Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity.

abstract：:N-nitrosation of glycine and its derivatives generates potent alkylating agents that can lead to the formation of O(6)-carboxymethylguanine (O(6)-CMG) in DNA. O(6)-CMG has been identified in DNA derived from human colon tissue, and its occurrence has been linked to diets high in red and processed meats. By analogy to ...

journal_title：Nucleic acids research

authors： Zhang F,Tsunoda M,Suzuki K,Kikuchi Y,Wilkinson O,Millington CL,Margison GP,Williams DM,Czarina Morishita E,Takénaka A

更新日期：2013-05-01 00:00:00

abstract：:The ribosomal frameshifting signal of the mouse embryonal carcinoma differentiation regulated (Edr) gene represents the sole documented example of programmed -1 frameshifting in mammalian cellular genes [Shigemoto,K., Brennan,J., Walls,E,. Watson,C.J., Stott,D., Rigby,P.W. and Reith,A.D. (2001), Nucleic Acids Res., 29...

journal_title：Nucleic acids research

authors： Manktelow E,Shigemoto K,Brierley I

更新日期：2005-03-14 00:00:00

abstract：:Pluripotency, the ability of embryonic stem cells to differentiate into specialized cell types, is determined by ESC-specific gene regulators such as transcription factors and chromatin modification factors. It is not well understood how ESCs are poised for differentiation, however, and methods are needed for prognosi...

journal_title：Nucleic acids research

authors： Ha M,Hong S

更新日期：2017-10-13 00:00:00

abstract：:Allele-specific DNA methylation, histone acetylation and histone methylation are recognized as epigenetic characteristics of imprinted genes and imprinting centers (ICs). These epigenetic modifications are also used to regulate tissue-specific gene expression. Epigenetic differences between alleles can be significant ...

journal_title：Nucleic acids research

authors： Lau JC,Hanel ML,Wevrick R

更新日期：2004-06-24 00:00:00

abstract：:Several proteins that have substantially diverged during evolution retain similar three-dimensional structures and biological function inspite of poor sequence identity. The database on Genomic Distribution of protein structural domain Superfamilies (GenDiS) provides record for the distribution of 4001 protein domains...

journal_title：Nucleic acids research

authors： Pugalenthi G,Bhaduri A,Sowdhamini R

更新日期：2005-01-01 00:00:00

abstract：:RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept o...

journal_title：Nucleic acids research

authors： Novichkov PS,Rodionov DA,Stavrovskaya ED,Novichkova ES,Kazakov AE,Gelfand MS,Arkin AP,Mironov AA,Dubchak I

更新日期：2010-07-01 00:00:00

abstract：:The Medaka Expression Pattern Database (MEPD) stores and integrates information of gene expression during embryonic development of the small freshwater fish Medaka (Oryzias latipes). Expression patterns of genes identified by ESTs are documented by images and by descriptions through parameters such as staining intensi...

journal_title：Nucleic acids research

authors： Henrich T,Ramialison M,Quiring R,Wittbrodt B,Furutani-Seiki M,Wittbrodt J,Kondoh H,Medaka Expression Pattern Database.

更新日期：2003-01-01 00:00:00

abstract：:The DNA sequence of a 225.4 kilobase segment of the Escherichia coli K-12 genome is described here, from 76.0 to 81.5 minutes on the genetic map. This brings the total of contiguous sequence from the E.coli genome project to 725.1 kb (76.0 to 92.8 minutes). We found 191 putative coding genes (ORFs) of which 72 genes w...

journal_title：Nucleic acids research

authors： Sofia HJ,Burland V,Daniels DL,Plunkett G 3rd,Blattner FR

更新日期：1994-07-11 00:00:00

abstract：:We report here spectroscopic and biochemical data of a novel series of sugar-modified oligodeoxy-nucleotides, the carbocyclic oligothymidylates, c(dT)3-20. In c(dT)n a methylene group has been substituted for the oxygen atom of the deoxyribose ring of the natural thymidylate unit. c(dT)10-20 form helical structures, i...

journal_title：Nucleic acids research

authors： Sági J,Szemzõ A,Szécsi J,Otvös L

更新日期：1990-04-25 00:00:00

abstract：:Multivalent cations are known to condense DNA into higher ordered structures, including toroids and rods. Here we report that solid supports treated with monovalent or multivalent cationic silanes, followed by removal of soluble molecules, can condense DNA. The mechanism of this surface-directed condensation depends o...

