Automatic assessment of alignment quality.

abstract：:The replication control circuit of the FII plasmids R1, R100 and R6-5 involves a small untranslated RNA molecule of about 93 nucleotides. This RNA, designated CopA RNA in plasmid R1, acts in vivo as a post-transcriptional inhibitor of the expression of the RepA protein whose synthesis is required for each round of pla...

journal_title：Nucleic acids research

authors： Gerhart E,Wagner H,Nordström K

更新日期：1986-03-25 00:00:00

abstract：:The 1.7 Å X-ray crystal structure of the B-DNA dodecamer, [d(CGCGAATTCGCG)]₂ (DDD)-bound non-covalently to a platinum(II) complex, [{Pt(NH₃)₃}₂-µ-{trans-Pt(NH₃)₂(NH₂(CH₂)₆NH₂)₂}](NO₃)₆ (1, TriplatinNC-A,) shows the trinuclear cation extended along the phosphate backbone and bridging the minor groove. The square planar...

journal_title：Nucleic acids research

authors： Komeda S,Moulaei T,Chikuma M,Odani A,Kipping R,Farrell NP,Williams LD

更新日期：2011-01-01 00:00:00

abstract：:A dot hybridization method is presented for rapidly determining the relative concentrations of nucleic acids in a mixture, as well as the extent of sequence homology between related RNA or DNA species. ...

journal_title：Nucleic acids research

authors： Kafatos FC,Jones CW,Efstratiadis A

更新日期：1979-11-24 00:00:00

abstract：:The nucleotide sequence of the 5S ribosomal RNA of Streptococcus cremoris has been determined. The sequence is 5' (sequence in text) 3'. Comparison of the S. cremoris 5S RNA sequence to an updated prokaryotic generalized 5S RNA structural model shows that this 5S RNA contains some unusual structural features. These fe...

journal_title：Nucleic acids research

authors： Neimark H,Andersen J,Delihas N

更新日期：1983-11-11 00:00:00

abstract：:Live-cell measurement of protein binding to chromatin allows probing cellular biochemistry in physiological conditions, which are difficult to mimic in vitro. However, different studies have yielded widely discrepant predictions, and so it remains uncertain how to make the measurements accurately. To establish a bench...

journal_title：Nucleic acids research

authors： Mazza D,Abernathy A,Golob N,Morisaki T,McNally JG

更新日期：2012-08-01 00:00:00

abstract：:Genotoxic stress induces alternative splicing of the oncogene MDM2 generating MDM2-ALT1, an isoform attributed with tumorigenic properties. However, the mechanisms underlying this event remain unclear. Here we explore MDM2 splicing regulation by utilizing a novel minigene that mimics endogenous MDM2 splicing in respon...

journal_title：Nucleic acids research

authors： Comiskey DF Jr,Jacob AG,Singh RK,Tapia-Santos AS,Chandler DS

更新日期：2015-04-30 00:00:00

abstract：:The oncogenic transformation of normal cells into malignant, rapidly proliferating cells requires major alterations in cell physiology. For example, the transformed cells remodel their metabolic processes to supply the additional demand for cellular building blocks. We have recently demonstrated essential metabolic pr...

journal_title：Nucleic acids research

authors： Shaul YD,Yuan B,Thiru P,Nutter-Upham A,McCallum S,Lanzkron C,Bell GW,Sabatini DM

更新日期：2016-01-04 00:00:00

abstract：:The apolipoprotein AI (apoAI) promoter/enhancer contains multiple cis -acting elements on which a variety of hepatocyte-enriched and ubiquitous transcription factors function synergistically to regulate liver-specific transcription. Adenovirus E1A proteins repress tissue-specific gene expression and disrupt the differ...

journal_title：Nucleic acids research

authors： Kilbourne EJ,Evans MJ,Karathanasis SK

更新日期：1998-04-01 00:00:00

abstract：:We show how to speed up sequence alignment algorithms of the type introduced by Needleman and Wunsch (and generalized by Sellers and others). Faster alignment algorithms have been introduced, but always at the cost of possibly getting sub-optimal alignments. Our modification results in the optimal alignment still bein...

journal_title：Nucleic acids research

authors： Fickett JW

更新日期：1984-01-11 00:00:00

abstract：:Preparations of chicken, rat and human nuclear 5S RNA contain two sets of molecules. The set with the lowest electrophoretic mobility (5Sa) contains RNAs identical or closely related to ribosomal 5S RNA from the corresponding animal species. In HeLa cells and rat brain, we only detected an RNA identical to the ribosom...

