Human Rad51 filaments on double- and single-stranded DNA: correlating regular and irregular forms with recombination function.

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：:In this paper, we present evidence that an efficient Rho-dependent terminator can be created by introducing a simple (AG/TC) n DNA repeat into a transcription unit. The Rho termination activity in vivo and in vitro is dependent on the length and the orientation of the insert. The transcription of at least 30 bp of the...

journal_title：Nucleic acids research

authors： Guérin M,Robichon N,Geiselmann J,Rahmouni AR

更新日期：1998-11-01 00:00:00

abstract：:SV40 DNA form I is expressed efficiently after its injection into the nuclei of Xenopus laevis oocytes, resulting in the synthesis of RNA and protein products of both viral late and early transcription units. However it was observed that injection of SV40 genes cloned into pBR322 or related plasmids yielded vastly red...

journal_title：Nucleic acids research

authors： Michaeli T,Prives C

更新日期：1987-02-25 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：:The HIV-1 nucleocapsid (NC) protein is a small, basic protein containing two retroviral zinc fingers. It is a highly active nucleic acid chaperone; because of this activity, it plays a crucial role in virus replication as a cofactor during reverse transcription, and is probably important in other steps of the replicat...

journal_title：Nucleic acids research

authors： Fisher RJ,Fivash MJ,Stephen AG,Hagan NA,Shenoy SR,Medaglia MV,Smith LR,Worthy KM,Simpson JT,Shoemaker R,McNitt KL,Johnson DG,Hixson CV,Gorelick RJ,Fabris D,Henderson LE,Rein A

更新日期：2006-01-24 00:00:00

abstract：:Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the identification and classification of new members of known sequence families, and distributes annotation of ncRNAs in over 200 comp...

journal_title：Nucleic acids research

authors： Griffiths-Jones S,Moxon S,Marshall M,Khanna A,Eddy SR,Bateman A

更新日期：2005-01-01 00:00:00

abstract：:Upstream open reading frame (uORF)-mediated translational inhibition is important in controlling key regulatory genes expression. However, understanding the underlying molecular mechanism of such uORF-mediated control system in vivo is challenging in the absence of an animal model. Therefore, we generated a zebrafish ...

journal_title：Nucleic acids research

authors： Lee HC,Chen YJ,Liu YW,Lin KY,Chen SW,Lin CY,Lu YC,Hsu PC,Lee SC,Tsai HJ

更新日期：2011-11-01 00:00:00

abstract：:The SeqA protein binds hemi-methylated GATC sites and forms structures that sequester newly replicated origins and trail the replication forks. Cells that lack SeqA display signs of replication fork disintegration. The broken forks could arise because of over-initiation (the launching of too many forks) or lack of dyn...

journal_title：Nucleic acids research

authors： Pedersen IB,Helgesen E,Flåtten I,Fossum-Raunehaug S,Skarstad K

更新日期：2017-06-20 00:00:00

abstract：:The multifunctional HCV core protein consists of a hydrophilic RNA interacting D1 domain and a hydrophobic D2 domain interacting with membranes and lipid droplets. The core D1 domain was found to possess nucleic acid annealing and strand transfer properties. To further understand these chaperone properties, we investi...

journal_title：Nucleic acids research

authors： Sharma Kk,Didier P,Darlix JL,de Rocquigny H,Bensikaddour H,Lavergne JP,Pénin F,Lessinger JM,Mély Y

更新日期：2010-06-01 00:00:00

abstract：:Extensive efforts have been directed at the discovery, investigation and clinical monitoring of targeted therapeutics. These efforts may be facilitated by the convenient access of the genetic, proteomic, interactive and other aspects of the therapeutic targets. Here, we describe an update of the Therapeutic target dat...

journal_title：Nucleic acids research

authors： Li YH,Yu CY,Li XX,Zhang P,Tang J,Yang Q,Fu T,Zhang X,Cui X,Tu G,Zhang Y,Li S,Yang F,Sun Q,Qin C,Zeng X,Chen Z,Chen YZ,Zhu F

更新日期：2018-01-04 00:00:00

abstract：:A novel expression system was established that allows expression and propagation of the human hepatitis B virus (HBV) genome in cultured animal cells. An overlength HBV genome encoding the viral pregenomic RNA was put under transcriptional control of the human metallothionein IIA promoter thereby replacing the endogen...

