Structural basis for uracil DNA glycosylase interaction with uracil: NMR study.

abstract：:Biological networks are a topic of great current interest, particularly with the publication of a number of large genome-wide interaction datasets. They are globally characterized by a variety of graph-theoretic statistics, such as the degree distribution, clustering coefficient, characteristic path length and diamete...

journal_title：Nucleic acids research

authors： Yu H,Zhu X,Greenbaum D,Karro J,Gerstein M

更新日期：2004-01-14 00:00:00

abstract：:The hexametric T7 helicase (gp4) adopts a spiral lock-washer form and encircles a coil-like DNA (tracking) strand with two nucleotides bound to each subunit. However, the chemo-mechanical coupling mechanism in unwinding has yet to be elucidated. Here, we utilized nanotensioner-enhanced Förster resonance energy transfe...

journal_title：Nucleic acids research

authors： Ma JB,Chen Z,Xu CH,Huang XY,Jia Q,Zou ZY,Mi CY,Ma DF,Lu Y,Zhang HD,Li M

更新日期：2020-04-06 00:00:00

abstract：:SynergyFinder (https://synergyfinder.fimm.fi) is a stand-alone web-application for interactive analysis and visualization of drug combination screening data. Since its first release in 2017, SynergyFinder has become a widely used web-tool both for the discovery of novel synergistic drug combinations in pre-clinical mo...

journal_title：Nucleic acids research

authors： Ianevski A,Giri AK,Aittokallio T

更新日期：2020-07-02 00:00:00

abstract：:We have isolated genomic clones from Xenopus borealis representing 3 different types of histone gene cluster. We show that the major type (H1, H2B, H2A, H4, H3), present at about 60-70 copies per haploid genome (1), is tandemly reiterated with a repeat length of 15 kb. In situ hybridization to mitotic chromosomes show...

journal_title：Nucleic acids research

authors： Turner PC,Bagenal EB,Vlad MT,Woodland HR

更新日期：1988-04-25 00:00:00

abstract：:A single-helical B-type geometry is presented based on 1H NMR observations on d(TATA) and several other small single-helical DNA fragments. The structure is extended to one complete turn of double-helical DNA and its characteristics are compared with other known B-type structures. ...

journal_title：Nucleic acids research

authors： Mellema JR,van Kampen PN,Carlson CN,Bosshard HE,Altona C

更新日期：1983-05-11 00:00:00

abstract：:Transfer RNAGlu4 was isolated from Drosophila melanogaster by affinity chromatography. The tRNA was iodinated "in vitro" with Na[25I] and hybridized "in situ" to salivary gland chromosomes from Drosophila. Subsequent autoradiography allowed the localization of the genes for tRNAGlu4 to the right arm of the second chro...

journal_title：Nucleic acids research

authors： Kubli E,Schmidt T

更新日期：1978-05-01 00:00:00

abstract：:Two dimensional PEI-cellulose thin layer chromatography can resolve sequentially degraded oligonucleotide fragments of tRNA. This technique entails the sequential degradation of the oligonucleotide with snake venom phosphodiesterase in the presence of bacterial alkaline phosphatase, and periodate oxidation followed by...

journal_title：Nucleic acids research

authors： Chen EY,Roe BA

更新日期：1977-10-01 00:00:00

abstract：:Human MitBASE is a database collecting human mtDNA variants. This database is part of a greater mitochondrial genome database (MitBASE) funded within the EU Biotech Program. The present paper reports the recent improvements in data structure, data quality and data quantity. As far as the database structure is concerne...

journal_title：Nucleic acids research

authors： Attimonelli M,Cooper JM,D'Elia D,de Montalvo A,De Robertis M,Lehväslaiho H,Malladi SB,Memeo F,Stevens K,Schapira AH,Saccone C

更新日期：1999-01-01 00:00:00

abstract：:In order to characterize structure-function relationships, the kinetic behavior of chimeric RNA/DNA ribozyme was compared with that of all RNA ribozyme. Determined kcat values were proven to represent the chemical-cleavage step and not the product-dissociation step. In agreement with the finding by Dahm and Uhlenbeck ...

journal_title：Nucleic acids research

authors： Sawata S,Shimayama T,Komiyama M,Kumar PK,Nishikawa S,Taira K

更新日期：1993-12-11 00:00:00

abstract：:The nucleotide sequence of the promoter region and the first five genes of the atp (or unc) operon of Escherichia coli has been determined. The first proposed gene in the operon contains four AUA codons and may be poorly expressed; it encodes a basic but yet hydrophobic protein which could function as a pilot protein ...

