Structural features and stability of an RNA triple helix in solution.

abstract：:Post-transcriptional methylation of ribose at position O-2' is one of the most common and conserved types of RNA modification. Details of the functional roles of these methylations are far from clear, although in tRNA they are involved at position 34 in regulation of codon recognition and in eukaryotic rRNAs they are ...

journal_title：Nucleic acids research

authors： Qiu F,McCloskey JA

更新日期：1999-09-15 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：:Proteins are highly dynamic molecules, whose function is intrinsically linked to their molecular motions. Despite the pivotal role of protein dynamics, their computational simulation cost has led to most structure-based approaches for assessing the impact of mutations on protein structure and function relying upon sta...

journal_title：Nucleic acids research

authors： Rodrigues CH,Pires DE,Ascher DB

更新日期：2018-07-02 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：:Enzymes of intermediary metabolism are often reported to have moonlighting functions as RNA-binding proteins and have regulatory roles beyond their primary activities. Human serine hydroxymethyltransferase (SHMT) is essential for the one-carbon metabolism, which sustains growth and proliferation in normal and tumour c...

journal_title：Nucleic acids research

authors： Guiducci G,Paone A,Tramonti A,Giardina G,Rinaldo S,Bouzidi A,Magnifico MC,Marani M,Menendez JA,Fatica A,Macone A,Armaos A,Tartaglia GG,Contestabile R,Paiardini A,Cutruzzolà F

更新日期：2019-05-07 00:00:00

abstract：:Metabolite-responsive RNA pseudoknots derived from prokaryotic riboswitches have been shown to stimulate -1 programmed ribosomal frameshifting (PRF), suggesting -1 PRF as a promising gene expression platform to extend riboswitch applications in higher eukaryotes. However, its general application has been hampered by d...

journal_title：Nucleic acids research

authors： Lin YH,Chang KY

更新日期：2016-10-14 00:00:00

abstract：:Cell-free extracts employed as chromatin assembly systems contain a myriad of proteins, polyanions and nucleic acids. The roles of ATP, MgCl2 and other cofactors in the catalysis of nucleosome formation by the Xenopus laevis oocyte S-150 have yet to be established unequivocally. In this study we examine the influence ...

journal_title：Nucleic acids research

authors： Sekiguchi JM,Kmiec EB

更新日期：1992-02-25 00:00:00

abstract：:We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 μs) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged ...

journal_title：Nucleic acids research

authors： Havrila M,Stadlbauer P,Kührová P,Banáš P,Mergny JL,Otyepka M,Šponer J

更新日期：2018-09-28 00:00:00

abstract：:Transcriptional regulatory networks specify regulatory proteins controlling the context-specific expression levels of genes. Inference of genome-wide regulatory networks is central to understanding gene regulation, but remains an open challenge. Expression-based network inference is among the most popular methods to i...

journal_title：Nucleic acids research

authors： Siahpirani AF,Roy S

更新日期：2017-02-28 00:00:00

abstract：:RNA levels in a cell are regulated by the relative rates of RNA synthesis and decay. We recently developed a new approach for measuring both RNA synthesis and decay in a single experimental setting by biosynthetic labeling of newly transcribed RNA. Here, we show that this provides measurements of RNA half-lives from m...

journal_title：Nucleic acids research

authors： Friedel CC,Dölken L,Ruzsics Z,Koszinowski UH,Zimmer R

更新日期：2009-09-01 00:00:00

abstract：:Two DNA hexadecamers containing one central 5'-GC-3' base step have been examined by footprinting methodology in the presence and absence of actinomycin D. The results of these studies, coupled with imino proton NMR measurements indicate that the antitumor drug causes a change in DNA conformation at a distance from th...

journal_title：Nucleic acids research

authors： Huang YQ,Rehfuss RP,LaPlante SR,Boudreau E,Borer PN,Lane MJ

更新日期：1988-12-09 00:00:00

abstract：:Enzymatic hydrolysis and base analysis by high performance liquid chromatography showed that mouse satellite DNA had 30-50% less 5-methylcytosine in sperm than in somatic tissue (1.59 mols % vs 2.40-3.11 mols %). Maxam-Gilbert sequencing and analysis of the intensity of the cytosine bands indicated that the level of m...