journal_title：Nucleic acids research

authors： Junker M,Galle P,Schaller H

更新日期：1987-12-23 00:00:00

abstract：:RegAnalyst is a user-friendly web interface that integrates MoPP (Motif Prediction Program), MyPatternFinder (pattern detection tool) and MycoRegDB (mycobacterial promoter and regulatory elements database). Since motif discovery is a challenging task, numerous tools have been developed over the past few years. Strikin...

journal_title：Nucleic acids research

authors： Sharma D,Mohanty D,Surolia A

更新日期：2009-07-01 00:00:00

abstract：:We describe a database of macromolecular motions meant to be of general use to the structural community. The database, which is accessible on the World Wide Web with an entry point at http://bioinfo.mbb.yale.edu/MolMovDB , attempts to systematize all instances of protein and nucleic acid movement for which there is at...

journal_title：Nucleic acids research

authors： Gerstein M,Krebs W

更新日期：1998-09-15 00:00:00

abstract：:The sequencing of the full transcriptome (RNA-seq) has become the preferred choice for the measurement of genome-wide gene expression. Despite its widespread use, challenges remain in RNA-seq data analysis. One often-overlooked aspect is normalization. Despite the fact that a variety of factors or 'batch effects' can ...

journal_title：Nucleic acids research

authors： Peixoto L,Risso D,Poplawski SG,Wimmer ME,Speed TP,Wood MA,Abel T

更新日期：2015-09-18 00:00:00

abstract：:RNA editing by adensosine deaminases is a widespread mechanism to alter genetic information in metazoa. In addition to modifications in non-coding regions, editing contributes to diversification of protein function, in analogy to alternative splicing. However, although splicing programs respond to external signals, fa...

journal_title：Nucleic acids research

authors： Balik A,Penn AC,Nemoda Z,Greger IH

更新日期：2013-01-01 00:00:00

abstract：:Bile acid biosynthesis is subjected to feedback regulation whereby bile acids down-regulate their own synthesis. The major point of this regulation is at the level of cholesterol 7alpha-hydroxylase (7alpha-hydroxylase), which controls bile acid output from the classic pathway. This regulation is at the level of transc...

journal_title：Nucleic acids research

authors： del Castillo-Olivares A,Gil G

更新日期：2000-09-15 00:00:00

abstract：:The SRPDB (signal recognition particle database) provides aligned SRP RNA and protein sequences, annotated and phylogenetically ordered. This release includes 82 SRP RNAs (including 22 bacterial and 9 archaeal homologs) and a total of 20 protein sequences representing SRP9, SRP14, SRP19, SRP54, SRP68, and SRP72. The o...

journal_title：Nucleic acids research

authors： Zwieb C,Larsen N

更新日期：1994-09-01 00:00:00

abstract：:Uracil may occur in DNA due to either cytosine deamination or thymine replacing incorporation. Its quantitative characterization is important in assessing DNA damages in cells with perturbed thymidylate metabolism or within different DNA segments involved in immunoglobulin gene diversification. The archaeal DNA polyme...

journal_title：Nucleic acids research

authors： Horváth A,Vértessy BG

更新日期：2010-11-01 00:00:00

abstract：:The nucleotide sequence of Drosophila melanogaster methionine tRNAi was determined to be: pA-G-C-A-G-A-G-U-m1G-m2G-C-G-C-A-G-U-G-G-A-A-G-C-G-U-m2G-C-U-G-G-G-C-C-C-A-U-t6A-A-C-C-C-A-G-A-G-m7G-D-m5C-C-C-G-A-G-G-A-U-C-G-m1A-A-A-C-C-U-U-G-C-U-C-U-G-C-U-A-C-C-A(OH). It differs from vertebrate initiator tRNAs in only 6 out ...

journal_title：Nucleic acids research

authors： Silverman S,Heckman J,Cowling GJ,Delaney AD,Dunn RJ,Gillam IC,Tener GM,Söll D,RajBhandary UL

更新日期：1979-02-01 00:00:00

abstract：:Rap1 is an essential DNA-binding factor from the yeast Saccharomyces cerevisiae involved in transcription and telomere maintenance. Its binding to DNA targets Rap1 at particular loci, and may optimize its ability to form functional macromolecular assemblies. It is a modular protein, rich in large potentially unfolded ...

journal_title：Nucleic acids research

authors： Matot B,Le Bihan YV,Lescasse R,Pérez J,Miron S,David G,Castaing B,Weber P,Raynal B,Zinn-Justin S,Gasparini S,Le Du MH

更新日期：2012-04-01 00:00:00

abstract：:RNA sequencing (RNA-Seq) is a powerful tool for analyzing the identity of cellular RNAs but is often limited by the amount of material available for analysis. In spite of extensive efforts employing existing protocols, we observed that it was not possible to obtain useful sequencing libraries from nuclear RNA derived ...