journal_title：Nucleic acids research

authors： Gay NJ,Walker JE

更新日期：1981-08-25 00:00:00

abstract：:We have sequenced mouse tRNA genes from two recombinant lambda phage. An 1800 bp sequence from one phage contains 3 tRNA genes, potentially encoding tRNAAsp, tRNAGly, and tRNAGlu, separated by spacer sequences of 587 bp and 436 bp, respectively. The mouse tRNA gene cluster is homologous to a rat sequence (Sekiya et al...

journal_title：Nucleic acids research

authors： Looney JE,Harding JD

更新日期：1983-12-20 00:00:00

abstract：:Splicing of mammalian introns requires that the intron possess at least 80 nucleotides. This length requirement presumably reflects the constraints of accommodating multiple snRNPs simultaneously in the same intron. In the free-living nematode, C. elegans, introns typically are 45 to 55 nucleotides in length. In this ...

journal_title：Nucleic acids research

authors： Ogg SC,Anderson P,Wickens MP

更新日期：1990-01-11 00:00:00

abstract：:We describe a rapid fluorescence indicator displacement assay (R-FID) to evaluate the affinity and the selectivity of compounds binding to different DNA structures. We validated the assay using a library of 30 well-known nucleic acid binders containing a variety chemical scaffolds. We used a combination of principal c...

journal_title：Nucleic acids research

authors： Del Villar-Guerra R,Gray RD,Trent JO,Chaires JB

更新日期：2018-04-20 00:00:00

abstract：:ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy datab...

journal_title：Nucleic acids research

authors： Brozovic M,Dantec C,Dardaillon J,Dauga D,Faure E,Gineste M,Louis A,Naville M,Nitta KR,Piette J,Reeves W,Scornavacca C,Simion P,Vincentelli R,Bellec M,Aicha SB,Fagotto M,Guéroult-Bellone M,Haeussler M,Jacox E,Lowe

更新日期：2018-01-04 00:00:00

abstract：:The last few years have witnessed significant changes in Pfam (https://pfam.xfam.org). The number of families has grown substantially to a total of 17,929 in release 32.0. New additions have been coupled with efforts to improve existing families, including refinement of domain boundaries, their classification into Pfa...

journal_title：Nucleic acids research

authors： El-Gebali S,Mistry J,Bateman A,Eddy SR,Luciani A,Potter SC,Qureshi M,Richardson LJ,Salazar GA,Smart A,Sonnhammer ELL,Hirsh L,Paladin L,Piovesan D,Tosatto SCE,Finn RD

更新日期：2019-01-08 00:00:00

abstract：:A method to purify histone groups H2A+H2B and H3+H4 using dissociation with NaCl and hydroxylapatite chromatography is presented. The procedure is simple, involves mild solvents, and provides milligram quantities of histones of high purity. The histone pairs prepared by this method can regenerate chromatin-like charac...

journal_title：Nucleic acids research

authors： Simon RH,Felsenfeld G

更新日期：1979-02-01 00:00:00

abstract：:The transactivator responsive region (TAR) present in the 5'-NTR of the HIV-1 genome represents a potential target for antiretroviral intervention and a model system for the development of specific inhibitors of RNA-protein interaction. Earlier, we have shown that an anti-TAR polyamide nucleotide analog (PNA(TAR)) con...

journal_title：Nucleic acids research

authors： Tripathi S,Chaubey B,Ganguly S,Harris D,Casale RA,Pandey VN

更新日期：2005-08-02 00:00:00

abstract：:Polymers of random 14 mer oligonucleotides are shown to detect discrete loci in the human genome. Eighteen different synthetic tandem repeats of random 14 base-pair units (STRs) have been generated and all of them turn out to detect polymorphic loci on southern blots of human DNA samples, presumably corresponding to a...

journal_title：Nucleic acids research

authors： Vergnaud G

更新日期：1989-10-11 00:00:00

abstract：:The triphosphate of the nucleoside deoxyribosyl dihydropyrimido[4,5-c][1,2]oxazin-7-one (dP) is known to be incorporated into DNA efficiently by Taq polymerase and is a useful tool for polymerase-mediated in vitro mutagenesis. It is shown here that dP is a potent mutagen in Escherichia coli and Salmonella typhimurium ...

journal_title：Nucleic acids research

authors： Negishi K,Williams DM,Inoue Y,Moriyama K,Brown DM,Hayatsu H

更新日期：1997-04-15 00:00:00

abstract：:The HAMSTeRS WWW site was set up in 1996 in order to facilitate easy access to, and aid understanding of, the causes of haemophilia A at the molecular level; previously, the first and second text editions of the database have been published in Nucleic Acids Research. This report describes the facilities originally ava...