journal_title：Nucleic acids research

authors： Krol A,Gallinaro H,Lazar E,Jacob M,Branlant C

更新日期：1981-02-25 00:00:00

abstract：:The gene encoding the DNA methyltransferase M.CviRI from Chlorella virus XZ-6E was cloned and expressed in Escherichia coli. M.CviRI methylates adenine in TGCA sequences. DNA containing the M.CviRI gene was sequenced and a single open reading frame of 1137 bp was identified which could code for a polypeptide of 379 am...

journal_title：Nucleic acids research

authors： Stefan C,Xia YN,Van Etten JL

更新日期：1991-01-25 00:00:00

abstract：:Selenoproteins contain the amino acid selenocysteine which is encoded by a UGA Sec codon. Recoding UGA Sec requires a complex mechanism, comprising the cis-acting SECIS RNA hairpin in the 3'UTR of selenoprotein mRNAs, and trans-acting factors. Among these, the SECIS Binding Protein 2 (SBP2) is central to the mechanism...

journal_title：Nucleic acids research

authors： Takeuchi A,Schmitt D,Chapple C,Babaylova E,Karpova G,Guigo R,Krol A,Allmang C

更新日期：2009-04-01 00:00:00

abstract：:Cloned DNA from the EcoRI J fragment of EBV has been used as template for in vitro transcription experiments using cell-free extracts prepared from HeLa or KB cells. Two EBV specific RNAs each about 175 bases in length were synthesised and nuclease 51 mapping experiments determined that these in vitro products corresp...

journal_title：Nucleic acids research

authors： Jat P,Arrand JR

更新日期：1982-06-11 00:00:00

abstract：:The effect of mutations in the highly conserved Y-GG/A motif of B-type DNA polymerases was studied in the DNA polymerase from the hyperthermophilic euryarchaeon Thermococcus aggregans. This motif plays a critical role in the balance between the synthesis and degradation of the DNA chain. Five different mutations of th...

journal_title：Nucleic acids research

authors： Böhlke K,Pisani FM,Vorgias CE,Frey B,Sobek H,Rossi M,Antranikian G

更新日期：2000-10-15 00:00:00

abstract：:Upon endocytosis, most oligodeoxynucleotides (ODNs) accumulate in vesicular compartments; a tiny number of them cross the vesicle membrane, reach the cytosol and by passive diffusion enter the nucleus where they are entrapped. So far, the compartment in which an antisense ODN interacts with its mRNA target has not bee...

journal_title：Nucleic acids research

authors： Meunier L,Mayer R,Monsigny M,Roche AC

更新日期：1999-07-01 00:00:00

abstract：:To organize data resulting from the phenotypic characterization of a library of 30,000 T-DNA enhancer trap (ET) insertion lines of rice (Oryza sativa L cv. Nipponbare), we developed the Oryza Tag Line (OTL) database (http://urgi.versailles.inra.fr/OryzaTagLine/). OTL structure facilitates forward genetic search for sp...

journal_title：Nucleic acids research

authors： Larmande P,Gay C,Lorieux M,Périn C,Bouniol M,Droc G,Sallaud C,Perez P,Barnola I,Biderre-Petit C,Martin J,Morel JB,Johnson AA,Bourgis F,Ghesquière A,Ruiz M,Courtois B,Guiderdoni E

更新日期：2008-01-01 00:00:00

abstract：:MPromDb (Mammalian Promoter Database) is a curated database that strives to annotate gene promoters identified from ChIP-seq results with the goal of providing an integrated resource for mammalian transcriptional regulation and epigenetics. We analyzed 507 million uniquely aligned RNAP-II ChIP-seq reads from 26 differ...

journal_title：Nucleic acids research

authors： Gupta R,Bhattacharyya A,Agosto-Perez FJ,Wickramasinghe P,Davuluri RV

更新日期：2011-01-01 00:00:00

abstract：:CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring 'spacer' sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR inter...

journal_title：Nucleic acids research

authors： Xue C,Seetharam AS,Musharova O,Severinov K,Brouns SJ,Severin AJ,Sashital DG

更新日期：2015-12-15 00:00:00

abstract：:Molecular Biology Database List (MBDL) includes brief descriptions and pointers to Web sites for the various databases described in this issue as well as other Web sites presenting data sets relevant to molecular biology. This information is compiled into a list (http://www.oup.co.uk/nar/Volume_27/Issue_01/summary/ gk...

journal_title：Nucleic acids research

authors： Burks C

更新日期：1999-01-01 00:00:00

abstract：:Protein-protein interactions regulate many essential enzymatic processes in the cell. Somatic mutations outside of an enzyme active site can therefore impact cellular function by disruption of critical protein-protein interactions. In our investigation of the cellular impact of the T304I cancer mutation of DNA Polymer...

