RNAMST: efficient and flexible approach for identifying RNA structural homologs.

abstract：:We have sequenced mouse tRNA genes from two recombinant lambda phage. An 1800 bp sequence from one phage contains 3 tRNA genes, potentially encoding tRNAAsp, tRNAGly, and tRNAGlu, separated by spacer sequences of 587 bp and 436 bp, respectively. The mouse tRNA gene cluster is homologous to a rat sequence (Sekiya et al...

journal_title：Nucleic acids research

authors： Looney JE,Harding JD

更新日期：1983-12-20 00:00:00

abstract：:We have synthesized a family of double-stranded cDNAs (ds cDNAs) using as a template the family of highly purified protamine mRNAs from rainbow trout testis. Individual pure protamine cDNA components were isolated by cloning this family of protamine ds cDNAs in a plasmid vector (pMB9). Clones containing protamine sequ...

journal_title：Nucleic acids research

authors： Gedamu L,Wosnick MA,Connor W,Watson DC,Dixon GH,Iatrou K

更新日期：1981-03-25 00:00:00

abstract：:The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with analysis services and a phylogenetically consistent taxonomic framework for these data. Updated monthly, these services are made available through the RDP-II website (http://rdp.cme.msu.ed...

journal_title：Nucleic acids research

authors： Cole JR,Chai B,Farris RJ,Wang Q,Kulam SA,McGarrell DM,Garrity GM,Tiedje JM

更新日期：2005-01-01 00:00:00

abstract：:The human transcription factor EF-1A binds to the purine-rich E1A core enhancer sequence in the adenovirus E1A and E4 and polyomavirus enhancer regions. The consensus binding site for EF-1A resembles that of members of the ets domain protein family. EF-1A activation of transcription requires a dimeric binding site. An...

journal_title：Nucleic acids research

authors： Bolwig GM,Bruder JT,Hearing P

更新日期：1992-12-25 00:00:00

abstract：:Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized Pseudomonas aeruginosa and Pseudomonas putida. Unlike these bacteria, the Acinetobacter ADP1 is highly competent for natural transformation which affords extraordinary convenience for ...

journal_title：Nucleic acids research

authors： Barbe V,Vallenet D,Fonknechten N,Kreimeyer A,Oztas S,Labarre L,Cruveiller S,Robert C,Duprat S,Wincker P,Ornston LN,Weissenbach J,Marlière P,Cohen GN,Médigue C

更新日期：2004-10-28 00:00:00

abstract：:Thyroglobulin (Tg), the precursor of thyroid hormones, is a 660.000 Da dimeric glycoprotein synthesized exclusively in the thyroid gland. We have cloned the human thyroglobulin gene from cosmid and phage libraries and constructed a complete restriction map. The gene encodes an 8.7 kb mRNA, covers at least 300 kb DNA a...

journal_title：Nucleic acids research

authors： Baas F,van Ommen GJ,Bikker H,Arnberg AC,de Vijlder JJ

更新日期：1986-07-11 00:00:00

abstract：:Altering zinc bioavailability to bacterial pathogens is a key component of host innate immunity. Thus, the ability to sense and adapt to the alterations in zinc concentrations is critical for bacterial survival and pathogenesis. To understand the adaptive responses of group A Streptococcus (GAS) to zinc limitation and...

journal_title：Nucleic acids research

authors： Sanson M,Makthal N,Flores AR,Olsen RJ,Musser JM,Kumaraswami M

更新日期：2015-01-01 00:00:00

abstract：:Single-nucleotide variation and gene expression of disease samples represent important resources for biomarker discovery. Many databases have been built to host and make available such data to the community, but these databases are frequently limited in scope and/or content. BioMuta, a database of cancer-associated si...

journal_title：Nucleic acids research

authors： Dingerdissen HM,Torcivia-Rodriguez J,Hu Y,Chang TC,Mazumder R,Kahsay R

更新日期：2018-01-04 00:00:00

abstract：:Chemically modified siRNAs are expected to have resistance toward nuclease degradation and good thermal stability in duplex formation for in vivo applications. We have recently found that 2'-OMe-4'-thioRNA, a hybrid chemical modification based on 2'-OMeRNA and 4'-thioRNA, has high hybridization affinity for complement...

