Nucleosomes undergo slow spontaneous gaping.

abstract：:The yeast protein Rrf1p encoded by the FIL1 nuclear gene bears significant sequence similarity to Escherichia coli ribosome recycling factor (RRF). Here, we call FIL1 Ribosome Recycling Factor of yeast, RRF1. Its gene product, Rrf1p, was localized in mitochondria. Deletion of RRF1 leads to a respiratory incompetent ph...

journal_title：Nucleic acids research

authors： Teyssier E,Hirokawa G,Tretiakova A,Jameson B,Kaji A,Kaji H

更新日期：2003-07-15 00:00:00

abstract：:Human ADAR3 is a catalytically inactive member of the Adenosine Deaminase Acting on RNA (ADAR) protein family, whose active members catalyze A-to-I RNA editing in metazoans. Until now, the reasons for the catalytic incapability of ADAR3 has not been defined and its biological function rarely explored. Yet, its exclusi...

journal_title：Nucleic acids research

authors： Wang Y,Chung DH,Monteleone LR,Li J,Chiang Y,Toney MD,Beal PA

更新日期：2019-11-18 00:00:00

abstract：:Actinomycin D (ActD) is a small molecule with strong antibiotic and anticancer activity. However, its biologically relevant DNA-binding mechanism has never been resolved, with some studies suggesting that the primary binding mode is intercalation, and others suggesting that single-stranded DNA binding is most importan...

journal_title：Nucleic acids research

authors： Paramanathan T,Vladescu I,McCauley MJ,Rouzina I,Williams MC

更新日期：2012-06-01 00:00:00

abstract：:Residual dipolar coupling (RDC) represents one of the most exciting emerging NMR techniques for protein structure studies. However, solving a protein structure using RDC data alone is still a highly challenging problem. We report here a computer program, RDC-PROSPECT, for protein structure prediction based on a struct...

journal_title：Nucleic acids research

authors： Qu Y,Guo JT,Olman V,Xu Y

更新日期：2004-01-26 00:00:00

abstract：:We have constructed simple test-plasmids to study transcriptional enhancers in yeast. In this paper the reporter-gene is a plasmid borne deletion-substitution derivative (his-del4) of the Saccharomyces cerevisiae HIS3 gene in which the native promoter has been replaced by a dormant, susceptible pseudopromoter. We inve...

journal_title：Nucleic acids research

authors： Ciaramella M,Sacco M,Pulitzer JF

更新日期：1988-09-26 00:00:00

abstract：:The single nucleotide polymorphisms (SNPs) in conserved protein regions have been thought to be strong candidates that alter protein functions. Thus, we have developed SNP@Domain, a web resource, to identify SNPs within human protein domains. We annotated SNPs from dbSNP with protein structure-based as well as sequenc...

journal_title：Nucleic acids research

authors： Han A,Kang HJ,Cho Y,Lee S,Kim YJ,Gong S

更新日期：2006-07-01 00:00:00

abstract：:PSF (a.k.a. SFPQ) is a ubiquitously expressed, essential nuclear protein with important roles in DNA damage repair and RNA biogenesis. In stimulated T cells, PSF binds to and suppresses the inclusion of CD45 exon 4 in the final mRNA; however, in resting cells, TRAP150 binds PSF and prevents access to the CD45 RNA, tho...

journal_title：Nucleic acids research

authors： Yarosh CA,Tapescu I,Thompson MG,Qiu J,Mallory MJ,Fu XD,Lynch KW

更新日期：2015-10-15 00:00:00

abstract：:Cadmium (Cd2+) is a known carcinogen that inactivates the DNA mismatch repair (MMR) pathway. In this study, we have tested the effect of Cd2+ exposure on the enzymatic activity of the mismatch binding complex MSH2-MSH6. Our results indicate that Cd2+ is highly inhibitory to the ATP binding and hydrolysis activities of...

journal_title：Nucleic acids research

authors： Banerjee S,Flores-Rozas H

更新日期：2005-03-03 00:00:00

abstract：:A detailed scheme of the Peptidyl Transferase Centre of bacterial ribosomes is proposed by summarizing the literature data on the substrate specificity of the acceptor and donor sites. According to the proposed scheme only the elements of the donor and acceptor having a stable structure bind with the ribosome. The pre...

journal_title：Nucleic acids research

authors： Krayevsky AA,Kukhanova MK,Gottikh BP

更新日期：1975-12-01 00:00:00

abstract：:Archaeal family-B DNA polymerases bind tightly to deaminated bases and stall replication on encountering uracil in template strands, four bases ahead of the primer-template junction. Should the polymerase progress further towards the uracil, for example, to position uracil only two bases in front of the junction, 3'-5...

