Cloning and functional analysis of spliced isoforms of human nuclear factor I-X: interference with transcriptional activation by NFI/CTF in a cell-type specific manner.

abstract：:Argonaute (Ago) proteins function in RNA silencing as components of the RNA-induced silencing complex (RISC). In lower organisms, the small interfering RNA and miRNA pathways diverge due in part to sorting mechanisms that direct distinct small RNA (sRNA) duplexes onto specific Ago-RISCs. However, such sorting mechanis...

journal_title：Nucleic acids research

authors： Yamakawa N,Okuyama K,Ogata J,Kanai A,Helwak A,Takamatsu M,Imadome K,Takakura K,Chanda B,Kurosaki N,Yamamoto H,Ando K,Matsui H,Inaba T,Kotani A

更新日期：2014-04-01 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：:TATA-binding protein (TBP) is central to the regulation of eukaryotic transcription initiation. Recruitment of TBP to target genes can be positively regulated by one of two basal transcription factor complexes: SAGA or TFIID. Negative regulation of TBP promoter association can be performed by Mot1p or the NC2 complex....

journal_title：Nucleic acids research

authors： Spedale G,Meddens CA,Koster MJ,Ko CW,van Hooff SR,Holstege FC,Timmers HT,Pijnappel WW

更新日期：2012-02-01 00:00:00

abstract：:dITP may be generated from dATP by a slow, nonenzymatic hydrolysis. While [3H]dITP was degraded rapidly to [3H]deoxyinosine by HeLa cell nuclear extracts, no net degradation of [3H]dITP was observed in the presence of physiological concentrations of ATP, apparently because the extract contained deoxynucleoside diphosp...

journal_title：Nucleic acids research

authors： Myrnes B,Guddal PH,Krokan H

更新日期：1982-06-25 00:00:00

abstract：:Pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). Here, we report on changes that ha...

journal_title：Nucleic acids research

authors： Punta M,Coggill PC,Eberhardt RY,Mistry J,Tate J,Boursnell C,Pang N,Forslund K,Ceric G,Clements J,Heger A,Holm L,Sonnhammer EL,Eddy SR,Bateman A,Finn RD

更新日期：2012-01-01 00:00:00

abstract：:Hepatitis C virus (HCV) infection is a major cause of human chronic liver disease and hepatocellular carcinoma. G-quadruplex (G4) is an important four-stranded secondary structure of nucleic acids. Recently, we discovered that the core gene of HCV contains a G4 RNA structure; however, the interaction between the HCV c...

journal_title：Nucleic acids research

authors： Bian WX,Xie Y,Wang XN,Xu GH,Fu BS,Li S,Long G,Zhou X,Zhang XL

更新日期：2019-01-10 00:00:00

abstract：:Properties of a mutant bacteriophage T2 DNA [N:(6)-adenine] methyltransferase (T2 Dam MTase) have been investigated for its potential utilization in RecA-assisted restriction endonuclease (RARE) cleavage. Steady-state kinetic analyses with oligonucleotide duplexes revealed that, compared to wild-type T4 Dam, both wild...

journal_title：Nucleic acids research

authors： Minko I,Hattman S,Lloyd RS,Kossykh V

更新日期：2001-04-01 00:00:00

abstract：:To explain the activation of transcription by a remote enhancer, two models are most often considered, namely looping and scanning. A scanning model, also referred to as 'polymerase entry site' model predicts that for two adjacent promoters the one proximal to an enhancer would be preferentially activated. Preferentia...

journal_title：Nucleic acids research

authors： Heuchel R,Matthias P,Schaffner W

更新日期：1989-11-25 00:00:00

abstract：:An improved method was developed for microdissection and cloning of metaphase as well as pachytene chromosomes. The protocol incorporates efficient ligation of chromosomal DNA with linker adaptors, abolishment of microcloning steps and the reduction of micromanipulation. The threshold for amplifying genomic DNA templa...

journal_title：Nucleic acids research

authors： Ponelies N,Stein N,Weber G

更新日期：1997-09-01 00:00:00

abstract：:Achiral pseudonucleosides bearing an anthraquinone moiety have been incorporated into deoxyoligonucleotides in internal, 3' and 5' positions. The ability of these modified deoxyoligonucleotides to hybridize to complementary RNA and DNA was investigated using Tm measurements. The anthraquinone was shown to enhance bind...

