Transfer RNA identity contributes to transition state stabilization during aminoacyl-tRNA synthesis.

abstract：:When the function of origins of replication in yeast was compromised by placing ARS sequences downstream of strong promoters, ARS activity might have been affected either by transcription or by an altered chromatin configuration induced by the construct. To distinguish between these possibilities, derivatives of the y...

journal_title：Nucleic acids research

authors： Tanaka S,Halter D,Livingstone-Zatchej M,Reszel B,Thoma F

更新日期：1994-09-25 00:00:00

abstract：:RegulonDB, first published 20 years ago, is a comprehensive electronic resource about regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from classic molecular biology experiments, and recently also from high-throughput genomic methodologies. We curated the literature to keep Reg...

journal_title：Nucleic acids research

authors： Santos-Zavaleta A,Salgado H,Gama-Castro S,Sánchez-Pérez M,Gómez-Romero L,Ledezma-Tejeida D,García-Sotelo JS,Alquicira-Hernández K,Muñiz-Rascado LJ,Peña-Loredo P,Ishida-Gutiérrez C,Velázquez-Ramírez DA,Del Moral-Chávez V,Bonavid

更新日期：2019-01-08 00:00:00

abstract：:CLASPIN is an essential mediator in the DNA replication checkpoint, responsible for ATR (ataxia telangiectasia and Rad3-related protein)-dependent activation of CHK1 (checkpoint kinase 1). Here we found a dynamic signaling pathway that regulates CLASPIN turn over. Under unperturbed conditions, the E3 ubiquitin ligase ...

journal_title：Nucleic acids research

authors： Zhu M,Zhao H,Liao J,Xu X

更新日期：2014-12-01 00:00:00

abstract：:A downstream G-rich sequence (GRS), GGGGGAGGUGUGGG, has been previously shown to influence the efficiency of 3' end processing of the SV40 late polyadenylation signal. We have now defined several important parameters for GRS-mediated polyadenylation. The ability of the GRS to influence 3' end processing efficiency was...

journal_title：Nucleic acids research

authors： Bagga PS,Ford LP,Chen F,Wilusz J

更新日期：1995-05-11 00:00:00

abstract：:This review takes a second look at a set of mRNAs that purportedly employ an alternative mechanism of initiation when cap-dependent translation is reduced during mitosis or stress conditions. A closer look is necessary because evidence cited in support of the internal initiation hypothesis is often flawed. When putati...

journal_title：Nucleic acids research

authors： Kozak M

更新日期：2005-11-28 00:00:00

abstract：:During the formation of a transcriptionally active macronucleus, ciliated protozoa excise large numbers of interstitial segments of DNA (internal eliminated sequences; IESs) from their chromosomes. In this study we analyze the published sequences of 20 IESs that interrupt surface protein genes of Paramecium and identi...

journal_title：Nucleic acids research

authors： Klobutcher LA,Herrick G

更新日期：1995-06-11 00:00:00

abstract：:The PRISM web server enables fast and accurate prediction of protein-protein interactions (PPIs). The prediction algorithm is knowledge-based. It combines structural similarity and accounts for evolutionary conservation in the template interfaces. The predicted models are stored in its repository. Given two protein st...

journal_title：Nucleic acids research

authors： Baspinar A,Cukuroglu E,Nussinov R,Keskin O,Gursoy A

更新日期：2014-07-01 00:00:00

abstract：:Minichromosome maintenance (MCM) proteins facilitate replication by licensing origins and unwinding the DNA double strand. Interestingly, the number of MCM hexamers greatly exceeds the number of firing origins suggesting additional roles of MCMs. Here we show a hitherto unanticipated function of MCM2 in cilia formatio...

journal_title：Nucleic acids research

authors： Casar Tena T,Maerz LD,Szafranski K,Groth M,Blätte TJ,Donow C,Matysik S,Walther P,Jeggo PA,Burkhalter MD,Philipp M

更新日期：2019-01-10 00:00:00

abstract：:Automated fluorescence-based DNA sequence analysis offers the possibility to undertake very large scale sequencing projects. Directed strategies, such as the specific-primer-directed sequencing approach ('gene walking'), should prove useful in such projects. Described herein is a study involving the use of this approa...

journal_title：Nucleic acids research

authors： Kaiser RJ,MacKellar SL,Vinayak RS,Sanders JZ,Saavedra RA,Hood LE

更新日期：1989-08-11 00:00:00

abstract：:Plasmid DNA incubated in interphase Xenopus egg extracts is normally assembled into chromatin and then into synthetic nuclei which undergo one round of regulated replication. During a study of restriction endonuclease cut plasmid replication intermediates (RIs) by the Brewer-Fangman 2D gel electrophoresis technique, w...