journal_title：Nucleic acids research

authors： Kemball-Cook G,Tuddenham EG

更新日期：1997-01-01 00:00:00

abstract：:The comprehensive multiplatform genomics data generated by The Cancer Genome Atlas (TCGA) Research Network is an enabling resource for cancer research. It includes an unprecedented amount of microRNA sequence data: ~11 000 libraries across 33 cancer types. Combined with initiatives like the National Cancer Institute G...

journal_title：Nucleic acids research

authors： Chu A,Robertson G,Brooks D,Mungall AJ,Birol I,Coope R,Ma Y,Jones S,Marra MA

更新日期：2016-01-08 00:00:00

abstract：:The human immunodeficiency virus (HIV) and other retroviruses show extensive genomic variation, which is primarily due to error-prone replication by the viral reverse transcriptase (RT) enzymes. RT errors include misincorporation with subsequent extension of the mismatched terminal base, and extension of realigned pri...

journal_title：Nucleic acids research

authors： Das AT,Berkhout B

更新日期：1995-04-25 00:00:00

abstract：:Helicobacter pylori is a Gram-negative bacterium that colonizes human stomach and causes gastric inflammation. The species is naturally competent and displays remarkable diversity. The presence of a large number of restriction-modification (R-M) systems in this bacterium creates a barrier against natural transformatio...

journal_title：Nucleic acids research

authors： Dwivedi GR,Sharma E,Rao DN

更新日期：2013-03-01 00:00:00

abstract：:Mitochondrial transcription factor A (mtTFA/TFAM) is a nucleus-encoded, high-mobility-group-box (HMG-box) protein that regulates transcription of the mitochondrial genome by specifically recognizing light-strand and heavy-strand promoters (LSP, HSP1). TFAM also binds mitochondrial DNA in a non-sequence specific (NSS) ...

journal_title：Nucleic acids research

authors： Malarkey CS,Bestwick M,Kuhlwilm JE,Shadel GS,Churchill ME

更新日期：2012-01-01 00:00:00

abstract：:Patients with Alzheimer's disease (AD) exhibit higher levels of 8-oxo-guanine (8-oxoG) DNA lesions in their brain, suggesting a reduced or defective 8-oxoG repair. To test this hypothesis, this study investigated 14 AD patients and 10 age-matched controls for mutations of the major 8-oxoG removal gene OGG1. Whereas no...

journal_title：Nucleic acids research

authors： Mao G,Pan X,Zhu BB,Zhang Y,Yuan F,Huang J,Lovell MA,Lee MP,Markesbery WR,Li GM,Gu L

更新日期：2007-01-01 00:00:00

abstract：:Sug1 and Sug2 are two of six ATPases in the 19S regulatory particle of the 26S proteasome. We have shown previously that these proteins play a non-proteolytic role in the transcription of the GAL genes in yeast. In this study, we probe the requirement for these factors in stress-induced transcription in yeast. It is k...

journal_title：Nucleic acids research

authors： Sulahian R,Sikder D,Johnston SA,Kodadek T

更新日期：2006-03-03 00:00:00

abstract：:Extensive research has characterized distinct exogenous RNAi pathways interfering in gene expression during vegetative growth of the unicellular model ciliate Paramecium. However, role of RNAi in endogenous transcriptome regulation, and environmental adaptation is unknown. Here, we describe the first genome-wide profi...

journal_title：Nucleic acids research

authors： Karunanithi S,Oruganti V,Marker S,Rodriguez-Viana AM,Drews F,Pirritano M,Nordström K,Simon M,Schulz MH

更新日期：2019-09-05 00:00:00

abstract：:A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized in the space group I4(1)22 with the unit-cell dimensions a = b = 53.4 A and c = 54.0 A, and the crystal structure has been determined at 2.5 A resolution. The four nucleotide residues CGAA of the first half o...

journal_title：Nucleic acids research

authors： Sunami T,Kondo J,Kobuna T,Hirao I,Watanabe K,Miura K,Takénaka A

更新日期：2002-12-01 00:00:00

abstract：:A cDNA clone which expresses a protein that cross-reacts immunologically with the human C1 and C2 hnRNP core proteins has been isolated. The clone was selected by a sensitive immunochemical assay employing an avidin-biotin complex for detection, and identified as a clone for the hnRNP C proteins by a highly sensitive ...

journal_title：Nucleic acids research

authors： Lahiri DK,Thomas JO

更新日期：1986-05-27 00:00:00

abstract：:Gene finding is complicated in organisms that exhibit insertional RNA editing. Here, we demonstrate how our new algorithm Predictor of Insertional Editing (PIE) can be used to locate genes whose mRNAs are subjected to multiple frameshifting events, and extend the algorithm to include probabilistic predictions for site...

journal_title：Nucleic acids research

authors： Gott JM,Parimi N,Bundschuh R

更新日期：2005-09-07 00:00:00