Structural and mechanistic insights into UHRF1-mediated DNMT1 activation in the maintenance DNA methylation.

abstract：:DNA methylation plays a crucial role in the establishment of tissue-specific gene expression and the regulation of key biological processes. However, our present inability to predict the effect of genome sequence variation on DNA methylation precludes a comprehensive assessment of the consequences of non-coding variat...

journal_title：Nucleic acids research

authors： Zeng H,Gifford DK

更新日期：2017-06-20 00:00:00

abstract：:The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC). d(GCTTCTCTTC) has been solved and refined at 2.5 A resolution. The refinement procedure converged at R = 0.181 for all reflections in the range 20.0-2.5 A. In the crystal, the RNA/DNA hybrid duplex has an A' conformation with all but one of the nucleotide suga...

journal_title：Nucleic acids research

authors： Conn GL,Brown T,Leonard GA

更新日期：1999-01-15 00:00:00

abstract：:We have developed a new COFACTOR webserver for automated structure-based protein function annotation. Starting from a structural model, given by either experimental determination or computational modeling, COFACTOR first identifies template proteins of similar folds and functional sites by threading the target structu...

journal_title：Nucleic acids research

authors： Roy A,Yang J,Zhang Y

更新日期：2012-07-01 00:00:00

abstract：:Although telomeres are not recognized as double-strand breaks (DSBs), some DSB repair proteins are present at telomeres and are required for telomere maintenance. To learn more about the telomeric function of proteins from the homologous recombination (HR) and non-homologous end joining pathways (NHEJ), we have screen...

journal_title：Nucleic acids research

authors： Wei C,Skopp R,Takata M,Takeda S,Price CM

更新日期：2002-07-01 00:00:00

abstract：:Optimization of primer sequences for polymerase chain reaction (PCR) and quantitative PCR (qPCR) and reaction conditions remains an experimental challenge. We have developed a resource, PrimerBank, which contains primers that can be used for PCR and qPCR under stringent and allele-invariant amplification conditions. A...

journal_title：Nucleic acids research

authors： Wang X,Spandidos A,Wang H,Seed B

更新日期：2012-01-01 00:00:00

abstract：:Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. We introduce PatternQuery, a web-based application designed for detection and fast extraction of such patterns. The application uses a...

journal_title：Nucleic acids research

authors： Sehnal D,Pravda L,Svobodová Vařeková R,Ionescu CM,Koča J

更新日期：2015-07-01 00:00:00

abstract：:Metnase is a human protein with methylase (SET) and nuclease domains that is widely expressed, especially in proliferating tissues. Metnase promotes non-homologous end-joining (NHEJ), and knockdown causes mild hypersensitivity to ionizing radiation. Metnase also promotes plasmid and viral DNA integration, and topoisom...

journal_title：Nucleic acids research

authors： De Haro LP,Wray J,Williamson EA,Durant ST,Corwin L,Gentry AC,Osheroff N,Lee SH,Hromas R,Nickoloff JA

更新日期：2010-09-01 00:00:00

abstract：:We have analyzed the DNaseI sensitivity of chromatin from the rat albumin and alpha-fetoprotein genes in the fetal liver (which synthesizes albumin and alpha-fetoprotein), adult liver (which synthesizes albumin), fetal yolk sac (which synthesizes alpha-fetoprotein), and adult kidney (which synthesizes neither). Active...

journal_title：Nucleic acids research

authors： Kunnath L,Locker J

更新日期：1985-01-11 00:00:00

abstract：:The MF alpha 1 gene of Saccharomyces cerevisiae is an alpha specific gene whose expression is regulated by two upstream activation sites (UASMF alpha 1S), which are the binding sites for activator proteins, MAT alpha 1 and MCM1. UASMF alpha 1 elements act in a synergistic fashion; lack of either element causes reduced...

journal_title：Nucleic acids research

authors： Inokuchi K,Nakayama A

更新日期：1991-06-11 00:00:00

abstract：:Proteomic and RNomic approaches have identified many components of different ribonucleoprotein particles (RNPs), yet still little is known about the organization and protein proximities within these heterogeneous and highly dynamic complexes. Here we describe a targeted cross-linking approach, which combines cross-lin...

