA-damaging agents. DNA damage can block DNA replication or alter base coding potential, resulting in mutations. In addition, the accumulation of damage in nonreplicating DNA can affect gene expression, which leads to the malfunction of many cellular processes. A number of DNA repair systems operate in cells to remove DNA lesions, and several DNA polymerases are known to be the key components of these repair systems. In the past few years, a number of novel DNA polymerases have been discovered that likely function in replicative bypass of DNA damage missed by DNA repair enzymes or in specialized forms of repair. Furthermore, DNA polymerases can act as sensors in cell cycle checkpoint pathways that prevent entry into mitosis until damaged DNA is repaired and replication is completed. The list of DNA template-dependent eukaryotic DNA polymerases now consists of 14 enzymes with amazingly different properties. In this review, we discuss the possible functions of these polymerases in DNA damage repair, the replication of intact and damaged chromosomes, and cell cycle checkpoints. PMID:12844548

Shcherbakova, Polina V; Bebenek, Katarzyna; Kunkel, Thomas A

2003-02-26

422

Gallus gallus aggrecan gene-based phylogenetic analysis of selected avian taxonomic groups  

Microsoft Academic Search

Mitochondrial DNA (mtDNA) sequences remain the most widely used for phylogenetic analysis in birds. A major limitation of mtDNA sequences, however, is that mitochondria genes are inherited as a single linkage group. Here we describe the use of a 540-bp DNA sequence corresponding to the G3 domain of Gallus gallus nuclear aggrecan gene (AGC1) for phylogenetic analysis of the main

Edward J. Smith; Li Shi; Zhijian Tu

2005-01-01

423

Tyrosyl-DNA phosphodiesterase I resolves both naturally and chemically induced DNA adducts and its potential as a therapeutic target.  

PubMed

Abstract DNA is subject to a wide range of insults, resulting from endogenous and exogenous sources that need to be metabolized/resolved to maintain genome integrity. Tyrosyl-DNA phosphodiesterase I (Tdp1) is a eukaryotic DNA repair enzyme that catalyzes the removal of covalent 3'-DNA adducts. As a phospholipase D superfamily member Tdp1 utilizes two catalytic histidines each within a His-Lys-Asn motif. Tdp1 was discovered for its ability to hydrolyze the 3'-phospho-tyrosyl that in the cell covalently links DNA Topoisomerase I (Topo1) and DNA. Tdp1's list of substrates has since grown and can be divided into two groups: protein-DNA adducts, such as camptothecin stabilized Topo1-DNA adducts, and modified nucleotides, including oxidized nucleotides and chain terminating nucleoside analogs. Since many of Tdp1's substrates are generated by clinically relevant chemotherapeutics, Tdp1 became a therapeutic target for molecularly targeted small molecules. Tdp1's unique catalytic cycle allows for two different targeting strategies: (1) the intuitive inhibition of Tdp1 catalysis to prevent Tdp1-mediated repair of chemotherapeutically induced DNA adducts, thereby enhancing their toxicity and (2) stabilization of the Tdp1-DNA covalent reaction intermediate, prevents resolution of Tdp1-DNA adduct and increases the half-life of this potentially toxic DNA adduct. This concept is best illustrated by a catalytic Tdp1 mutant that forms the molecular basis of the autosomal recessive neurodegenerative disease spinocerebellar ataxia with axonal neuropathy, and results in an increased stability of its Tdp1-DNA reaction intermediate. Here, we will discuss Tdp1 catalysis from a structure-function perspective, Tdp1 substrates and Tdp1 potential as a therapeutic target. PMID:25327705

Comeaux, Evan Q; van Waardenburg, Robert C A M

2014-11-01

424

Group Cohesiveness in the Industrial Work Group.  

ERIC Educational Resources Information Center

Originally published in 1954, this investigation was designed to explore the formation of cohesiveness within work groups in an industrial setting, and the relationship of cohesiveness to productivity and to group members' mental health and adjustment. A company wide questionnaire survey, involving 228 groups totaling 5,871 workers, was made of…

Seashore, Stanley E.

