Localized structural frustration for evaluating the impact of sequence variants.

abstract：:Bacteriophage DNA packaging motors translocate their genomic DNA into viral heads, compacting it to near-crystalline density. The Bacillus subtilis phage 29 has a unique ring of RNA (pRNA) that is an essential component of its motor, serving as a scaffold for the packaging ATPase. Previously, deletion of a three-base ...

journal_title：Nucleic acids research

authors： Harjes E,Kitamura A,Zhao W,Morais MC,Jardine PJ,Grimes S,Matsuo H

更新日期：2012-10-01 00:00:00

abstract：:We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5'-alternative splicing, 3'-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein s...

journal_title：Nucleic acids research

authors： Huang HD,Horng JT,Lin FM,Chang YC,Huang CC

更新日期：2005-01-01 00:00:00

abstract：:The vitamin D receptor mediates the signal of 1 alpha, 25-dihydroxyvitamin D3 by binding to vitamin D responsive elements in DNA as a homodimer or as a heterodimer composed of one vitamin D receptor subunit and one retinoid X receptor subunit. We have mapped the dimerization interfaces of the vitamin D receptor that i...

journal_title：Nucleic acids research

authors： Nishikawa J,Kitaura M,Imagawa M,Nishihara T

更新日期：1995-02-25 00:00:00

abstract：:Phylogenetic analysis of Y-family DNA polymerases suggests that it can be subdivided into several discrete branches consisting of UmuC/DinB/Rev1/Rad30/Rad30A and Rad30B. The most diverse is the DinB family that is found in all three kingdoms of life. Searches of the complete genome of the crenarchaeon Sulfolobus solfa...

journal_title：Nucleic acids research

authors： Boudsocq F,Iwai S,Hanaoka F,Woodgate R

更新日期：2001-11-15 00:00:00

abstract：:Genetic recombination in meiosis plays an important role in generating diversity of genetic information. In yeast an Escherichia coli RecA-like gene, DMC1, is expressed in meiotic prophase and its product co-localizes with Rad51 protein on zygotene chromosomes. We have cloned the mouse and human homologs of the yeast ...

journal_title：Nucleic acids research

authors： Habu T,Taki T,West A,Nishimune Y,Morita T

更新日期：1996-02-01 00:00:00

abstract：:To study the role of the poly(A) tail length during the replication of poly(A)-containing plus-strand RNA virus, we have developed a simple reverse transcription polymerase chain reaction (RT-PCR)-based method that substantially improves the previously reported PAT [poly(A) test] assay. In contrast to the PAT assay, t...

journal_title：Nucleic acids research

authors： Kusov YY,Shatirishvili G,Dzagurov G,Gauss-Müller V

更新日期：2001-06-15 00:00:00

abstract：:We had shown previously (3) that the E. coli argE gene could be turned-on by an IS3 element inserted in orientation II near the 5' end of the gene. Here we show that this effect is due to the presence of an outward promoter located on IS3. The exact site of insertion of IS3 was determined by DNA sequencing. Using the ...

journal_title：Nucleic acids research

authors： Charlier D,Piette J,Glansdorff N

更新日期：1982-10-11 00:00:00

abstract：:We describe here the cloning, characterization and expression in E. coli of the gene coding for a DNA methylase from Spiroplasma sp. strain MQ1 (M.SssI). This enzyme methylates completely and exclusively CpG sequences. The Spiroplasma gene was transcribed in E. coli using its own promoter. Translation of the entire me...

journal_title：Nucleic acids research

authors： Renbaum P,Abrahamove D,Fainsod A,Wilson GG,Rottem S,Razin A

更新日期：1990-03-11 00:00:00

abstract：:Tumor formation is partially driven by DNA copy number changes, which are typically measured using array comparative genomic hybridization, SNP arrays and DNA sequencing platforms. Many techniques are available for detecting recurring aberrations across multiple tumor samples, including CMAR, STAC, GISTIC and KC-SMART...

journal_title：Nucleic acids research

authors： van Dyk E,Reinders MJ,Wessels LF

更新日期：2013-05-01 00:00:00

abstract：:We have determined the genomic structure of the fosB gene and shown that it consists of 4 exons and 3 introns at positions also found in the c-fos gene. By deletion analysis we have characterized a region upstream of the TATA box which is the promoter region of the gene. Several consensus sequences have been identifie...

journal_title：Nucleic acids research

authors： Lazo PS,Dorfman K,Noguchi T,Mattéi MG,Bravo R

更新日期：1992-01-25 00:00:00

abstract：:We present a new publicly accessible web-service, RiboSoft, which implements a comprehensive hammerhead ribozyme design procedure. It accepts as input a target sequence (and some design parameters) then generates a set of ranked hammerhead ribozymes, which target the input sequence. This paper describes the implemente...