journal_title：Nucleic acids research

authors： Trahan C,Oeffinger M

更新日期：2016-02-18 00:00:00

abstract：:REV1 and DNA Polymerase ζ (REV3 and REV7) play important roles in translesion DNA synthesis (TLS) in which DNA replication bypasses blocking lesions. REV1 and Polζ have also been implicated in promoting repair of DNA double-stranded breaks (DSBs). However, the mechanism by which these two TLS polymerases increase tole...

journal_title：Nucleic acids research

authors： Sharma S,Hicks JK,Chute CL,Brennan JR,Ahn JY,Glover TW,Canman CE

更新日期：2012-01-01 00:00:00

abstract：:HIV-1 reverse transcriptase (RT) is a primary target for anti-AIDS drugs. Structures of HIV-1 RT, usually determined at approximately 2.5-3.0 A resolution, are important for understanding enzyme function and mechanisms of drug resistance in addition to being helpful in the design of RT inhibitors. Despite hundreds of ...

journal_title：Nucleic acids research

authors： Bauman JD,Das K,Ho WC,Baweja M,Himmel DM,Clark AD Jr,Oren DA,Boyer PL,Hughes SH,Shatkin AJ,Arnold E

更新日期：2008-09-01 00:00:00

abstract：:A terminator of transcription with bidirectional activity has been located between the translation termination codons of the genes tetA and orfL on Tn10. These genes are transcribed towards each other. Each orientation of the intervening sequence is shown to reduce the expression of the lacZ and galK genes when cloned...

journal_title：Nucleic acids research

authors： Schollmeier K,Gärtner D,Hillen W

更新日期：1985-06-25 00:00:00

abstract：:Cpf1 nucleases were recently reported to be highly specific and programmable nucleases with efficiencies comparable to those of SpCas9. AsCpf1 and LbCpf1 require a single crRNA and recognize a 5'-TTTN-3' protospacer adjacent motif (PAM) at the 5' end of the protospacer for genome editing. For widespread application in...

journal_title：Nucleic acids research

authors： Tu M,Lin L,Cheng Y,He X,Sun H,Xie H,Fu J,Liu C,Li J,Chen D,Xi H,Xue D,Liu Q,Zhao J,Gao C,Song Z,Qu J,Gu F

更新日期：2017-11-02 00:00:00

abstract：:Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database (http://merops.sanger.ac.uk) aims to fulfil the need for an integrated source of information about these. The database has hierarchical classifications in which homologous sets of peptidases a...

journal_title：Nucleic acids research

authors： Rawlings ND,Barrett AJ,Bateman A

更新日期：2012-01-01 00:00:00

abstract：:Three clones of non-repetitive sequences and six clones containing repetitive sequences were obtained from micronuclear DNA of Tetrahymena thermophila. All the non-repetitive and three repetitive sequences had the same organization in micro- and macronuclear DNAs as revealed by blot hybridization. On the other hand, t...

journal_title：Nucleic acids research

authors： Iwamura Y,Sakai M,Muramatsu M

更新日期：1982-07-24 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：:The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification ex...

journal_title：Nucleic acids research

authors： Riffle M,Malmström L,Davis TN

更新日期：2005-01-01 00:00:00

abstract：:This work presents the Apo-Holo DataBase (AH-DB, http://ahdb.ee.ncku.edu.tw/ and http://ahdb.csbb.ntu.edu.tw/), which provides corresponding pairs of protein structures before and after binding. Conformational transitions are commonly observed in various protein interactions that are involved in important biological f...

journal_title：Nucleic acids research

authors： Chang DT,Yao TJ,Fan CY,Chiang CY,Bai YH

更新日期：2012-01-01 00:00:00

abstract：:The mRNA export complex TREX (TREX) is known to contain Aly, UAP56, Tex1 and the THO complex, among which UAP56 is required for TREX assembly. Here, we systematically investigated the role of each human TREX component in TREX assembly and its association with the mRNA. We found that Tex1 is essentially a subunit of th...

journal_title：Nucleic acids research

authors： Chi B,Wang Q,Wu G,Tan M,Wang L,Shi M,Chang X,Cheng H

更新日期：2013-01-01 00:00:00

abstract：:The development of genetic switches and their integrated forms (genetic circuits) with desired specifications/functions is key for success in synthetic biology. Due to the difficulty in rational design, genetic switches and circuits with desirable specifications are mostly obtained by directed evolution. Based on a vi...