journal_title：Nucleic acids research

authors： Fang Y,Hoh JH

更新日期：1998-01-15 00:00:00

abstract：:In the most extensive examination to date of the relationship between the pausing of reverse transcrip-tase (RT) and RNA secondary structures, pause events were found to be correlated to inverted repeats both ahead of, and behind the catalytic site in vitro. In addition pausing events were strongly associated with pol...

journal_title：Nucleic acids research

authors： Harrison GP,Mayo MS,Hunter E,Lever AM

更新日期：1998-07-15 00:00:00

abstract：:This paper describes a method for predicting a supersecondary structural motif, beta-hairpins, in a protein sequence. The method was trained and tested on a set of 5102 hairpins and 5131 non-hairpins, obtained from a non-redundant dataset of 2880 proteins using the DSSP and PROMOTIF programs. Two machine-learning tech...

journal_title：Nucleic acids research

authors： Kumar M,Bhasin M,Natt NK,Raghava GP

更新日期：2005-07-01 00:00:00

abstract：:The reaction of fluorescamine with primary amino groups of tRNAs was investigated. The reagent was attached under mild conditions to the 3'-end of tRNAPhe-C-C-A(3'NH) from yeast and to the minor nucleoside x in E. coli tRNAArg, tRNALys, tRNAMet, tRNAIle and tRNAPhe. The primary aliphatic amino groups of these tRNAs re...

journal_title：Nucleic acids research

authors： Sprinzl M,Faulhammer HG

更新日期：1978-12-01 00:00:00

abstract：:Cleavage of phosphodiester bonds by small ribonuclease mimics within different bulge-loops of RNA was investigated. Bulge-loops of different size (1-7 nt) and sequence composition were formed in a 3' terminal fragment of influenza virus M2 RNA (96 nt) by hybridization of complementary oligodeoxynucleotides. Small bulg...

journal_title：Nucleic acids research

authors： Kuznetsova IL,Zenkova MA,Gross HJ,Vlassov VV

更新日期：2005-02-24 00:00:00

abstract：:During the splicing process, spliceosomal snRNAs undergo numerous conformational rearrangements that appear to be catalyzed by proteins belonging to the DEAD/H-box superfamily of RNA helicases. We have cloned a new RNA helicase gene, designated DBP2 (DEAH-boxprotein), homologous to the Schizosaccaromyces pombe cdc28(+...

journal_title：Nucleic acids research

authors： Imamura O,Saiki K,Tani T,Ohshima Y,Sugawara M,Furuichi Y

更新日期：1998-05-01 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：:The gene co-expression analysis toolbox (GeneCAT) introduces several novel microarray data analyzing tools. First, the multigene co-expression analysis, combined with co-expressed gene networks, provides a more powerful data mining technique than standard, single-gene co-expression analysis. Second, the high-throughpu...

journal_title：Nucleic acids research

authors： Mutwil M,Obro J,Willats WG,Persson S

更新日期：2008-07-01 00:00:00

abstract：:The R-Coffee web server produces highly accurate multiple alignments of noncoding RNA (ncRNA) sequences, taking into account predicted secondary structures. R-Coffee uses a novel algorithm recently incorporated in the T-Coffee package. R-Coffee works along the same lines as T-Coffee: it uses pairwise or multiple seque...

journal_title：Nucleic acids research

authors： Moretti S,Wilm A,Higgins DG,Xenarios I,Notredame C

更新日期：2008-07-01 00:00:00

abstract：:Insertion/deletion (indel) is one of the most common methods of protein sequence variation. Recent studies showed that indels could affect their flanking regions and they are important for protein function and evolution. Here, we describe the Indel Flanking Region Database (IndelFR, http://indel.bioinfo.sdu.edu.cn), w...

journal_title：Nucleic acids research

authors： Zhang Z,Xing C,Wang L,Gong B,Liu H

更新日期：2012-01-01 00:00:00

abstract：:The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is the model organism database for the fully sequenced and intensively studied model plant Arabidopsis thaliana. Data in TAIR is derived in large part from manual curation of the Arabidopsis research literature and direct submissions from the research...

journal_title：Nucleic acids research

authors： Swarbreck D,Wilks C,Lamesch P,Berardini TZ,Garcia-Hernandez M,Foerster H,Li D,Meyer T,Muller R,Ploetz L,Radenbaugh A,Singh S,Swing V,Tissier C,Zhang P,Huala E

更新日期：2008-01-01 00:00:00

abstract：:The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these ...

journal_title：Nucleic acids research

authors： Bult CJ,Eppig JT,Blake JA,Kadin JA,Richardson JE,Mouse Genome Database Group.

