DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites.

abstract：:Phosphorylation of the easily accessible 3',5'-diesters 1a-d with diphenyl phosphorochloridate, followed by selective 5'-deacylation, affords the phosphotriester derivatives 2a-d in good yields. Alkaline treatment of 2a-d results in the formation of the 2',3'-cyclic phosphates (3a-d). The usefulness of the phosphotrie...

journal_title：Nucleic acids research

authors： van Boom JH,Burgers PM,Haasnoot CA

更新日期：1976-10-01 00:00:00

abstract：:The p53 protein is crucial for adapting programs of gene expression in response to stress. Recently, we revealed that this occurs partly through the formation of stress-specific p53 binding patterns. However, the mechanisms that generate these binding patterns remain largely unknown. It is not established whether the ...

journal_title：Nucleic acids research

authors： Millau JF,Bandele OJ,Perron J,Bastien N,Bouchard EF,Gaudreau L,Bell DA,Drouin R

更新日期：2011-04-01 00:00:00

abstract：:Signal recognition particle (SRP) is a stable cytoplasmic ribonucleoprotein complex that serves to translocate secretory proteins across membranes during translation. The SRP Database (SRPDB) provides compilations of SRP components, ordered alphabetically and phylogenetically. Alignments emphasize phylogenetically-sup...

journal_title：Nucleic acids research

authors： Gorodkin J,Knudsen B,Zwieb C,Samuelsson T

更新日期：2001-01-01 00:00:00

abstract：:Members of the basic helix-loop-helix (bHLH) family of transcription factors regulate a wide array of developmental processes in many cell types, including cell fate specification, differentiation and morphogenesis. Our studies describe the cloning of a gene from the nematode Caenorhabditis elegans that is closely rel...

journal_title：Nucleic acids research

authors： Nguyen L,Round J,O'Connell R,Geurts P,Funes-Duran M,Wong J,Jongeward G,Vierra CA

更新日期：2001-11-01 00:00:00

abstract：:Heat shock genes are activated by the binding of the heat shock transcription factor (HSF) to heat shock elements (HSEs), consisting of arrays of the 5-bp unit NGAAN arranged as inverted repeats. Here, we have investigated the interaction of the 5-bp unit with HSFs of Drosophila and Saccharomyces. Mutations within the...

journal_title：Nucleic acids research

authors： Fernandes M,Xiao H,Lis JT

更新日期：1994-01-25 00:00:00

abstract：:ST1710, a member of the multiple antibiotic resistance regulator (MarR) family of regulatory proteins in bacteria and archaea, plays important roles in development of antibiotic resistance, a global health problem. Here, we present the crystal structure of ST1710 from Sulfolobus tokodaii strain 7 complexed with salicy...

journal_title：Nucleic acids research

authors： Kumarevel T,Tanaka T,Umehara T,Yokoyama S

更新日期：2009-08-01 00:00:00

abstract：:Hepatitis B virus (HBV) infection remains a major health problem worldwide. The role played by microRNAs (miRNAs) in HBV replication and pathogenesis is being increasingly recognized. In this study, we found that miR-15b, an important miRNA during HBV infection and hepatocellular carcinoma development, directly binds ...

journal_title：Nucleic acids research

authors： Dai X,Zhang W,Zhang H,Sun S,Yu H,Guo Y,Kou Z,Zhao G,Du L,Jiang S,Zhang J,Li J,Zhou Y

更新日期：2014-06-01 00:00:00

abstract：:We have partially purified replicating simian virus 40 (SV40) chromosomes in a form which allows continued DNA synthesis in vitro. We first prepare a soluble DNA-synthesizing system from SV40-infected monkey cells and then sediment the components through a neutral sucrose gradient of extremely low ionic strength. Repl...

journal_title：Nucleic acids research

authors： Edenberg HJ,Waqar MA,Huberman JA

更新日期：1977-09-01 00:00:00

abstract：:RNA editing of miRNAs, especially in the seed region, adds another layer to miRNA mediated gene regulation which can modify its targets, altering cellular signaling involved in important processes such as differentiation. In this study, we have explored the role of miRNA editing in CD4(+) T cell differentiation. CD4(+...

journal_title：Nucleic acids research

authors： Negi V,Paul D,Das S,Bajpai P,Singh S,Mukhopadhyay A,Agrawal A,Ghosh B

更新日期：2015-09-18 00:00:00

abstract：:N7-Methyl-2'-deoxyguanosine (m7dG) is the predominant lesion formed by methylating agents. A systematic investigation on the effect of m7dG on DNA replication has been difficult due to the chemical instability of m7dG. To gain insights into the m7dG effect, we employed a 2'-fluorine-mediated transition-state destabilz...

journal_title：Nucleic acids research

authors： Koag MC,Kou Y,Ouzon-Shubeita H,Lee S

更新日期：2014-07-01 00:00:00

abstract：:GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 9.9 trillion base pairs from over 2.1 billion nucleotide sequences for 478 000 formally described species. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverag...