journal_title：Nucleic acids research

authors： Takahashi M,Nagai C,Hatakeyama H,Minakawa N,Harashima H,Matsuda A

更新日期：2012-07-01 00:00:00

abstract：:Bacterial Rho-independent terminators (RITs) are important genomic landmarks involved in gene regulation and terminating gene expression. In this investigation we present RNIE, a probabilistic approach for predicting RITs. The method is based upon covariance models which have been known for many years to be the most a...

journal_title：Nucleic acids research

authors： Gardner PP,Barquist L,Bateman A,Nawrocki EP,Weinberg Z

更新日期：2011-08-01 00:00:00

abstract：:One of the master regulators of placental cell fusion in mammals leading to multi-nucleated syncytiotrophoblasts is the transcription factor GCMa. Recently, we proved that the cAMP-driven protein kinase A signaling pathway is fundamental for up-regulation of GCMa transcript levels and protein stability. Here, we show ...

journal_title：Nucleic acids research

authors： Schubert SW,Abendroth A,Kilian K,Vogler T,Mayr B,Knerr I,Hashemolhosseini S

更新日期：2008-06-01 00:00:00

abstract：:The advances of next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole collection of genetic material within an environmental sample (i.e. the metagenome). Identification of genes directly from short reads has become an important yet challenging probl...

journal_title：Nucleic acids research

authors： Rho M,Tang H,Ye Y

更新日期：2010-11-01 00:00:00

abstract：:The eukaryotic genome evolves under the dual constraint of maintaining coordinated gene transcription and performing effective DNA replication and cell division, the coupling of which brings about inevitable DNA topological tension. DNA supercoiling is resolved and, in some cases, even harnessed by the genome through ...

journal_title：Nucleic acids research

authors： Tsochatzidou M,Malliarou M,Papanikolaou N,Roca J,Nikolaou C

更新日期：2017-06-02 00:00:00

abstract：:Global run-on sequencing (GRO-seq) is a recent addition to the series of high-throughput sequencing methods that enables new insights into transcriptional dynamics within a cell. However, GRO-sequencing presents new algorithmic challenges, as existing analysis platforms for ChIP-seq and RNA-seq do not address the uniq...

journal_title：Nucleic acids research

authors： Allison KA,Kaikkonen MU,Gaasterland T,Glass CK

更新日期：2014-02-01 00:00:00

abstract：:A normal human population has been screened for the existence of further restriction fragment length polymorphisms (RFLPs) in the clotting factor IX gene in addition to the TaqI polymorphism already characterised (1,2). Two polymorphic loci were found, both within 6 Kb of the TaqI polymorphism within the body of the f...

journal_title：Nucleic acids research

authors： Winship PR,Anson DS,Rizza CR,Brownlee GG

更新日期：1984-12-11 00:00:00

abstract：:The role of thymine dimerization for previously reported U.V. induced conformational changes has been proved using acetophenone as sensitizer for the specific thymine dimerization upon irradiation at 313 nm. CD results demonstrate that formation of pyrimidine dimers cause typical conformational changes of the DNA B he...

journal_title：Nucleic acids research

authors： Lang H

更新日期：1975-02-01 00:00:00

abstract：:SV40 DNA form I is expressed efficiently after its injection into the nuclei of Xenopus laevis oocytes, resulting in the synthesis of RNA and protein products of both viral late and early transcription units. However it was observed that injection of SV40 genes cloned into pBR322 or related plasmids yielded vastly red...

journal_title：Nucleic acids research

authors： Michaeli T,Prives C

更新日期：1987-02-25 00:00:00

abstract：:Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteri...

journal_title：Nucleic acids research

authors： Wilson KA,Kellie JL,Wetmore SD

更新日期：2014-06-01 00:00:00

abstract：:Superhelical PM2 DNA can be photochemically modified by u.v. irradiation. The variation of S20,w with dose shows the following characteristics. There is a linear increase from 28 to 31s produced by a low dose of u.v. irradiation (4,000 ergs/mm2). A plateau in S20,w occurs between 4,000 and 10,000 ergs/mm2. The S20,w t...

journal_title：Nucleic acids research

authors： Woodworth-Gutai M,Lebowitz J,Kato AC,Denhardt DT

更新日期：1977-01-01 00:00:00

abstract：:The rpoH genes encoding homologs of Escherichia coli sigma 32 (heat shock sigma factor) were isolated and sequenced from five gram negative proteobacteria (gamma or alpha subgroup): Enterobacter cloacae (gamma), Serratia marcescens (gamma), Proteus mirabilis (gamma), Agrobacterium tumefaciens (alpha) and Zymomonas mob...