journal_title：Nucleic acids research

authors： Tashiro Y,Fukutomi H,Terakubo K,Saito K,Umeno D

更新日期：2011-02-01 00:00:00

abstract：:The channel proteins belonging to the major intrinsic proteins (MIP) superfamily are diverse and are found in all forms of life. Water-transporting aquaporin and glycerol-specific aquaglyceroporin are the prototype members of the MIP superfamily. MIPs have also been shown to transport other neutral molecules and gases...

journal_title：Nucleic acids research

authors： Gupta AB,Verma RK,Agarwal V,Vajpai M,Bansal V,Sankararamakrishnan R

更新日期：2012-01-01 00:00:00

abstract：:Cdc13 is an essential protein from Saccharomyces cerevisiae that caps telomeres by protecting the C-rich telomeric DNA strand from degradation and facilitates telomeric DNA replication by telomerase. In vitro, Cdc13 binds TG-rich single-stranded telomeric DNA with high affinity and specificity. A previously identified...

journal_title：Nucleic acids research

authors： Anderson EM,Halsey WA,Wuttke DS

更新日期：2002-10-01 00:00:00

abstract：:Quantitative real-time PCR has revolutionized many aspects of genetic research, biomedical diagnostics and pathogen detection. Nevertheless, the full potential of this technology has yet to be realized, primarily due to the limitations of the threshold-based methodologies that are currently used for quantitative analy...

journal_title：Nucleic acids research

authors： Rutledge RG

更新日期：2004-12-15 00:00:00

abstract：UNLABELLED:Partial cleavage of DNA with the restriction endonuclease NotI (5'...GC/GGCCGC...3') is an important technique for genomic mapping. However, partial genomic cleavage with this enzyme is impaired by the agarose matrix in which the DNA must be suspended. To solve this problem we have purified the blocking meth...

journal_title：Nucleic acids research

authors： Hanish J,McClelland M

更新日期：1990-06-11 00:00:00

abstract：:As large-scale re-sequencing of genomes reveals many protein mutations, especially in human cancer tissues, prediction of their likely functional impact becomes important practical goal. Here, we introduce a new functional impact score (FIS) for amino acid residue changes using evolutionary conservation patterns. The ...

journal_title：Nucleic acids research

authors： Reva B,Antipin Y,Sander C

更新日期：2011-09-01 00:00:00

abstract：:Understanding the cellular uptake and intracellular trafficking of dendrimer-DNA complexes is an important prerequisite for improving the transfection efficiency of non-viral vector-mediated gene delivery. Dendrimers are synthetic polymers used for gene transfer. Although these cationic molecules show promise as versa...

journal_title：Nucleic acids research

authors： Manunta M,Tan PH,Sagoo P,Kashefi K,George AJ

更新日期：2004-05-17 00:00:00

abstract：:The 279-bp major breakpoint region (mbr) within the 3'-untranslated region (3'-UTR) of the BCL2 gene is a binding site of special AT-rich sequence binding protein 1 (SATB1) that is well known to participate in the long-range regulation of gene transcription. Our previous studies have revealed that the mbr could regula...

journal_title：Nucleic acids research

authors： Gong F,Sun L,Wang Z,Shi J,Li W,Wang S,Han X,Sun Y

更新日期：2011-06-01 00:00:00

abstract：:DNA breaks occur during many processes in mammalian cells, including recombination, repair, mutagenesis and apoptosis. Here we report a simple and rapid method for assaying DNA breaks and identifying DNA breaksites. Breaksites are first tagged and amplified by ligation-mediated PCR (LM-PCR), using nested PCR primers t...

journal_title：Nucleic acids research

authors： Kong Q,Maizels N

更新日期：2001-03-15 00:00:00

abstract：:Oxoguanine DNA glycosylase (OGG1) initiates the repair of 8-oxoguanine (8-oxoG), a major oxidative DNA base modification that has been directly implicated in cancer and aging. OGG1 functions in the base excision repair pathway, for which a molecular hand-off mechanism has been proposed. To date, only one functional an...

journal_title：Nucleic acids research

authors： Hu J,Imam SZ,Hashiguchi K,de Souza-Pinto NC,Bohr VA

更新日期：2005-06-07 00:00:00