425

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.

2006-01-01

426

Information Society Technologies Advisory Group Working Group  

E-print Network

Challenges to assess the future of IST technologies and their influence on European society. The group's aims1 Information Society Technologies Advisory Group Working Group "Grand Challenges in the Evolution of the Information Society" W. Wahlster (ed.) July 2004 Contents 1. Executive Summary 2. Introduction 3. Research

Wahlster, Wolfgang - Deutsche Forschungszentrum für Künstliche Intelligenz & FR 6.2

427

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.

NONE

1997-09-01

428

Twisted group algebras II  

Microsoft Academic Search

Wendel showed that norm non-increasing isomorphisms between the group algebras of locally compact groups could be expressed in terms of group characters and topological isomorphisms. His results are extended to twisted group algebras. In particular, by applying a generalisation ofWendel's main result to twisted group algebras over the same group, it is shown that the number of such algebras is

C. M. Edwards; J. T. Lewis

1969-01-01

429

Molecular dynamics simulations of DNA-polycation complexes  

NASA Astrophysics Data System (ADS)

A necessary step in the preparation of DNA for use in gene therapy is the packaging of DNA with a vector that can condense DNA and provide protection from degrading enzymes. Because of the immunoresponses caused by viral vectors, there has been interest in developing synthetic gene therapy vectors, with polycations emerging as promising candidates. Molecular dynamics simulations of the DNA duplex CGCGAATTCGCG in the presence of 20 monomer long sequences of the polycations, poly-L-lysine (PLL) and polyethyleneimine (PEI), with explicit counterions and TIP3P water, are performed to provide insight into the structure and formation of DNA polyplexes. After an initial separation of approximately 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 upon complexation and remains in the B-form. In the formed complex, the charged amine groups of the polycation mainly interact with DNA phosphate groups, and rarely occupy electronegative sites in either the major or minor grooves. Differences between complexation with PEI and PLL will be discussed.

Ziebarth, Jesse; Wang, Yongmei

2008-03-01

430

Energy and Technology Review: Unlocking the mysteries of DNA repair  

SciTech Connect

DNA, the genetic blueprint, has the remarkable property of encoding its own repair following diverse types of structural damage induced by external agents or normal metabolism. We are studying the interplay of DNA damaging agents, repair genes, and their protein products to decipher the complex biochemical pathways that mediate such repair. Our research focuses on repair processes that correct DNA damage produced by chemical mutagens and radiation, both ionizing and ultraviolet. The most important type of DNA repair in human cells is called excision repair. This multistep process removes damaged or inappropriate pieces of DNA -- often as a string of 29 nucleotides containing the damage -- and replaces them with intact ones. We have isolated, cloned, and mapped several human repair genes associated with the nucleotide excision repair pathway and involved in the repair of DNA damage after exposure to ultraviolet light or mutagens in cooked food. We have shown that a defect in one of these repair genes, ERCC2, is responsible for the repair deficiency in one of the groups of patients with the recessive genetic disorder xeroderma pigmentosum (XP group D). We are exploring ways to purify sufficient quantities (milligrams) of the protein products of these and other repair genes so that we can understand their functions. Our long-term goals are to link defective repair proteins to human DNA repair disorders that predispose to cancer, and to produce DNA-repair-deficient mice that can serve as models for the human disorders.

Quirk, W.A.