journal_title：Nucleic acids research

authors： Lin KY,Matteucci M

更新日期：1991-06-11 00:00:00

abstract：:DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polym...

journal_title：Nucleic acids research

authors： Satange R,Chuang CY,Neidle S,Hou MH

更新日期：2019-09-19 00:00:00

abstract：:Sequence-dependent variation in structure and dynamics of a DNA duplex, collectively referred to as 'DNA shape', critically impacts interactions between DNA and proteins. Here, a method based on the technique of site-directed spin labeling was developed to experimentally map shapes of two DNA duplexes that contain res...

journal_title：Nucleic acids research

authors： Ding Y,Zhang X,Tham KW,Qin PZ

更新日期：2014-10-01 00:00:00

abstract：:The 'sandwich' binding format, which uses two reagents that can bind simultaneously to a given analyte, is the gold standard in diagnostics and many biochemical techniques. One of the bottlenecks in creating a sandwich assay is identifying pairs of reagents that bind non-competitively to the target. To bridge this gap...

journal_title：Nucleic acids research

authors： Gorman KT,Roby LC,Giuffre A,Huang R,Kay BK

更新日期：2017-10-13 00:00:00

abstract：:DNA mismatches that occur between vector homology arms and chromosomal target sequences reduce gene targeting frequencies in several species; however, this has not been reported in human cells. Here we demonstrate that even a single mismatched base pair can significantly decrease human gene targeting frequencies. In a...

journal_title：Nucleic acids research

authors： Deyle DR,Li LB,Ren G,Russell DW

更新日期：2014-03-01 00:00:00

abstract：:The STE2 gene of the yeast Saccharomyces cerevisiae encodes a component of the receptor for the oligopeptide pheromone alpha-factor. We have cloned and determined the nucleotide sequence of the STE2 gene. A sequence involved in the control of cell-type expression of the STE2 gene was found 5' of an open reading frame ...

journal_title：Nucleic acids research

authors： Burkholder AC,Hartwell LH

更新日期：1985-12-09 00:00:00

abstract：:We have analysed DNA modification in a HapII site (CCGG) present in the major intron of the discontinuous rabbit beta-globin gene. In most somatic tissues, including erythroid and non-erythroid tissues, about 50% of the DNA is resistant to cleavage at this site by HapII, though 100% cleavage is found with the isoschiz...

journal_title：Nucleic acids research

authors： Waalwijk C,Flavell RA

更新日期：1978-12-01 00:00:00

abstract：:Microarrays are an effective tool for monitoring genome-wide gene expression levels. In current microarray analyses, the majority of genes on arrays are frequently eliminated for further analysis because the changes in their expression levels (ratios) are considered to be not significant. This strategy risks failure t...

journal_title：Nucleic acids research

authors： Yano K,Imai K,Shimizu A,Hanashita T

更新日期：2006-03-14 00:00:00

abstract：:Long Interspersed Element-1 (LINE-1) retrotransposition contributes to inter- and intra-individual genetic variation and occasionally can lead to human genetic disorders. Various strategies have been developed to identify human-specific LINE-1 (L1Hs) insertions from short-read whole genome sequencing (WGS) data; howev...

journal_title：Nucleic acids research

authors： Zhou W,Emery SB,Flasch DA,Wang Y,Kwan KY,Kidd JM,Moran JV,Mills RE

更新日期：2020-02-20 00:00:00

abstract：:A multipurpose plasmid, pUR 250, has been constructed. It contains seven unique cloning sites (Hind III, Xba I, Sal I, Acc I, Hinc II, BamH I and EcoR I) in a small region of its lac Z gene part. Insertion of foreign DNA into the plasmid can be easily detected. Plasmid DNA isolated from a clone by a rapid method can b...

journal_title：Nucleic acids research

authors： Rüther U

更新日期：1982-10-11 00:00:00

abstract：:Eucaryotic transcription initiation by RNA polymerase II involves protein:DNA interactions during the formation of a transcription complex. In addition to RNA polymerase II there are at least five other general transcription factors necessary for initiation with the adenovirus major late promoter. One of these, TFIIA,...

journal_title：Nucleic acids research

authors： Burke C,Yu XB,Marchitelli L,Davis EA,Ackerman S

更新日期：1990-06-25 00:00:00

abstract：:The Saccharomyces cerevisiae viruses are non-infectious double-stranded (ds) RNA viruses present in most laboratory strains of yeast. Their genome consists of one or more dsRNAs separately encapsidated in particles composed mainly of one polypeptide, which has a Mr of 88 kdaltons in the best-studied viral subtype. A l...