journal_title：Nucleic acids research

authors： Kharma N,Varin L,Abu-Baker A,Ouellet J,Najeh S,Ehdaeivand MR,Belmonte G,Ambri A,Rouleau G,Perreault J

更新日期：2016-02-29 00:00:00

abstract：:The nucleotide sequence of the portion of a Bacillus subtilis (strain PAP115) 3 kb Pst I fragment which contains an endo-beta-1, 4-glucanase gene has been determined. This gene encodes a protein of 499 amino acid residues (Mr = 55,234) with a typical B. subtilis signal peptide. Escherichia coli which has been transfor...

journal_title：Nucleic acids research

authors： MacKay RM,Lo A,Willick G,Zuker M,Baird S,Dove M,Moranelli F,Seligy V

更新日期：1986-11-25 00:00:00

abstract：:MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates high-quality DNA methylomes across a variety of species and provides an interactive browser for visualization of methylation data. Here, we present an updated implementation of MethBank (version 3.0) by incorporating more DNA methylomes from multi...

journal_title：Nucleic acids research

authors： Li R,Liang F,Li M,Zou D,Sun S,Zhao Y,Zhao W,Bao Y,Xiao J,Zhang Z

更新日期：2018-01-04 00:00:00

abstract：:The solid phase synthesis of oligoribonucleotides using the H-phosphonate approach and the 1-[(2-chloro-4-methyl)phenyl]-4-methoxypiperidin-4-yl (Ctmp) and dimethoxytrityl (DMTr) groups, respectively, for the protection of the 2'- and 5'-hydroxy functions is described. The use of a new reagent, tris-(1,1,1,3,3,3-hexaf...

journal_title：Nucleic acids research

authors： Sakatsume O,Ohtsuki M,Takaku H,Reese CB

更新日期：1989-05-25 00:00:00

abstract：:In eukaryotic ribosome, the N domain of polypeptide release factor eRF1 is involved in decoding stop signals in mRNAs. However, structure of the decoding site remains obscure. Here, we specifically altered the stop codon recognition pattern of human eRF1 by point mutagenesis of the invariant Glu55 and Tyr125 residues ...

journal_title：Nucleic acids research

authors： Kolosov P,Frolova L,Seit-Nebi A,Dubovaya V,Kononenko A,Oparina N,Justesen J,Efimov A,Kisselev L

更新日期：2005-11-10 00:00:00

abstract：:Homing endonucleases (HEs) cut long DNA target sites with high specificity to initiate and target the lateral transfer of mobile introns or inteins. This high site specificity of HEs makes them attractive reagents for gene targeting to promote DNA modification or repair. We have generated several hundred catalytically...

journal_title：Nucleic acids research

authors： Li H,Pellenz S,Ulge U,Stoddard BL,Monnat RJ Jr

更新日期：2009-04-01 00:00:00

abstract：:It is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. ConSurf (http://consurf.tau.ac.il) and ConSeq (http://conseq.tau.ac.il) are two well-established web servers for calculating the evolutionar...

journal_title：Nucleic acids research

authors： Ashkenazy H,Erez E,Martz E,Pupko T,Ben-Tal N

更新日期：2010-07-01 00:00:00

abstract：:Tissue-specific gene expression is critical in understanding biological processes, physiological conditions, and disease. The identification and appropriate use of tissue-specific genes (TissGenes) will provide important insights into disease mechanisms and organ-specific therapeutic targets. To better understand the ...

journal_title：Nucleic acids research

authors： Kim P,Park A,Han G,Sun H,Jia P,Zhao Z

更新日期：2018-01-04 00:00:00

abstract：:Retinoic acid-inducible gene I (RIG-I) is a pattern recognition receptor expressed in metazoan cells that is responsible for eliciting the production of type I interferons and pro-inflammatory cytokines upon detection of intracellular, non-self RNA. Structural studies of RIG-I have identified a novel Pincer domain com...

journal_title：Nucleic acids research

authors： Rawling DC,Kohlway AS,Luo D,Ding SC,Pyle AM

更新日期：2014-10-01 00:00:00

abstract：:After ionising radiation double-strand breaks (dsb) are lethal if not repaired or misrepaired. Cell killing is greatly enhanced by hyperthermia and it is questioned here whether heat not only affects dsb repair capacity but also fidelity in a chromosomal context. dsb repair experiments were designed so as to mainly sc...

journal_title：Nucleic acids research

authors： El-Awady RA,Dikomey E,Dahm-Daphi J

更新日期：2001-05-01 00:00:00

abstract：:From a recombinant lambda phage, we have determined a 387 bp sequence containing a mouse lysine tRNA gene. The putative lys tRNA (anticodon UUU) differs from rabbit liver lys tRNA at five positions. The flanking regions of the mouse gene are not generally homologous to published human and Drosophila lys tRNA genes. Ho...