journal_title：Nucleic acids research

authors： Lucas I,Hyrien O

更新日期：2000-05-15 00:00:00

abstract：:A formaldehyde denaturation map of the replicative form of phiX174 DNA is obtained. The RFI DNA was converted into a linear state by restriction endonuclease pst I which introduces into this DNA a single double-stranded break. The map has four clear-cut peaks. Their positions excellently correlate with the peak positi...

journal_title：Nucleic acids research

authors： Karataev GI,Permogorov VI,Vologodskii AV,Frank-Kamenetskii MD

更新日期：1978-07-01 00:00:00

abstract：:The compilation of 5S rRNA and 5S rRNA gene nucleotide sequences as of 30 September 1996, contains a total of 1661 primary structures of 5S rRNAs or their genes, which is an increase of 928 new sequence entries over the last compilation. It covers sequences from 54 archaea, 449 eubacteria, 34 plastids, nine mitochondr...

journal_title：Nucleic acids research

authors： Specht T,Szymanski M,Barciszewska MZ,Barciszewski J,Erdmann VA

更新日期：1997-01-01 00:00:00

abstract：:Human immunodeficiency virus-1 (HIV-1) leader RNA, which contains double-stranded regions due to inverted repeats, was shown to activate the dsRNA-dependent enzymes associated with the interferon system. HIV-1 leader RNA produced in vitro using SP6 RNA polymerase was characterized using probes for antisense and sense-...

journal_title：Nucleic acids research

authors： SenGupta DN,Silverman RH

更新日期：1989-02-11 00:00:00

abstract：:A new procedure has been developed for the efficient cloning of complex PCR mixtures, resulting in libraries exclusively consisting of recombinant clones. Recombinants are generated between PCR products and a PCR-amplified plasmid vector. The procedure does not require the use of restriction enzymes, T4 DNA ligase or ...

journal_title：Nucleic acids research

authors： Aslanidis C,de Jong PJ

更新日期：1990-10-25 00:00:00

abstract：:We have previously characterized an extracellular nuclease from Pseudomonas BAL 31 which, in addition to other activities, displays a double-strand exonuclease activity which progressively shortens both strands of linear duplex DNA molecules from both termini. This degradation is accomplished without the introduction ...

journal_title：Nucleic acids research

authors： Legerski RJ,Hodnett JL,Gray HB Jr

更新日期：1978-05-01 00:00:00

abstract：:We have carried out a survey of potential quadruplex structure sequences (PQSS), which occur in the immediate upstream region (500 bp) of human genes. By examining the number and distribution of these we have established that there is a clear link between them and the occurrence of the SP1-binding element 'GGGCGG', su...

journal_title：Nucleic acids research

authors： Todd AK,Neidle S

更新日期：2008-05-01 00:00:00

abstract：:We have purified to near homogeneity a novel nuclear protein from HeLa cells, that specifically binds to scaffold or matrix attachment region DNA elements (S/MAR DNA). The protein, designated SAF-B for scaffold attachment factor B, is an abundant component of chromatin, but not of the nuclear matrix and is expressed i...

journal_title：Nucleic acids research

authors： Renz A,Fackelmayer FO

更新日期：1996-03-01 00:00:00

abstract：:As the formation of ribonucleoprotein complexes is a major mechanism of angiotensin II type 1 receptor (AT1R) regulation, we sought to identify novel AT1R mRNA binding proteins. By affinity purification and mass spectroscopy, we identified TIA-1. This interaction was confirmed by colocalization of AT1R mRNA and TIA-1 ...

journal_title：Nucleic acids research

authors： Backlund M,Paukku K,Kontula KK,Lehtonen JY

更新日期：2016-04-20 00:00:00

abstract：:We have prepared several novel phosphoramidites and have synthesised oligonucleotides incorporating them internally. The presence of these residues in an oligonucleotide template presents an impossible barrier to primed synthesis by Taq DNA polymerase. When extended as polymerase chain reaction products, these oligonu...

journal_title：Nucleic acids research

authors： Newton CR,Holland D,Heptinstall LE,Hodgson I,Edge MD,Markham AF,McLean MJ

更新日期：1993-03-11 00:00:00

abstract：:Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we discover an HRP2-DPF3a-BAF epigenetic pathway that coordinates methylated histone H3 ly...

journal_title：Nucleic acids research

authors： Zhu X,Lan B,Yi X,He C,Dang L,Zhou X,Lu Y,Sun Y,Liu Z,Bai X,Zhang K,Li B,Li MJ,Chen Y,Zhang L