journal_title：Nucleic acids research

authors： Sayers EW,Cavanaugh M,Clark K,Pruitt KD,Schoch CL,Sherry ST,Karsch-Mizrachi I

更新日期：2021-01-08 00:00:00

abstract：:The C/D box scaRNA2 is predicted to guide specific 2'-O-methylation of U2 snRNA. In contrast to other SCARNA genes, SCARNA2 appears to be independently transcribed. By transient expression of SCARNA2-reporter gene constructs, we have demonstrated that this gene is transcribed by RNA polymerase II and that the promoter...

journal_title：Nucleic acids research

authors： Gérard MA,Myslinski E,Chylak N,Baudrey S,Krol A,Carbon P

更新日期：2010-01-01 00:00:00

abstract：:The hepatocyte nuclear factor (HNF)4alpha, a member of the nuclear receptor superfamily, regulates genes that play a critical role in embryogenesis and metabolism. Recent studies have shown that mutations in the human HNF4alpha gene cause a rare form of type 2 diabetes, maturity onset diabetes of the young (MODY1). To...

journal_title：Nucleic acids research

authors： Lausen J,Thomas H,Lemm I,Bulman M,Borgschulze M,Lingott A,Hattersley AT,Ryffel GU

更新日期：2000-01-15 00:00:00

abstract：:Ribosome synthesis involves the concomitance of pre-rRNA processing and ribosomal protein assembly. In eukaryotes, this is a complex process that requires the participation of specific sequences and structures within the pre-rRNAs, at least 200 trans-acting factors and the ribosomal proteins. There is little informati...

journal_title：Nucleic acids research

authors： Babiano R,de la Cruz J

更新日期：2010-08-01 00:00:00

abstract：:The nuclear suppressor allele NSM3 in strain FF1210-6C/170-E22 (E22), which suppresses a mutation of the yeast mitochondrial tRNA(Asp)gene in Saccharomyces cerevisiae, was cloned and identified. To isolate the NSM3 allele, a genomic DNA library using the vector YEp13 was constructed from strain E22. Nine YEp13 recombi...

journal_title：Nucleic acids research

authors： Chiang CS,Liaw GJ

更新日期：2000-04-01 00:00:00

abstract：:The open state of human topoisomerase I has been probed by molecular dynamics simulation, starting from the coordinates of the closed structure of the protein complexed with DNA, after elimination of the 22-bp DNA duplex oligonucleotide. A repulsion force between the two lips of the protein has been introduced for a s...

journal_title：Nucleic acids research

authors： Chillemi G,Bruselles A,Fiorani P,Bueno S,Desideri A

更新日期：2007-01-01 00:00:00

abstract：:EMAGE (http://genex.hgu.mrc.ac.uk/Emage/database) is a database of in situ gene expression patterns in the developing mouse embryo. Domains of expression from raw data images are spatially integrated into a set of standard 3D virtual mouse embryos at different stages of development, allowing data interrogation by spat...

journal_title：Nucleic acids research

authors： Venkataraman S,Stevenson P,Yang Y,Richardson L,Burton N,Perry TP,Smith P,Baldock RA,Davidson DR,Christiansen JH

更新日期：2008-01-01 00:00:00

abstract：:Melting of DNA in a segment bounded at both ends by regions of greater stability during electrophoresis in denaturing gradient gels show complex properties, not accommodated with standard melting theory. Compact bands of some DNA molecules become anomalously broadened at the retardation level in a denaturing gradient,...

journal_title：Nucleic acids research

authors： Abrams ES,Murdaugh SE,Lerman LS

更新日期：1995-07-25 00:00:00

abstract：:RNase III enzymes cleave double stranded (ds)RNA. This is an essential step for regulating the processing of mRNA, rRNA, snoRNA and other small RNAs, including siRNA and miRNA. Arabidopsis thaliana encodes nine RNase III: four DICER-LIKE (DCL) and five RNASE THREE LIKE (RTL). To better understand the molecular functio...

journal_title：Nucleic acids research

authors： Charbonnel C,Niazi AK,Elvira-Matelot E,Nowak E,Zytnicki M,de Bures A,Jobet E,Opsomer A,Shamandi N,Nowotny M,Carapito C,Reichheld JP,Vaucheret H,Sáez-Vásquez J

更新日期：2017-11-16 00:00:00

abstract：:CDK12 (cyclin-dependent kinase 12) is a regulatory kinase with evolutionarily conserved roles in modulating transcription elongation. Recent tumor genome studies of breast and ovarian cancers highlighted recurrent CDK12 mutations, which have been shown to disrupt DNA repair in cell-based assays. In breast cancers, CDK...