journal_title：Nucleic acids research

authors： Richardson TT,Wu X,Keith BJ,Heslop P,Jones AC,Connolly BA

更新日期：2013-02-01 00:00:00

abstract：:We recently identified a region of preferential replication initiation, oriGNAI3, near the 3' end of the Chinese hamster GNAI3 gene. oriGNAI3 is co-amplified in mutants selected for AMPD2 amplification, a process generating chromosomal rearrangements. In this report we have taken advantage of cell lines with truncated...

journal_title：Nucleic acids research

authors： Toledo F,Lachagès AM,Mayau V,Debatisse M

更新日期：1999-04-01 00:00:00

abstract：:Yeast tRNA Lys2 codes preferentially for AAA and contains a 2-thiouridine derivative (U) at the 5'-position of the anticodon. Removal of the 2-thio group from U by treatment with CNBr did not affect the amino acid accepting activity of the modified tRNA Lys2. CNBr treated tRNA Lys2 was active in protein synthesis but ...

journal_title：Nucleic acids research

authors： Sen GC,Ghosh HP

更新日期：1976-03-01 00:00:00

abstract：:The nucleotide sequence of Drosophila melanogaster tRNA 5 Lys is pGCCCGGAUAm2GCUCAGDCGGDAGAGCA psi psi GGACUsU*UUt6A*A psi CCAAGGm7GDm5CCAGGGTm psi CAm1AGUCCCUGUUCGGGCGCCA. The sU* is probably 5-methylcarboxymethyl-2-thiouridine and t6A* is a mixture of modified derivatives of t6A including t6A itself and a component ...

journal_title：Nucleic acids research

authors： Cribbs DL,Gillam IC,Tener GM

更新日期：1982-10-25 00:00:00

abstract：:A highly sensitive method to detect traces of aldehyde-containing apurinic/apyrimidinic (AP) sites in nucleic acids has been developed. Based on this method, a novel approach to detect DNA base mismatches recognized by the mismatch repair glycosylase MutY is demonstrated. Open chain aldehydes generated in nucleic acid...

journal_title：Nucleic acids research

authors： Maulik G,Botchway S,Chakrabarti S,Tetradis S,Price B,Makrigiorgos GM

更新日期：1999-03-01 00:00:00

abstract：:Telomerase is a ribonucleoprotein reverse transcriptase that synthesizes and maintains telomeric DNA. Studies of telomeres and telomerase are facilitated by the large number of linear DNA molecules found in ciliated protozoa, such as Tetrahymena thermophila. To examine the expression of telomerase, we investigated the...

journal_title：Nucleic acids research

authors： Hargrove BW,Bhattacharyya A,Domitrovich AM,Kapler GM,Kirk K,Shippen DE,Kunkel GR

更新日期：1999-11-01 00:00:00

abstract：:Despite the increasing wealth of available data, the structure of cancer transcriptional space remains largely unknown. Analysis of this space would provide novel insights into the complexity of cancer, assess relative implications in complex biological processes and responses, evaluate the effectiveness of cancer mod...

journal_title：Nucleic acids research

authors： Gadaleta E,Cutts RJ,Kelly GP,Crnogorac-Jurcevic T,Kocher HM,Lemoine NR,Chelala C

更新日期：2011-10-01 00:00:00

abstract：:Deletion of Hop2 in mice eliminates homologous chromosome synapsis and disrupts double-strand break (DSB) repair through homologous recombination. HOP2 in vitro shows two distinctive activities: when it is incorporated into a HOP2-MND1 complex it stimulates DMC1 and RAD51 recombination activities and the purified HOP2...

journal_title：Nucleic acids research

authors： Pezza RJ,Voloshin ON,Volodin AA,Boateng KA,Bellani MA,Mazin AV,Camerini-Otero RD

更新日期：2014-02-01 00:00:00

abstract：:Translation regulation plays an important role in eukaryotic gene expression. Upstream open reading frames (uORFs) are potent regulatory elements located in 5' mRNA transcript leaders. Translation of uORFs usually inhibit the translation of downstream main open reading frames, but some enhance expression. While a mino...

journal_title：Nucleic acids research

authors： Lin Y,May GE,Kready H,Nazzaro L,Mao M,Spealman P,Creeger Y,McManus CJ

更新日期：2019-09-26 00:00:00

abstract：:Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) ...

journal_title：Nucleic acids research

authors： Wu X,Kim TK,Baxter D,Scherler K,Gordon A,Fong O,Etheridge A,Galas DJ,Wang K

更新日期：2017-12-01 00:00:00

abstract：:Abasic sites are common DNA lesions resulting from spontaneous depurination and excision of damaged nucleobases by DNA repair enzymes. However, the influence of the local sequence context on the structure of the abasic site and ultimately, its recognition and repair, remains elusive. In the present study, duplex DNAs ...