更新日期：2020-07-09 00:00:00

abstract：:U4 RNA from chicken, rat and man was examined for nucleotide sequence and secondary structure. Three molecular species, U4A, U4B and U4C were detected in the three animal species. U4A is 146 nucleotide long and U4B RNA only lacks the 3' terminal G. four nucleotides are missing at the 3'-end of U4C RNA which, in additi...

journal_title：Nucleic acids research

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

更新日期：1981-06-25 00:00:00

abstract：:We have generated transgenic mice that express a diverse repertoire of human sequence immunoglobulins. The expression of this repertoire is directed by light and heavy chain minilocus transgenes comprised of human protein coding sequences in an unrearranged, germ-line configuration. In this paper we describe the const...

journal_title：Nucleic acids research

authors： Taylor LD,Carmack CE,Schramm SR,Mashayekh R,Higgins KM,Kuo CC,Woodhouse C,Kay RM,Lonberg N

更新日期：1992-12-11 00:00:00

abstract：:Actinomycin D (ActD) is a small molecule with strong antibiotic and anticancer activity. However, its biologically relevant DNA-binding mechanism has never been resolved, with some studies suggesting that the primary binding mode is intercalation, and others suggesting that single-stranded DNA binding is most importan...

journal_title：Nucleic acids research

authors： Paramanathan T,Vladescu I,McCauley MJ,Rouzina I,Williams MC

更新日期：2012-06-01 00:00:00

abstract：:Genome browsers are widely used for individually exploring various types of genomic data. A handful of genome browsers offer limited tools for collaboration among multiple users. Here, we describe PBrowse, an integrated real-time collaborative genome browser that enables multiple users to simultaneously view and acces...

journal_title：Nucleic acids research

authors： Szot PS,Yang A,Wang X,Parsania C,Röhm U,Wong KH,Ho JWK

更新日期：2017-05-19 00:00:00

abstract：:With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; representing cellular processes or pathways is no exception. VISIBIOweb is a free, open-source, we...

journal_title：Nucleic acids research

authors： Dilek A,Belviranli ME,Dogrusoz U

更新日期：2010-07-01 00:00:00

abstract：:The nuclear receptor vitamin D receptor (VDR) is known to associate with two vitamin D response element (VDRE) containing chromatin regions of the insulin-like growth factor binding protein 3 (IGFBP3) gene. In non-malignant MCF-10A human mammary cells, we show that the natural VDR ligand 1α,25-dihydroxyvitamin D(3) (1...

journal_title：Nucleic acids research

authors： Malinen M,Ryynänen J,Heinäniemi M,Väisänen S,Carlberg C

更新日期：2011-01-01 00:00:00

abstract：:In vitro enzymatic amplification of nucleic acids by PCR or other techniques is a very sensitive method to detect rare DNA segments. We present here a protocol that allows the rapid, sensitive and precise quantification of DNA molecules using PCR amplification run to saturation. The DNA (or cDNA) to be assayed is co-a...

journal_title：Nucleic acids research

authors： Pannetier C,Delassus S,Darche S,Saucier C,Kourilsky P

更新日期：1993-02-11 00:00:00

abstract：:CS23D (chemical shift to 3D structure) is a web server for rapidly generating accurate 3D protein structures using only assigned nuclear magnetic resonance (NMR) chemical shifts and sequence data as input. Unlike conventional NMR methods, CS23D requires no NOE and/or J-coupling data to perform its calculations. CS23D ...

journal_title：Nucleic acids research

authors： Wishart DS,Arndt D,Berjanskii M,Tang P,Zhou J,Lin G

更新日期：2008-07-01 00:00:00

abstract：:Hepatocyte Nuclear Factor 4 (HNF-4), a liver-enriched orphan receptor of the nuclear receptor superfamily, is required for the expression of a wide variety of liver-specific genes including apoAI. To explore the possibility that site A of the apoAI gene enhancer might also be the target for HNF-4 without the interfere...

journal_title：Nucleic acids research

authors： Fuernkranz HA,Wang Y,Karathanasis SK,Mak P

更新日期：1994-12-25 00:00:00

abstract：:Molecular models of six anthracycline antibiotics and their complexes with 32 distinct DNA octamer sequences were created and analyzed using HINT (Hydropathic INTeractions) to describe binding. The averaged binding scores were then used to calculate the free energies of binding for comparison with experimentally deter...

journal_title：Nucleic acids research

authors： Cashman DJ,Scarsdale JN,Kellogg GE

更新日期：2003-08-01 00:00:00