Impact of CpG methylation on structure, dynamics and solvation of cAMP DNA responsive element.

abstract：:Three protein isoforms (74, 54 and 42 kDa) are expressed from repressor gene c in the Streptomyces temperate bacteriophage phiC31. Because expression of the two smaller isoforms, 54 and 42 kDa, is sufficient for superinfection immunity, the interaction between these isoforms was studied. The native 42 kDa repressor (N...

journal_title：Nucleic acids research

authors： Wilson SE,Smith MC

更新日期：1998-05-15 00:00:00

abstract：:Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers...

journal_title：Nucleic acids research

authors： Zheng X,Yang J,Zhou C,Zhang C,Zhang Q,Wei X

更新日期：2019-02-20 00:00:00

abstract：:The Gibbs Motif Sampler is a software package for locating common elements in collections of biopolymer sequences. In this paper we describe a new variation of the Gibbs Motif Sampler, the Gibbs Recursive Sampler, which has been developed specifically for locating multiple transcription factor binding sites for multip...

journal_title：Nucleic acids research

authors： Thompson W,Rouchka EC,Lawrence CE

更新日期：2003-07-01 00:00:00

abstract：:Pyrimidine adducts in cellular DNA arise from modification of the pyrimidine 5,6-double bond by oxidation, reduction or hydration. The biological outcome includes increased mutation rate and potential lethality. A major DNA N:-glycosylase responsible for the excision of modified pyrimidine bases is the base excision r...

journal_title：Nucleic acids research

authors： Yang H,Phan IT,Fitz-Gibbon S,Shivji MK,Wood RD,Clendenin WM,Hyman EC,Miller JH

更新日期：2001-02-01 00:00:00

abstract：:Nucleotide excision DNA repair is mechanistically conserved across all kingdoms of life. In prokaryotes, this multi-enzyme process requires six proteins: UvrA-D, DNA polymerase I and DNA ligase. To examine how UvrC locates the UvrB-DNA pre-incision complex at a site of damage, we have labeled UvrB and UvrC with differ...

journal_title：Nucleic acids research

authors： Hughes CD,Wang H,Ghodke H,Simons M,Towheed A,Peng Y,Van Houten B,Kad NM

更新日期：2013-05-01 00:00:00

abstract：:DNA-damage response machinery is crucial to maintain the genomic integrity of cells, by enabling effective repair of even highly lethal lesions such as DNA double-strand breaks (DSBs). Defects in specific genes acquired through mutations, copy-number alterations or epigenetic changes can alter the balance of these pat...

journal_title：Nucleic acids research

authors： Liu C,Srihari S,Cao KA,Chenevix-Trench G,Simpson PT,Ragan MA,Khanna KK

更新日期：2014-06-01 00:00:00

abstract：:MicroRNAs (miRNA) are short single-stranded RNA molecules derived from hairpin-forming precursors that play a crucial role as post-transcriptional regulators in eukaryotes and viruses. In the past years, many microRNA target genes (MTGs) have been identified experimentally. However, because of the high costs of experi...

journal_title：Nucleic acids research

authors： Leclercq M,Diallo AB,Blanchette M

更新日期：2017-01-25 00:00:00

abstract：:The expression pattern and regulatory functions of microRNAs (miRNAs) are intensively investigated in various tissues, cell types and disorders. Differential miRNA expression signatures have been revealed in healthy and unhealthy tissues using high-throughput profiling methods. For further analyses of miRNA signatures...

journal_title：Nucleic acids research

authors： Arefian E,Kiani J,Soleimani M,Shariati SA,Aghaee-Bakhtiari SH,Atashi A,Gheisari Y,Ahmadbeigi N,Banaei-Moghaddam AM,Naderi M,Namvarasl N,Good L,Faridani OR

更新日期：2011-07-01 00:00:00

abstract：:The Transcription Regulatory Regions Database (TRRD) is a curated database designed for accumulation of experimental data on extended regulatory regions of eukaryotic genes, the regulatory elements they contain, i.e., transcription factor binding sites, promoters, enhancers, silencers, etc., and expression patterns of...

journal_title：Nucleic acids research

authors： Kolchanov NA,Ananko EA,Podkolodnaya OA,Ignatieva EV,Stepanenko IL,Kel-Margoulis OV,Kel AE,Merkulova TI,Goryachkovskaya TN,Busygina TV,Kolpakov FA,Podkolodny NL,Naumochkin AN,Romashchenko AG

更新日期：1999-01-01 00:00:00

abstract：:Motor proteins that translocate on nucleic acids are key players in gene expression and maintenance. While the function of these proteins is diverse, they are driven by highly conserved core motor domains. In transcription-coupled DNA repair, motor activity serves to remove RNA polymerase stalled on damaged DNA, makin...