journal_title：Nucleic acids research

authors： Feinstein SI,Racaniello VR,Ehrlich M,Gehrke CW,Miller DA,Miller OJ

更新日期：1985-06-11 00:00:00

abstract：:The single nucleotide polymorphisms (SNPs) in conserved protein regions have been thought to be strong candidates that alter protein functions. Thus, we have developed SNP@Domain, a web resource, to identify SNPs within human protein domains. We annotated SNPs from dbSNP with protein structure-based as well as sequenc...

journal_title：Nucleic acids research

authors： Han A,Kang HJ,Cho Y,Lee S,Kim YJ,Gong S

更新日期：2006-07-01 00:00:00

abstract：:The side chains of the 20 types of amino acids, owing to a large extent to their different physical properties, have characteristic distributions in interior/surface regions of individual proteins and in interface/non-interface portions of protein surfaces that bind proteins or nucleic acids. These distributions have ...

journal_title：Nucleic acids research

authors： Tjong H,Qin S,Zhou HX

更新日期：2007-07-01 00:00:00

abstract：:Key components of the translational apparatus, i.e. ribosomes, elongation factor EF-Tu and most aminoacyl-tRNA synthetases, are stereoselective and prevent incorporation of d-amino acids (d-aa) into polypeptides. The rare appearance of d-aa in natural polypeptides arises from post-translational modifications or non-ri...

journal_title：Nucleic acids research

authors： Achenbach J,Jahnz M,Bethge L,Paal K,Jung M,Schuster M,Albrecht R,Jarosch F,Nierhaus KH,Klussmann S

更新日期：2015-07-13 00:00:00

abstract：:Tight cell-cycle regulation of the histone H4-K20 methyltransferase PR-Set7 is essential for the maintenance of genome integrity. In mammals, this mainly involves the interaction of PR-Set7 with the replication factor PCNA, which triggers the degradation of the enzyme by the CRL4CDT2 E3 ubiquitin ligase. PR-Set7 is al...

journal_title：Nucleic acids research

authors： Zouaz A,Fernando C,Perez Y,Sardet C,Julien E,Grimaud C

更新日期：2018-04-06 00:00:00

abstract：:Ribosome-inactivating proteins (RIP) are a family of plant enzymes for which a unique activity was determined: rRNAN-glycosidase at a specific universally conserved position, A4324in the case of rat ribosomes. Recently we have shown that the RIP from Saponaria officinalis have a much wider substrate specificity: they ...

journal_title：Nucleic acids research

authors： Barbieri L,Valbonesi P,Bonora E,Gorini P,Bolognesi A,Stirpe F

更新日期：1997-02-01 00:00:00

abstract：:Restriction endonucleases are highly specific in recognizing the particular DNA sequence they act on. However, their activity is affected by sequence context, enzyme concentration and buffer composition. Changes in these factors may lead to either ineffective cleavage at the cognate restriction site or relaxed specifi...

journal_title：Nucleic acids research

authors： Kamps-Hughes N,Quimby A,Zhu Z,Johnson EA

更新日期：2013-06-01 00:00:00

abstract：:A limited number of Methicillin-resistant Staphylococcus aureus (MRSA) clones are responsible for MRSA infections worldwide, and those of different lineages carry unique Type I restriction-modification (RM) variants. We have identified the specific DNA sequence targets for the dominant MRSA lineages CC1, CC5, CC8 and ...

journal_title：Nucleic acids research

authors： Roberts GA,Houston PJ,White JH,Chen K,Stephanou AS,Cooper LP,Dryden DT,Lindsay JA

更新日期：2013-08-01 00:00:00

abstract：:GenBank is a comprehensive database that contains publicly available DNA sequences for more than 140 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the BankIt (web) or Sequin program an...

journal_title：Nucleic acids research

authors： Benson DA,Karsch-Mizrachi I,Lipman DJ,Ostell J,Wheeler DL

更新日期：2004-01-01 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：:The HSV gene encoding ICP4 is negatively regulated and the HSV gene encoding thymidine kinase is positively regulated by ICP4 in vivo. We report that ICP4 is a component of a stable complex that contains protein and a sequence of approximately 28 nucleotides that span the ICP4 gene transcription initiation site. The a...