journal_title：Nucleic acids research

authors： Nakahigashi K,Yanagi H,Yura T

更新日期：1995-11-11 00:00:00

abstract：:An efficient procedure for the synthesis of unnatural alpha-anomeric oligodeoxyribonucleotides is described. This solid-phase procedure is based on the use of alpha-nucleoside phosphoramidites and alpha-nucleoside derivatized solid supports corresponding to the four natural bases and allow rapid synthesis of oligonucl...

journal_title：Nucleic acids research

authors： Morvan F,Rayner B,Leonetti JP,Imbach JL

更新日期：1988-02-11 00:00:00

abstract：:Gene expression profiling has gradually become a routine procedure for disease diagnosis and classification. In the past decade, many computational methods have been proposed, resulting in great improvements on various levels, including feature selection and algorithms for classification and clustering. In this study,...

journal_title：Nucleic acids research

authors： Ren X,Wang Y,Zhang XS,Jin Q

更新日期：2013-08-01 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：:Telomerase is a ribonucleoprotein reverse transcriptase that synthesizes and maintains telomeric DNA. Studies of telomeres and telomerase are facilitated by the large number of linear DNA molecules found in ciliated protozoa, such as Tetrahymena thermophila. To examine the expression of telomerase, we investigated the...

journal_title：Nucleic acids research

authors： Hargrove BW,Bhattacharyya A,Domitrovich AM,Kapler GM,Kirk K,Shippen DE,Kunkel GR

更新日期：1999-11-01 00:00:00

abstract：:BRCA1 expression is repressed by aberrant cytosine methylation in sporadic breast cancer. We hypothesized that aberrant cytosine methylation of the BRCA1 promoter was associated with the transcriptionally repressive effects of histone hypoacetylation and chromatin condensation. To address this question, we developed a...

journal_title：Nucleic acids research

authors： Rice JC,Futscher BW

更新日期：2000-09-01 00:00:00

abstract：:The mammalian transcription factor SRF and the yeast regulatory protein MCM1 contain DNA binding domains that are 70% identical; moreover, both proteins can bind the serum response element in the human c-fos promoter. Here we present an analysis of MCM1 sequence specificity by selection of sites from random sequence o...

journal_title：Nucleic acids research

authors： Wynne J,Treisman R

更新日期：1992-07-11 00:00:00

abstract：:Calf thymus DNA polymerase alpha (pol alpha) and bacteriophage T4 DNA polymerase (pol T4) were exploited as model enzymes to investigate the molecular mechanism of inhibitory action of N2-(p-n-butylphenyl)dGTP (BuPdGTP) and 2-(p-n-butyl-anilino)dATP (BuAdATP) on the BuPdNTP-susceptible alpha polymerase family. Kinetic...

journal_title：Nucleic acids research

authors： Khan NN,Wright GE,Brown NC

更新日期：1991-04-11 00:00:00

abstract：:An oligodeoxyribonucleotide, d(GCTCACAAT-X-ATTGTGAGC), where X represents a hexaethylene glycol chain, was studied using circular dichroism spectroscopy. Its conformation and conformational stability were compared to those of compounds where X was replaced by four thymines and to the duplex of same sequence without lo...

journal_title：Nucleic acids research

authors： Durand M,Chevrie K,Chassignol M,Thuong NT,Maurizot JC

更新日期：1990-11-11 00:00:00

abstract：:We report that greA expression is driven by two strong, overlapping P1 and P2 promoters. The P1 promoter is sigma(70)-dependent and P2 is sigma(E)-dependent. Two-thirds of transcripts terminate within the leader region and the remaining third comprises greA mRNA. Termination efficiency seems to be unaffected by growth...

journal_title：Nucleic acids research

authors： Potrykus K,Murphy H,Chen X,Epstein JA,Cashel M

更新日期：2010-03-01 00:00:00

abstract：:Transgenic mice suitable for the in vivo assay of suspected mutagens at the chromosome level have been constructed by stable integration of a lambda phage shuttle vector. The shuttle vector, which contains a beta-galactosidase (beta-gal) target gene, can be rescued from genomic DNA with in vitro packaging extracts. Mu...

journal_title：Nucleic acids research

authors： Kohler SW,Provost GS,Kretz PL,Dycaico MJ,Sorge JA,Short JM

更新日期：1990-05-25 00:00:00