1993-04-01

431

Single Nucleotide Polymorphism Analysis of European Archaeological M. leprae DNA  

PubMed Central

Background Leprosy was common in Europe eight to twelve centuries ago but molecular confirmation of this has been lacking. We have extracted M. leprae ancient DNA (aDNA) from medieval bones and single nucleotide polymorphism (SNP) typed the DNA, this provides insight into the pattern of leprosy transmission in Europe and may assist in the understanding of M. leprae evolution. Methods and Findings Skeletons have been exhumed from 3 European countries (the United Kingdom, Denmark and Croatia) and are dated around the medieval period (476 to 1350 A.D.). we tested for the presence of 3 previously identified single nucleotide polymorphisms (SNPs) in 10 aDNA extractions. M. leprae aDNA was extracted from 6 of the 10 bone samples. SNP analysis of these 6 extractions were compared to previously analysed European SNP data using the same PCR assays and were found to be the same. Testing for the presence of SNPs in M. leprae DNA extracted from ancient bone samples is a novel approach to analysing European M. leprae DNA and the findings concur with the previously published data that European M. leprae strains fall in to one group (SNP group 3). Conclusions These findings support the suggestion that the M. leprae genome is extremely stable and show that archaeological M. leprae DNA can be analysed to gain detailed information about the genotypic make-up of European leprosy, which may assist in the understanding of leprosy transmission worldwide. PMID:19847306

Watson, Claire L.; Lockwood, Diana N. J.

2009-01-01

432

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. PMID:21095241

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.

2010-01-01

433

DNA Knots: Theory and Experiments  

NASA Astrophysics Data System (ADS)

Cellular DNA is a long, thread-like molecule with remarkably complex topology. Enzymes that manipulate the geometry and topology of cellular DNA perform many vital cellular processes (including segregation of daughter chromosomes, gene regulation, DNA repair, and generation of antibody diversity). Some enzymes pass DNA through itself via enzyme-bridged transient breaks in the DNA; other enzymes break the DNA apart and reconnect it to different ends. In the topological approach to enzymology, circular DNA is incubated with an enzyme, producing an enzyme signature in the form of DNA knots and links. By observing the changes in DNA geometry (supercoiling) and topology (knotting and linking) due to enzyme action, the enzyme binding and mechanism can often be characterized. This paper will discuss some personal research history, and the tangle model for the analysis of site-specific recombination experiments on circular DNA.

Sumners, D. W.

434

Defects of mitochondrial DNA replication.  

PubMed

Mitochondrial DNA is replicated by DNA polymerase ? in concert with accessory proteins such as the mitochondrial DNA helicase, single-stranded DNA binding protein, topoisomerase, and initiating factors. Defects in mitochondrial DNA replication or nucleotide metabolism can cause mitochondrial genetic diseases due to mitochondrial DNA deletions, point mutations, or depletion, which ultimately cause loss of oxidative phosphorylation. These genetic diseases include mitochondrial DNA depletion syndromes such as Alpers or early infantile hepatocerebral syndromes, and mitochondrial DNA deletion disorders, such as progressive external ophthalmoplegia, ataxia-neuropathy, or mitochondrial neurogastrointestinal encephalomyopathy. This review focuses on our current knowledge of genetic defects of mitochondrial DNA replication (POLG, POLG2, C10orf2, and MGME1) that cause instability of mitochondrial DNA and mitochondrial disease. PMID:24985751

Copeland, William C

2014-09-01

435

Study on the relation between occupational fenvalerate exposure and spermatozoa DNA damage of pesticide factory workers  

PubMed Central

Aims: To determine sperm nuclear DNA integrity and to investigate the relation between fenvalerate (FE) exposure and spermatozoa DNA damage. Methods: Sperm DNA fragmentation was detected by a modified alkaline single cell gel electrophoresis (Comet) assay and a terminal deoxynucleotidyl transferase mediated dUTP nick end labelling (TUNEL) assay. The olive tail moment (OTM) and percentage tail DNA were measured by the Comet assay, and cell positive percentage was measured by the TUNEL assay for DNA damage evaluation. Results: The DNA integrity of spermatozoa of external and internal control groups were both significantly greater than that of the FE exposed group. The median value of tail DNA percentage in the exposure group was 11.30, which was significantly higher than 5.60 in the internal control group and 5.10 in the external control group. The median value of OTM was 3.80 in the exposure group, significantly higher than 1.50 in the internal control group and 2.00 in the external control group. Mean cell positive was 31.2% in the exposure group, significantly higher than 17.4% in the internal control and 19.6% in the external control groups. Cell positive (%) was significantly correlated with tail DNA percentage and with OTM of whole subjects (n = 63). Conclusions: Results showed that occupational FE exposure is associated with an increase in sperm DNA damage. A combination of the Comet and TUNEL assays would offer more comprehensive information for a better understanding of sperm DNA damage, and the biological significance of sperm DNA damage in sperm function and male infertility. PMID:15550606