journal_title：Nucleic acids research

authors： Faber SW,Wilcox KW

更新日期：1988-01-25 00:00:00

abstract：:Gene trapping is a method of generating murine embryonic stem (ES) cell lines containing insertional mutations in known and novel genes. A number of international groups have used this approach to create sizeable public cell line repositories available to the scientific community for the generation of mutant mouse str...

journal_title：Nucleic acids research

authors： Nord AS,Chang PJ,Conklin BR,Cox AV,Harper CA,Hicks GG,Huang CC,Johns SJ,Kawamoto M,Liu S,Meng EC,Morris JH,Rossant J,Ruiz P,Skarnes WC,Soriano P,Stanford WL,Stryke D,von Melchner H,Wurst W,Yamamura K,Young SG,

更新日期：2006-01-01 00:00:00

abstract：:Double-stranded (ds) oligodeoxynucleotides (29mers) containing an O6-ethylguanine (O6-EtGua) flanked 5' and 3' by different bases (5'..TGT..3'; 5'..CGG..3', 5'..GGT..3'; 5'..GGG..3'; 5'..GGA..3') were synthesized to investigate the binding and repair characteristics of recombinant human O6-alkylguanine-DNA alkyltransf...

journal_title：Nucleic acids research

authors： Bender K,Federwisch M,Loggen U,Nehls P,Rajewsky MF

更新日期：1996-06-01 00:00:00

abstract：:Human Protein Reference Database (HPRD) (http://www.hprd.org) was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein-protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest...

journal_title：Nucleic acids research

authors： Mishra GR,Suresh M,Kumaran K,Kannabiran N,Suresh S,Bala P,Shivakumar K,Anuradha N,Reddy R,Raghavan TM,Menon S,Hanumanthu G,Gupta M,Upendran S,Gupta S,Mahesh M,Jacob B,Mathew P,Chatterjee P,Arun KS,Sharma S,Chand

更新日期：2006-01-01 00:00:00

abstract：:Protein-RNA interactions play essential roles in a number of regulatory mechanisms for gene expression such as RNA splicing, transport, translation and post-transcriptional control. As the number of available protein-RNA complex 3D structures has increased, it is now possible to statistically examine protein-RNA inter...

journal_title：Nucleic acids research

authors： Kim OT,Yura K,Go N

更新日期：2006-01-01 00:00:00

abstract：:Variable (diversity) joining [V(D)J] recombination of immune gene loci proceeds in an ordered manner with D to J portions recombining first and then an upstream V joins that recombinant. We present evidence that the non-core domain of recombination activating gene (RAG) protein 2 is involved in the regulation of recom...

journal_title：Nucleic acids research

authors： Curry JD,Schlissel MS

更新日期：2008-10-01 00:00:00

abstract：:It has been recently reported that the pR plasmid enhances the UV survival in E.coli c600. In order to test whether this function may be expressed also in mammalian cells, LTA (tk- aprt-) mouse cells were cotransformed with pR plasmid DNA and ptk1 plasmid as selectable marker. Tk+ transformants were analyzed for their...

journal_title：Nucleic acids research

authors： Elli R,Marcucci L,Bosi R,Oppi C,Battaglia PA,Gigliani F

更新日期：1983-06-11 00:00:00

abstract：:Reversible methylation of the N6 or N1 position of adenine in RNA has recently been shown to play significant roles in regulating the functions of RNA. RNA can also be alkylated upon exposure to endogenous and exogenous alkylating agents. Here we examined how regio-specific methylation at the hydrogen bonding edge of ...

journal_title：Nucleic acids research

authors： You C,Dai X,Wang Y

更新日期：2017-09-06 00:00:00

abstract：:Every bulky lesion in DNA can potentially inhibit the Taq DNA polymerase and thereby decrease the amplification produced in the polymerase chain reaction. We investigated the feasibility of using this inhibition to quantify DNA lesions produced by the anticancer drug cisplatin. Products were detected by electrophoresi...

journal_title：Nucleic acids research

authors： Jennerwein MM,Eastman A

更新日期：1991-11-25 00:00:00