更新日期：2016-01-04 00:00:00

abstract：:The crp gene of E. coli, which codes for cAMP receptor protein (CRP), has been cloned in the plasmid pBR322 on the basis of a genetic complementation. One of the recombinant plasmids, pHA1, was shown to direct the synthesis of CRP in a cell-free system. The location of the crp gene was determined by constructing subcl...

journal_title：Nucleic acids research

authors： Aiba H,Fujimoto S,Ozaki N

更新日期：1982-02-25 00:00:00

abstract：:Hepatitis C virus (HCV) translation initiation is directed by an internal ribosome entry site (IRES) and regulated by distant regions at the 3'-end of the viral genome. Through a combination of improved RNA chemical probing methods, SHAPE structural analysis and screening of RNA accessibility using antisense oligonucl...

journal_title：Nucleic acids research

authors： Romero-López C,Barroso-Deljesus A,García-Sacristán A,Briones C,Berzal-Herranz A

更新日期：2012-12-01 00:00:00

abstract：:Bloom's syndrome helicase (BLM) is a member of the RecQ family of DNA helicases, which play key roles in the maintenance of genome integrity in all organism groups. We describe crystal structures of the BLM helicase domain in complex with DNA and with an antibody fragment, as well as SAXS and domain association studie...

journal_title：Nucleic acids research

authors： Newman JA,Savitsky P,Allerston CK,Bizard AH,Özer Ö,Sarlós K,Liu Y,Pardon E,Steyaert J,Hickson ID,Gileadi O

更新日期：2015-05-26 00:00:00

abstract：:We attempted to use the polymerase chain reaction (PCR) to monitor in vitro recombination in a plasmid containing directly repeated sequences. Some of the plasmid preparations which had not been exposed to recombination conditions were however found to behave in the PCR test as if they had undergone homologous recombi...

journal_title：Nucleic acids research

authors： Marton A,Delbecchi L,Bourgaux P

更新日期：1991-05-11 00:00:00

abstract：:PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB). Started at the Real World Computing Partnership (RWCP) in August 1997, it developed to the present system of PDB-REPRDB. In April 2001, the system was moved to the Computational Biology Research Center (CBRC), National Institut...

journal_title：Nucleic acids research

authors： Noguchi T,Akiyama Y

更新日期：2003-01-01 00:00:00

abstract：:We have isolated a unique fragment of the HLA-DR alpha gene and probed human genomic DNA at low stringency to search for homologous sequences. A minimum of six non-polymorphic cross-hybridizing high molecular weight fragments were found in all DNAs examined. In order to obtain molecular clones of these cross-hybridizi...

journal_title：Nucleic acids research

authors： Lawrance SK,Das HK,Pan J,Weissman SM

更新日期：1985-10-25 00:00:00

abstract：:Many types of DNA structures are generated in response to DNA damage, repair and recombination that require processing via specialized nucleases. DNA hairpins represent one such class of structures formed during V(D)J recombination, palindrome extrusion, DNA transposition and some types of double-strand breaks. Here w...

journal_title：Nucleic acids research

authors： Tiefenbach T,Junop M

更新日期：2012-03-01 00:00:00

abstract：:A direct correlation exists between the level of histone H4 hyperacetylation induced by sodium butyrate and the extent to which nucleosomes lose their compact shape and become elongated (62.0% of the particles have a length/width ratio over 1.6; overall mean in the length/width ratio = 1.83 +/- 0.48) when bound to ele...

journal_title：Nucleic acids research

authors： Oliva R,Bazett-Jones DP,Locklear L,Dixon GH

更新日期：1990-05-11 00:00:00

abstract：:MicroRNAs are small non-coding RNAs that modulate gene expression at post-transcriptional level, playing a crucial role in cell differentiation and development. Recently, some reports have shown that a limited number of mammalian microRNAs are also involved in anti-viral defense. In this study, the analysis of the hep...

journal_title：Nucleic acids research

authors： Potenza N,Papa U,Mosca N,Zerbini F,Nobile V,Russo A

更新日期：2011-07-01 00:00:00