journal_title：Nucleic acids research

authors： Han JH,Harding JD

更新日期：1983-04-11 00:00:00

abstract：:Arabidopsis microRNA (miRNA) genes (MIR) give rise to 20- to 22-nt miRNAs that are generated predominantly by the type III endoribonuclease Dicer-like 1 (DCL1) but do not require any RNA-dependent RNA Polymerases (RDRs) or RNA Polymerase IV (Pol IV). Here, we identify a novel class of non-conserved MIR genes that give...

journal_title：Nucleic acids research

authors： Chellappan P,Xia J,Zhou X,Gao S,Zhang X,Coutino G,Vazquez F,Zhang W,Jin H

更新日期：2010-11-01 00:00:00

abstract：:Contrary to the expectation, the Merrifield polystyrene resin, 2% cross-linked by divinylbenzene, is as efficient as the polyacrylmorpholide resin for the synthesis of polydeoxyribonucleotides using a phosphotriester method. On the Merrifield resin, the tetradecamer, dTpCpGpTpCpApApCpTpGpGpCpTpT, and the hexadecamer, ...

journal_title：Nucleic acids research

authors： Miyoshi K,Arentzen R,Huang T,Itakura K

更新日期：1980-11-25 00:00:00

abstract：:We have reported that an upstream stimulatory factor (USF) binding site is functional in transcription of the heme oxygenase-1 gene. In this study, we examined the role of USF in the induced state. By transient expression analyses with the chloramphenicol acetyl-transferase gene, we found that the USF binding site pla...

journal_title：Nucleic acids research

authors： Maeshima H,Sato M,Ishikawa K,Katagata Y,Yoshida T

更新日期：1996-08-01 00:00:00

abstract：:High-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP, also called CLIP-Seq) has been used to map global RNA-protein interactions. However, a critical caveat of HITS-CLIP results is that they contain non-linear background noise-different extent of non-specific interactions caused b...

journal_title：Nucleic acids research

authors： Park S,Ahn SH,Cho ES,Cho YK,Jang ES,Chi SW

更新日期：2018-11-30 00:00:00

abstract：:VA RNA(I) is a non-coding adenoviral transcript that counteracts the host cell anti-viral defenses such as immune responses mediated via PKR. We investigated potential alternate secondary structure conformations within the PKR-binding domain of VA RNA(I) using site-directed mutagenesis, RNA UV-melting analysis and enz...

journal_title：Nucleic acids research

authors： Wahid AM,Coventry VK,Conn GL

更新日期：2009-09-01 00:00:00

abstract：:Signal Transducers and Activators of Transcription (STAT) 5A/B regulate cytokine-inducible genes upon binding to GAS motifs. It is not known what percentage of genes with GAS motifs bind to and are regulated by STAT5. Moreover, it is not clear whether genome-wide STAT5 binding is modulated by its concentration. To cla...

journal_title：Nucleic acids research

authors： Zhu BM,Kang K,Yu JH,Chen W,Smith HE,Lee D,Sun HW,Wei L,Hennighausen L

更新日期：2012-05-01 00:00:00

abstract：:Apolipoprotein B (apoB) mRNA editing is a nuclear event that minimally requires the RNA substrate, APOBEC-1 and APOBEC-1 Complementation Factor (ACF). The co-localization of these macro-molecules within the nucleus and the modulation of hepatic apoB mRNA editing activity have been described following a variety of meta...

journal_title：Nucleic acids research

authors： Lehmann DM,Galloway CA,Sowden MP,Smith HC

更新日期：2006-07-04 00:00:00

abstract：:We searched for nucleotide excision repair in human cell-free extracts using two assays: damage-specific incision of DNA (the nicking assay) and damage-stimulated DNA synthesis (the repair synthesis assay). HeLa cell-free extract prepared by the method of Manley et al. (1980) has a weak nicking activity on UV irradiat...

journal_title：Nucleic acids research

authors： Sibghatullah,Husain I,Carlton W,Sancar A

更新日期：1989-06-26 00:00:00

abstract：:Short interfering RNAs (siRNAs) are valuable reagents for sequence-specific inhibition of gene expression via the RNA interference (RNAi) pathway. Although it has been proposed that the relative thermodynamic stability at the 5'-ends of siRNAs plays a crucial role in siRNA strand selection, we demonstrate here that a ...

journal_title：Nucleic acids research

authors： Sano M,Sierant M,Miyagishi M,Nakanishi M,Takagi Y,Sutou S

更新日期：2008-10-01 00:00:00