journal_title：Nucleic acids research

authors： Murphy MN,Gong P,Ralto K,Manelyte L,Savery NJ,Theis K

更新日期：2009-10-01 00:00:00

abstract：:Deamination of cytosine (C), 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) occurs spontaneously in mammalian DNA with several hundred deaminations occurring in each cell every day. The resulting potentially mutagenic mispairs of uracil (U), thymine (T) or 5-hydroxymethyluracil (hmU) with guanine (G) are subs...

journal_title：Nucleic acids research

authors： Kemmerich K,Dingler FA,Rada C,Neuberger MS

更新日期：2012-07-01 00:00:00

abstract：:We constructed several deletion mutants of Escherichia coli single-stranded DNA binding protein (EcoSSB) lacking different parts of the C-terminal region. This region of EcoSSB is composed of two parts: a glycine and proline-rich sequence of approximately 60 amino acids followed by an acidic region of the last 10 amin...

journal_title：Nucleic acids research

authors： Curth U,Genschel J,Urbanke C,Greipel J

更新日期：1996-07-15 00:00:00

abstract：:Evidence is presented that the editing mechanisms of aminoacyl-tRNA synthetase operate by two alternative pathways: pre-transfer, by hydrolysis of the non-cognate aminoacyl adenylate; post-transfer, by hydrolysis of the mischarged tRNA. The methionyl-tRNA synthetases from Escherichia coli and Bacillus stearothermophil...

journal_title：Nucleic acids research

authors： Jakubowski H,Fersht AR

更新日期：1981-07-10 00:00:00

abstract：:A fiber optic biosensor was used for the fluorimetric detection of T/AT triple-helical DNA formation. The surfaces of two sets of fused silica optical fibers were functionalized with hexaethylene oxide linkers from which decaadenylic acid oligonucleotides were grown in the 3'to 5'and 5'to 3'direction, respectively, us...

journal_title：Nucleic acids research

authors： Uddin AH,Piunno PA,Hudson RH,Damha MJ,Krull UJ

更新日期：1997-10-15 00:00:00

abstract：:PrimPol is a primase-polymerase involved in nuclear and mitochondrial DNA replication in eukaryotic cells. Although PrimPol is predicted to possess an archaeo-eukaryotic primase and a UL52-like zinc finger domain, the role of these domains has not been established. Here, we report that the proposed zinc finger domain ...

journal_title：Nucleic acids research

authors： Keen BA,Jozwiakowski SK,Bailey LJ,Bianchi J,Doherty AJ

更新日期：2014-05-01 00:00:00

abstract：:A cDNA clone named 1A11 was isolated in a screen for genes that are activated by both mesoderm inducing factors FGF and activin in animal explants of Xenopus laevis embryos. In undisturbed embryos, 1A11 is expressed during the gastrula stage in the entire marginal zone where mesoderm originates, and later in the somit...

journal_title：Nucleic acids research

authors： Greene JM,Otani H,Good PJ,Dawid IB

更新日期：1993-05-25 00:00:00

abstract：:Myocyte enhancer binding factor 2 (MEF2) proteins belong to the MADS box family of transcription factors and four MEF2 proteins, MEF2A, MEF2B, MEF2C and MEF2D, have been found. MEF2 proteins have been shown to play critical roles in differentiation of muscles and neuronal tissues. How transactivational activity of MEF...

journal_title：Nucleic acids research

authors： Choi SJ,Park SY,Han TH

更新日期：2001-07-01 00:00:00

abstract：:Upon activation of the ERK and p38 MAPK pathways, the MSK1/2-mediated nucleosomal response, including H3 phosphorylation at serine 28 or 10, is coupled with the induction of immediate-early (IE) gene transcription. The outcome of this response, varying with the stimuli and cellular contexts, ranges from neoplastic tra...

journal_title：Nucleic acids research

authors： Drobic B,Pérez-Cadahía B,Yu J,Kung SK,Davie JR

更新日期：2010-06-01 00:00:00

abstract：:Previous work has demonstrated that the yeast SPT3 gene is required for transcription from delta sequences, the long terminal repeats that flank yeast Ty elements. In spt3 null mutants, transcription fails to initiate in delta sequences and instead initiates farther downstream. Null mutations in SPT3 cause other mutan...

journal_title：Nucleic acids research

authors： Winston F,Minehart PL

更新日期：1986-09-11 00:00:00

abstract：:Homologous recombination provides a means for the in vivo construction of recombinant DNA molecules that may be problematic to assemble in vitro. We have investigated the efficiency of recombination within the Caenorhabditis elegans germ line as a function of the length of homology between recombining molecules. Our f...

journal_title：Nucleic acids research

authors： Kemp BJ,Hatzold J,Sternick LA,Cornman-Homonoff J,Whitaker JM,Tieu PJ,Lambie EJ

更新日期：2007-01-01 00:00:00

abstract：:HBV genotypes differ in pathogenicity. In addition, genotype-specific differences in the regulation of transcription and virus replication exist in HBV, but the underlying mechanisms are unknown. Here, we show the presence of a G-quadruplex motif in the promoter of the preS2/S gene; this G-quadruplex is highly conserv...