journal_title：Nucleic acids research

authors： Chen J,Dupradeau FY,Case DA,Turner CJ,Stubbe J

更新日期：2008-01-01 00:00:00

abstract：:Neuroserpin is an axonally secreted serine protease inhibitor expressed in the nervous system that protects neurons from ischemia-induced apoptosis. Mutant neuroserpin forms have been found polymerized in inclusion bodies in a familial autosomal encephalopathy causing dementia, or associated with epilepsy. Regulation ...

journal_title：Nucleic acids research

authors： Cuadrado A,Navarro-Yubero C,Furneaux H,Kinter J,Sonderegger P,Muñoz A

更新日期：2002-05-15 00:00:00

abstract：:Next-generation DNA sequencing platforms provide exciting new possibilities for in vitro genetic analysis of functional nucleic acids. However, the size of the resulting data sets presents computational and analytical challenges. We present an open-source software package that employs a locality-sensitive hashing algo...

journal_title：Nucleic acids research

authors： Pitt JN,Rajapakse I,Ferré-D'Amaré AR

更新日期：2010-12-01 00:00:00

abstract：:We describe the unique features of an aberrantly rearranged mu immunoglobulin heavy chain gene isolated from MPC-11 cells (a gamma 2b producing Balb/c plasmacytoma). A novel rearrangement has occurred 1.5 Kb 5' of the MPC-11 mu gene (denoted 18b mu) resulting in the deletion of the majority of the repetitive switch re...

journal_title：Nucleic acids research

authors： Greenberg R,Lang RB,Diamond MS,Marcu KB

更新日期：1982-12-11 00:00:00

abstract：:Zinc finger protein with KRAB and SCAN domains 3 (ZKSCAN3) has long been known as a master transcriptional repressor of autophagy. Here, we identify a novel role for ZKSCAN3 in alleviating senescence that is independent of its autophagy-related activity. Downregulation of ZKSCAN3 is observed in aged human mesenchymal ...

journal_title：Nucleic acids research

authors： Hu H,Ji Q,Song M,Ren J,Liu Z,Wang Z,Liu X,Yan K,Hu J,Jing Y,Wang S,Zhang W,Liu GH,Qu J

更新日期：2020-06-19 00:00:00

abstract：:Controller (C) proteins regulate the timing of the expression of restriction and modification (R-M) genes through a combination of positive and negative feedback circuits. A single dimer bound to the operator switches on transcription of the C-gene and the endonuclease gene; at higher concentrations, a second dimer bo...

journal_title：Nucleic acids research

authors： McGeehan JE,Streeter SD,Thresh SJ,Ball N,Ravelli RB,Kneale GG

更新日期：2008-08-01 00:00:00

abstract：:Microarrays are invaluable high-throughput tools used to snapshot the gene expression profiles of cells and tissues. Among the most basic and fundamental questions asked of microarray data is whether individual genes are significantly activated or repressed by a particular stimulus. We have previously presented two Ba...

journal_title：Nucleic acids research

authors： Hsiao A,Ideker T,Olefsky JM,Subramaniam S

更新日期：2005-07-01 00:00:00

abstract：:One of the most intensively studied chromatin binding factors is HP1α. HP1α is associated with silenced, heterochromatic regions of the genome and binds to H3K9me3. While H3K9me3 is necessary for HP1α recruitment to heterochromatin, it is becoming apparent that it is not sufficient suggesting that additional factors a...

journal_title：Nucleic acids research

authors： Ryan DP,Tremethick DJ

更新日期：2018-10-12 00:00:00

abstract：:Although Dicer is essential for general microRNA (miRNA) biogenesis, vertebrate mir-451 is Dicer independent. Instead, its short pre-miRNA hairpin is 'sliced' by Ago2, then 3'-resected into mature miRNAs. Here, we show that Drosophila cells and animals generate functional small RNAs from mir-451-type precursors. Howev...

journal_title：Nucleic acids research

authors： Yang JS,Smibert P,Westholm JO,Jee D,Maurin T,Lai EC

更新日期：2014-02-01 00:00:00

abstract：:Bacteriophage T4 Dda helicase has recently been shown to be active as a monomer for unwinding of short duplex oligonucleotides and for displacing streptavidin from 3'-biotinylated oligonucleotides. However, its activity for streptavidin displacement and DNA unwinding has been shown to increase as the number of Dda mol...

journal_title：Nucleic acids research

authors： Byrd AK,Raney KD

更新日期：2006-05-31 00:00:00

abstract：:A small library of 49 peptide-oligonucleotide conjugates were synthesized to explore the influence of various peptide side chains on the hybridization properties of the DNA. An invariant 8mer oligonucleotide was coupled to a peptide portion that contained a five residue variable region composed of the cationic amino a...

journal_title：Nucleic acids research

authors： Harrison JG,Balasubramanian S

更新日期：1998-07-01 00:00:00