Bian, Q; Xu, L; Wang, S; Xia, Y; Tan, L; Chen, J; Song, L; Chang, H; Wang, X

2004-01-01

436

Oxidative DNA Damage in Blood of CVD Patients Taking Detralex  

PubMed Central

The main goal of the work reported here was to determine the degree of oxidative/alkali-labile DNA damages in peripheral blood as well as in the blood stasis from varicose vein of (chronic venous disorder) CVD patients. Moreover, determination of the impact of Detralex usage on the level of (oxidative) DNA damages in CVD patients was evaluated as well. The degree of oxidative DNA damages was studied in a group consisted of thirty patients with diagnosed chronic venous insufficiency (CVI) in the 2nd and 3rd degree, according to clinical state, etiology, anatomy and pathophysiology (CEAP), and qualified to surgical procedure. The control group consisted of normal volunteers (blood donors) qualified during standard examinations at Regional Centers of Blood Donation and Blood Therapy. The comet assay was used for determination of DNA damages. Analyses of the obtained results showed increase in the level of oxidative/alkali-labile DNA damages in lymphocytes originating from antebrachial blood of CVD patients as compared to the control group (Control) (p < 0.002; ANOVA). In addition, it was demonstrated that the usage of Detralex® resulted in decrease of the level of oxidative/alkali-labile DNA damages in CVD patients as compared to patients without Detralex® treatment (p < 0.001; ANOVA). Based on findings from the study, it may be hypothesized about occurrence of significant oxidative DNA damages as the consequence of strong oxidative stress in CVD. In addition, antioxidative effectiveness of Detralexu® was observed at the recommended dose, one tablet twice daily. PMID:21912579

Krzysciak, Wirginia; Cierniak, Agnieszka; Kozka, Mariusz; Koziel, Joanna

2011-01-01

437

DNA-catalyzed lysine side chain modification.  

PubMed

Catalyzing the covalent modification of aliphatic amino groups, such as the lysine (Lys) side chain, by nucleic acids has been challenging to achieve. Such catalysis will be valuable, for example, for the practical preparation of Lys-modified proteins. We previously reported the DNA-catalyzed modification of the tyrosine and serine hydroxy side chains, but Lys modification has been elusive. Herein, we show that increasing the reactivity of the electrophilic reaction partner by using 5'-phosphorimidazolide (5'-Imp) rather than 5'-triphosphate (5'-ppp) enables the DNA-catalyzed modification of Lys in a DNA-anchored peptide substrate. The DNA-catalyzed reaction of Lys with 5'-Imp is observed in an architecture in which the nucleophile and electrophile are not preorganized. In contrast, previous efforts showed that catalysis was not observed when Lys and 5'-ppp were used in a preorganized arrangement. Therefore, substrate reactivity is more important than preorganization in this context. These findings will assist ongoing efforts to identify DNA catalysts for reactions of protein substrates at lysine side chains. PMID:24981820

Brandsen, Benjamin M; Velez, Tania E; Sachdeva, Amit; Ibrahim, Nora A; Silverman, Scott K

2014-08-18

438

Forensic DNA profiling and database.  

PubMed

The incredible power of DNA technology as an identification tool had brought a tremendous change in crimnal justice . DNA data base is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. This article discusses the essential steps in compilation of COmbined DNA