journal_title：Nucleic acids research

authors： Biswas B,Kandpal M,Vivekanandan P

更新日期：2017-11-02 00:00:00

abstract：:alpha2-Macroglobulin covalently linked to poly(L)-lysine can be used as a vehicle for receptor-mediated gene transfer. This modified alpha2-macroglobulin maintains its ability to bind to the alpha2-macroglobulin receptor, and was shown to introduce a luciferase reporter gene plasmid into HepG2 human hepatoma cells in ...

journal_title：Nucleic acids research

authors： Schneider H,Huse K,Birkenmeier G,Otto A,Scholz GH

更新日期：1996-10-01 00:00:00

abstract：:MicroRNAs (miRNAs) are small non-coding RNAs of approximately 22 nucleotides, which negatively regulate the gene expression at the post-transcriptional level. This study describes an update of the miRTarBase (http://miRTarBase.mbc.nctu.edu.tw/) that provides information about experimentally validated miRNA-target inte...

journal_title：Nucleic acids research

authors： Chou CH,Chang NW,Shrestha S,Hsu SD,Lin YL,Lee WH,Yang CD,Hong HC,Wei TY,Tu SJ,Tsai TR,Ho SY,Jian TY,Wu HY,Chen PR,Lin NC,Huang HT,Yang TL,Pai CY,Tai CS,Chen WL,Huang CY,Liu CC,Weng SL,Liao KW,Hsu WL,Hu

更新日期：2016-01-04 00:00:00

abstract：:We have determined the three-dimensional structure of a non-selfcomplementary nonanucleotide duplex which contains an abasic (apyrimidinic) site in the centre, i.e. a deoxyribose residue opposite an adenosine. The majority of the base and sugar proton resonances were assigned by NOESY, COSY and 2DQF spectra in D2O and...

journal_title：Nucleic acids research

authors： Cuniasse P,Sowers LC,Eritja R,Kaplan B,Goodman MF,Cognet JA,LeBret M,Guschlbauer W,Fazakerley GV

更新日期：1987-10-12 00:00:00

abstract：:PCAF and hGCN5 are distinct human genes that encode proteins related to the yeast histone acetyltransferase and transcriptional adapter GCN5. The PCAF protein shares extensive similarity with the 439 amino acids of yGCN5, but it has an approximately 350 amino acid N-terminal extension that interacts with the transcrip...

journal_title：Nucleic acids research

authors： Smith ER,Belote JM,Schiltz RL,Yang XJ,Moore PA,Berger SL,Nakatani Y,Allis CD

更新日期：1998-06-15 00:00:00

abstract：:The multiprotein complexes involved in active dis-ruption of chromatin structure, homologous to yeast SWI/SNF complex, have been described for human and Drosophila cells. In all SWI/SNF-class complexes characterised so far, one of the key components is the SNF5-type protein. Here we describe the isolation of a plant (...

journal_title：Nucleic acids research

authors： Brzeski J,Podstolski W,Olczak K,Jerzmanowski A

更新日期：1999-06-01 00:00:00

abstract：:The chromatographic profiles of isoaccepting tRNAs were analyzed at five time points during the 96 hr, dimethylsulfoxide induced, erythroid-like differentiation of Friend leukemia cells. Sixty-four isoaccepting species of tRNA for 16 amino acids were resolved by RPC-5 chromatography. The relative amounts of tRNAphe, t...

journal_title：Nucleic acids research

authors： Lin VK,Agris PF

更新日期：1980-08-11 00:00:00

abstract：:The convergently transcribed restriction (R) and methylase (M) genes of the Restriction-Modification system Esp1396I are tightly regulated by a controller (C) protein that forms part of the CR operon. We have mapped the transcriptional start sites from each promoter and examined the regulatory role of C.Esp1396I in vi...

journal_title：Nucleic acids research

authors： Bogdanova E,Zakharova M,Streeter S,Taylor J,Heyduk T,Kneale G,Severinov K

更新日期：2009-06-01 00:00:00

abstract：:We studied fluorescence intensity, polarization and lifetime of some commonly used fluorophores conjugated to oligodeoxyribonucleotides with different primary and secondary structures. We found that fluorescence intensity can increase or decrease upon hybridization of the labeled strand to its complement depending on ...

journal_title：Nucleic acids research

authors： Nazarenko I,Pires R,Lowe B,Obaidy M,Rashtchian A

更新日期：2002-05-01 00:00:00

abstract：:SPRING (http://algorithm.cs.nthu.edu.tw/tools/SPRING/) is a tool for the analysis of genome rearrangement between two chromosomal genomes using reversals and/or block-interchanges. SPRING takes two or more chromosomes as its input and then computes a minimum series of reversals and/or block-interchanges between any tw...

journal_title：Nucleic acids research

authors： Lin YC,Lu CL,Liu YC,Tang CY

更新日期：2006-07-01 00:00:00