journal_title：Nucleic acids research

authors： Bruenn J,Madura K,Siegel A,Miner Z,Lee M

更新日期：1985-03-11 00:00:00

abstract：:To gain insight into the mechanistic link between translation termination and nonsense-mediated mRNA decay (NMD), we depleted the ribosome recycling factor ABCE1 in human cells, resulting in an upregulation of NMD-sensitive mRNAs. Suppression of NMD on these mRNAs occurs prior to their SMG6-mediated endonucleolytic cl...

journal_title：Nucleic acids research

authors： Annibaldis G,Domanski M,Dreos R,Contu L,Carl S,Kläy N,Mühlemann O

更新日期：2020-10-09 00:00:00

abstract：:During culture, a chicken B cell line DT40 spontaneously mutates immunoglobulin (Ig) genes by gene conversion, which involves activation-induced cytidine deaminase (AID)-dependent homologous recombination of the variable (V) region gene with upstream pseudo-V genes. To explore whether this mutation mechanism can targe...

journal_title：Nucleic acids research

authors： Kanayama N,Todo K,Takahashi S,Magari M,Ohmori H

更新日期：2006-01-18 00:00:00

abstract：:LOCtarget is a web server and database that predicts and annotates sub-cellular localization for structural genomics targets; LOCnet is one of the methods used in LOCtarget that can predict sub-cellular localization for all eukaryotic and prokaryotic proteins. Targets are taken from the central registration database f...

journal_title：Nucleic acids research

authors： Nair R,Rost B

更新日期：2004-07-01 00:00:00

abstract：:The properties of the interaction of 5-fluorocytosine-containing DNA with the EcoRII methyltransferase were studied. The DNA used was either a polymer synthesized in vitro, or a 20-mer containing one CCA/TGG sequence. The DNA could be methylated by the enzyme. In the process the enzyme formed a tight binding adduct wi...

journal_title：Nucleic acids research

authors： Friedman S,Ansari N

更新日期：1992-06-25 00:00:00

abstract：:A list of DNA sequences cloned from the human genome is presented. Intended as a guide to clone availability, this list includes published reports of cDNA, genomic and synthetic clones comprising gene and pseudogene sequences, uncharacterised DNA segments and repetitive DNA elements. ...

journal_title：Nucleic acids research

authors： Schmidtke J,Cooper DN

更新日期：1988-01-01 00:00:00

abstract：:The recognition of human tRNA(Leu) or tRNA(Ser) by cognate aminoacyl- tRNA synthetases has distinct requirements. Only one base change (A73-->G) in tRNA(Leu) is required to generate an efficient serine acceptor in vitro, whereas several changes in three structural domains (the acceptor stem, DHU loop and long extra ar...

journal_title：Nucleic acids research

authors： Breitschopf K,Gross HJ

更新日期：1996-02-01 00:00:00

abstract：:Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell M...

journal_title：Nucleic acids research

authors： Smyth RP,Smith MR,Jousset AC,Despons L,Laumond G,Decoville T,Cattenoz P,Moog C,Jossinet F,Mougel M,Paillart JC,von Kleist M,Marquet R

更新日期：2018-05-18 00:00:00

abstract：:Here we report proof-of-principle for a microsphere-based genotyping assay that detects single nucleotide polymorphisms (SNPs) directly from human genomic DNA samples. This assay is based on a structure-specific cleavage reaction that achieves single base discrimination with a 5'-nuclease which recognizes a tripartite...

journal_title：Nucleic acids research

authors： Rao KV,Stevens PW,Hall JG,Lyamichev V,Neri BP,Kelso DM

更新日期：2003-06-01 00:00:00

abstract：:RNA can directly bind to purine-rich DNA via Hoogsteen base pairing, forming a DNA:RNA triple helical structure that anchors the RNA to specific sequences and allows guiding of transcription regulators to distinct genomic loci. To unravel the prevalence of DNA:RNA triplexes in living cells, we have established a fast ...

journal_title：Nucleic acids research

authors： Sentürk Cetin N,Kuo CC,Ribarska T,Li R,Costa IG,Grummt I

更新日期：2019-03-18 00:00:00