journal_title：Nucleic acids research

authors： Tien JF,Mazloomian A,Cheng SG,Hughes CS,Chow CCT,Canapi LT,Oloumi A,Trigo-Gonzalez G,Bashashati A,Xu J,Chang VC,Shah SP,Aparicio S,Morin GB

更新日期：2017-06-20 00:00:00

abstract：:Interaction detection methods have led to the discovery of thousands of interactions between proteins, and discerning relevance within large-scale data sets is important to present-day biology. Here, a spectral method derived from graph theory was introduced to uncover hidden topological structures (i.e. quasi-cliques...

journal_title：Nucleic acids research

authors： Bu D,Zhao Y,Cai L,Xue H,Zhu X,Lu H,Zhang J,Sun S,Ling L,Zhang N,Li G,Chen R

更新日期：2003-05-01 00:00:00

abstract：:The interaction of Hoechst 33258 with the minor groove of the adenine-tract DNA duplex d(CTTTTGCAAAAG)2 has been studied in both D2O and H2O solutions by 1D and 2D 1H NMR spectroscopy. Thirty-one nuclear Overhauser effects between drug and nucleotide protons within the minor groove of the duplex, together with ring-cu...

journal_title：Nucleic acids research

authors： Searle MS,Embrey KJ

更新日期：1990-07-11 00:00:00

abstract：:Different helical conformations of DNA (D), RNA (R), and DNA.RNA (DR) hybrid double and triple helices have been detected using affinity cleavage analysis. Synthetic methods were developed to attach EDTA.Fe to a single nucleotide on RNA as well as DNA oligonucleotides. Cleavage patterns generated by a localized diffus...

journal_title：Nucleic acids research

authors： Han H,Dervan PB

更新日期：1994-07-25 00:00:00

abstract：:TRF1, a duplex telomeric DNA-binding protein, plays an important role in telomere metabolism. We have previously reported that a fraction of endogenous TRF1 can stably exist free of telomere chromatin when it is phosphorylated at T371 by Cdk1; however, the role of this telomere-free (pT371)TRF1 has yet to be fully cha...

journal_title：Nucleic acids research

authors： McKerlie M,Walker JR,Mitchell TR,Wilson FR,Zhu XD

更新日期：2013-12-01 00:00:00

abstract：:The anti-cancer drug 2',2'-difluoro-2'-deoxycytidine (dFdC) is internally incorporated into DNA in vitro. To determine the effects of this incorporation on DNA structure and function, the beta-cyanoethyl phosphoramidite of dFdC was synthesized and oligodeoxyribonucleotides containing dFdC were made using automated sol...

journal_title：Nucleic acids research

authors： Richardson FC,Richardson KK,Kroin JS,Hertel LW

更新日期：1992-04-11 00:00:00

abstract：:This article describes recent developments of Europe PMC (http://europepmc.org), the leading database for life science literature. Formerly known as UKPMC, the service was rebranded in November 2012 as Europe PMC to reflect the scope of the funding agencies that support it. Several new developments have enriched Europ...

journal_title：Nucleic acids research

authors： Europe PMC Consortium.

更新日期：2015-01-01 00:00:00

abstract：:The swi4+ gene of Schizosaccharomyces pombe is involved in termination of copy-synthesis during mating-type switching. The gene was cloned by functional complementation of a swi4 mutant transformed with a genomic library. Determination of the nucleotide sequence revealed an open reading frame of 2979 nucleotides which...

journal_title：Nucleic acids research

authors： Fleck O,Michael H,Heim L

更新日期：1992-05-11 00:00:00

abstract：:We have previously shown that in vivo estradiol-dependent dephosphorylation of MDBP-2-H1 (a member of the histone H1 family) correlates with the loss of in vitro preferential binding to methylated DNA. To study the effects of the phosphorylation/dephosphorylation of MDBP-2-H1 on the expression of the avian vitellogeni...

journal_title：Nucleic acids research

authors： Bruhat A,Jost JP

更新日期：1996-05-15 00:00:00

abstract：:The GenBank(R) sequence database (http://www.ncbi.nlm.nih.gov/) incorporates DNA sequences from all available public sources, primarily through the direct submission of sequence data from individual laboratories and from large-scale sequencing projects. Most submitters use the BankIt (WWW) or Sequin programs to send t...

journal_title：Nucleic acids research

authors： Benson DA,Boguski MS,Lipman DJ,Ostell J,Ouellette BF

更新日期：1998-01-01 00:00:00

abstract：:Regulation of CLB2 is important both for completion of the normal vegetative cell cycle in Saccharomyces cerevisiae and for departure from the vegetative cell cycle upon nitrogen deprivation. Cell cycle-regulated transcription of CLB2 in the G2/M phase is known to be brought about by a set of proteins including Mcm1p,...

journal_title：Nucleic acids research

authors： Van Slyke C,Grayhack EJ

更新日期：2003-08-01 00:00:00