journal_title：Nucleic acids research

authors： Chu Y,Wang T,Dodd D,Xie Y,Janowski BA,Corey DR

更新日期：2015-06-23 00:00:00

abstract：:Silencing gene expression by siRNAs is rapidly becoming a powerful tool for the genetic analysis of mammalian cells. However, the rapid degradation of siRNA and the limited duration of its action call for an efficient delivery technology. Accordingly, we describe here that Atelocollagen complexed with siRNA is resista...

journal_title：Nucleic acids research

authors： Minakuchi Y,Takeshita F,Kosaka N,Sasaki H,Yamamoto Y,Kouno M,Honma K,Nagahara S,Hanai K,Sano A,Kato T,Terada M,Ochiya T

更新日期：2004-07-22 00:00:00

abstract：:The detailed principles of the hierarchical folding of eukaryotic chromosomes have been revealed during the last two decades. Along with structures composing three-dimensional (3D) genome organization (chromatin compartments, topologically associating domains, chromatin loops, etc.), the molecular mechanisms that are ...

journal_title：Nucleic acids research

authors： Kantidze OL,Razin SV

更新日期：2020-05-21 00:00:00

abstract：:High performance liquid chromatography analysis of imidazole open ring 7-methylguanine, 2-6 diamino-4-hydroxy-5N-methyl-formamidopyrimidine (rom7G), showed two well-separated peaks (fI and fII) of the same magnitude. Rechromatography of each isolated component indicated that they are slowly interconverted to give a 1:...

journal_title：Nucleic acids research

authors： Boiteux S,Belleney J,Roques BP,Laval J

更新日期：1984-07-11 00:00:00

abstract：:The 5' processing of rat pre-tRNA(Lys) and a series of mutant derivatives by rat cytosolic RNase P was examined. In standard, non-kinetic assays, mutant precursors synthesized in vitro with 5' leader sequences of 10, 17, 24, 25, and 46 nucleotides were processed to approximately equal levels and yielded precisely clea...

journal_title：Nucleic acids research

authors： Paisley TE,Van Tuyle GC

更新日期：1994-08-25 00:00:00

abstract：:DAXX displays complex biological functions. Remarkably, DAXX overexpression is a common feature in diverse cancers, which correlates with tumorigenesis, disease progression and treatment resistance. Structurally, DAXX is modular with an N-terminal helical bundle, a docking site for many DAXX interactors (e.g. p53 and ...

journal_title：Nucleic acids research

authors： Mahmud I,Liao D

更新日期：2019-09-05 00:00:00

abstract：:Most E2F-binding sites repress transcription through the recruitment of Retinoblastoma (RB) family members until the end of the G1 cell-cycle phase. Although the MYB promoter contains an E2F-binding site, its transcription is activated shortly after the exit from quiescence, before RB family members inactivation, by u...

journal_title：Nucleic acids research

authors： Álvaro-Blanco J,Urso K,Chiodo Y,Martín-Cortázar C,Kourani O,Arco PG,Rodríguez-Martínez M,Calonge E,Alcamí J,Redondo JM,Iglesias T,Campanero MR

更新日期：2017-09-29 00:00:00

abstract：:DNA binding of heat shock factor 2 (HSF2) is induced during hemin-induced differentiation of human erythroleukemia cell line K562. To identify the transcriptional activation and the regulatory domains of HSF2, we constructed a series of deletion derivatives fused to the yeast GAL4 DNA binding domain and analyzed their...

journal_title：Nucleic acids research

authors： Yoshima T,Yura T,Yanagi H

更新日期：1998-06-01 00:00:00

abstract：:Human tissue-specific genes were reported to be longer than housekeeping genes (both in coding and intronic parts). The competing neutralist and adaptationist models were proposed to explain this observation. Here I show that in human genome the longest are genes with the intermediate expression pattern. From the stan...

journal_title：Nucleic acids research

authors： Vinogradov AE

更新日期：2006-01-01 00:00:00

abstract：:MicA is a trans-encoded small non-coding RNA, which downregulates porin-expression in stationary-phase. In this work, we focus on the role of endoribonucleases III and E on Salmonella typhimurium sRNA MicA regulation. RNase III is shown to regulate MicA in a target-coupled way, while RNase E is responsible for the con...

journal_title：Nucleic acids research

authors： Viegas SC,Silva IJ,Saramago M,Domingues S,Arraiano CM

更新日期：2011-04-01 00:00:00