journal_title：Nucleic acids research

authors： Fang Q,Andrews J,Sharma N,Wilk A,Clark J,Slyskova J,Koczor CA,Lans H,Prakash A,Sobol RW

更新日期：2019-07-09 00:00:00

abstract：:The Cox protein from bacteriophage P2 forms oligomeric filaments and it has been proposed that DNA can be wound up around these filaments, similar to how histones condense DNA. We here use fluorescence microscopy to study single DNA-Cox complexes in nanofluidic channels and compare how the Cox homologs from phages P2 ...

journal_title：Nucleic acids research

authors： Frykholm K,Berntsson RP,Claesson M,de Battice L,Odegrip R,Stenmark P,Westerlund F

更新日期：2016-09-06 00:00:00

abstract：:The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. By combining the different types of expression data, GXD aims to provide increasingly complete information about the expression profiles of genes in different mouse strains and mutants, thus enabling val...

journal_title：Nucleic acids research

authors： Ringwald M,Eppig JT,Begley DA,Corradi JP,McCright IJ,Hayamizu TF,Hill DP,Kadin JA,Richardson JE

更新日期：2001-01-01 00:00:00

abstract：:DNA synthesized by in vitro transcription on rat interferon (IFN) mRNA has been cloned and amplified as recombinant DNA. The nucleotide sequence of these rat IFN cDNA clones revealed i. the partial presence of the coding region of the gene and ii all cDNA clones were derived from the same subtype of rat IFN-alpha mRNA...

journal_title：Nucleic acids research

authors： Dijkema R,Pouwels P,de Reus A,Schellekens H

更新日期：1984-01-25 00:00:00

abstract：:A growing body of evidence suggests that genes transcribed by RNA polymerase III exhibit multiple functions within a chromosome. While the predominant function of these genes is the synthesis of RNA molecules, certain RNA polymerase III genes also function as genomic landmarks. Transfer RNA genes are known to exhibit ...

journal_title：Nucleic acids research

authors： Simms TA,Miller EC,Buisson NP,Jambunathan N,Donze D

更新日期：2004-09-30 00:00:00

abstract：:This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology software environment: the lack of both a fast and user-friendly visualization tool and a standard for structural analyses of simulated systems. We introduce here oxView, a web browser-based visualizer that can load structures with ov...

journal_title：Nucleic acids research

authors： Poppleton E,Bohlin J,Matthies M,Sharma S,Zhang F,Šulc P

更新日期：2020-07-09 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：:4'-Acylated thymidines represent a new class of DNA chain terminators, since they have been shown to act as post-incorporation chain-terminating nucleotides despite the presence of a free 3'-hydroxyl group. Here, we describe the action of the 4'-acetyl- (MeTTP) and 4'-propanoylthymidine 5'-triphosphate (EtTTP) on HIV-...

journal_title：Nucleic acids research

authors： Marx A,Amacker M,Stucki M,Hübscher U,Bickle TA,Giese B

更新日期：1998-09-01 00:00:00

abstract：:The interaction specificity of salmon sperm DNA with 2-hydroxyethanethionlato(2,2',2''-terpyridine)platinum(II),PtTS has been studied. The results of 1H and 13C nuclear magnetic resonance, flow dichroism and circular dichroism studies are found to be consistent with an intercalation mode of binding as has been propose...

journal_title：Nucleic acids research

authors： Gabbay EJ,Adkins MA,Yen S

更新日期：1979-10-25 00:00:00

abstract：:The nucleoside analogs 1-(2'-deoxy-beta-D-ribofuranosyl)- 3-nitropyrrole (9), 1-(2'-deoxy-beta-D-ribofuranosyl)-4-nitropyrazole (10), 1-(2'-deoxy-beta-D-ribofuranosyl)-4-nitroimidazole (11) and 1-(2'-deoxy-beta-D-ribofuranosyl)-5-nitroindole (21) were incorporated into the oligonucleotide 5'-d(CGCXAATTYGCG)-3'in the f...

journal_title：Nucleic acids research

authors： Bergstrom DE,Zhang P,Johnson WT

更新日期：1997-05-15 00:00:00

abstract：:A large number of signalling pathways converge on p53 to induce different cellular stress responses that aim to promote cell cycle arrest and repair or, if the damage is too severe, to induce irreversible senescence or apoptosis. The differentiation of p53 activity towards specific cellular outcomes is tightly regulat...

journal_title：Nucleic acids research

authors： Haronikova L,Olivares-Illana V,Wang L,Karakostis K,Chen S,Fåhraeus R

更新日期：2019-04-23 00:00:00