ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage.

abstract：:Eukaryotic genomes contain many endogenous retroviral sequences (ERVs). ERVs are often severely mutated, therefore difficult to detect. A platform independent (Java) program package, RetroTector (ReTe), was constructed. It has three basic modules: (i) detection of candidate long terminal repeats (LTRs), (ii) detection...

journal_title：Nucleic acids research

authors： Sperber GO,Airola T,Jern P,Blomberg J

更新日期：2007-01-01 00:00:00

abstract：:Nucleotide excision repair is initiated by two different damage recognition subpathways, global genome repair (GGR) and transcription-coupled repair (TCR). In GGR, XPC detects DNA lesions and recruits TFIIH via interaction with the pleckstrin homology (PH) domain of TFIIH subunit p62. In TCR, an elongating form of RNA...

journal_title：Nucleic acids research

authors： Okuda M,Nakazawa Y,Guo C,Ogi T,Nishimura Y

更新日期：2017-12-15 00:00:00

abstract：:Structures of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 have been determined by NMR spectroscopy under low salt conditions. All protons and phosphorus nuclei resonances have been assigned. Signals of H5'/5" have been assigned stereospecifically. All 3JH,H and 3JP,H coupling constants have been measured. The structures were dete...

journal_title：Nucleic acids research

authors： Popenda M,Biala E,Milecki J,Adamiak RW

更新日期：1997-11-15 00:00:00

abstract：:Sequencing of RNAs (RNA-Seq) has revolutionized the field of transcriptomics, but the reads obtained often contain errors. Read error correction can have a large impact on our ability to accurately assemble transcripts. This is especially true for de novo transcriptome analysis, where a reference genome is not availab...

journal_title：Nucleic acids research

authors： Le HS,Schulz MH,McCauley BM,Hinman VF,Bar-Joseph Z

更新日期：2013-05-01 00:00:00

abstract：:In Euplotes crassus millions of telomeres are synthesized during the sexual phase of the life cycle. Since these newly synthesized telomeres are longer than normal macronuclear telomeres, they must be trimmed to the mature size. We have examined the timing and mechanism of this trimming step. We have shown that a sudd...

journal_title：Nucleic acids research

authors： Vermeesch JR,Williams D,Price CM

更新日期：1993-11-25 00:00:00

abstract：:JSNP is a repository of Japanese Single Nucleotide Polymorphism (SNP) data, begun in 2000 and developed through the Prime Minister's Millennium Project. The aim of this undertaking is to identify and collate up to 150 000 SNPs from the Japanese population, located in genes or in adjacent regions that might influence t...

journal_title：Nucleic acids research

authors： Hirakawa M,Tanaka T,Hashimoto Y,Kuroda M,Takagi T,Nakamura Y

更新日期：2002-01-01 00:00:00

abstract：:The development of biosensors based on DNA hybridization requires a more precise knowledge of the thermodynamics of the hybridization at a solid interface. In particular, the selectivity of hybridization can be affected by a lot of parameters such as the single-strand (ss)DNA density, the pH, the ionic strength or the...

journal_title：Nucleic acids research

authors： Meunier-Prest R,Raveau S,Finot E,Legay G,Cherkaoui-Malki M,Latruffe N

更新日期：2003-12-01 00:00:00

abstract：:The engineering of new enzymes that efficiently and specifically modify DNA sequences is necessary for the development of enhanced gene therapies and genetic studies. To address this need, we developed a robust strategy for evolving site-specific recombinases with novel substrate specificities. In this system, recombi...

journal_title：Nucleic acids research

authors： Gersbach CA,Gaj T,Gordley RM,Barbas CF 3rd

更新日期：2010-07-01 00:00:00

abstract：:Nucleoside 3'-phosphoramidite and chlorophosphite reagents have been found to react with the lactam function of guanine. This reaction caused unsatisfactory results when oligodeoxyribonucleotides containing a large number of guanine bases were prepared in an automated solid phase synthesizer. The guanine modification ...

journal_title：Nucleic acids research

authors： Pon RT,Damha MJ,Ogilvie KK

更新日期：1985-09-25 00:00:00

abstract：:Inadequate cellular compartmentalisation of plasmid DNA and antisense oligodeoxynucleotides (ODNs) is generally considered as a major limitation in their use. In this study, an approach combining in situ visual-isation of rhodamine-labelled ODNs and affinity modification of proteins by radiolabelled-alkylating ODN der...

journal_title：Nucleic acids research

authors： Laktionov PP,Dazard JE,Vives E,Rykova EY,Piette J,Vlassov VV,Lebleu B

更新日期：1999-06-01 00:00:00

abstract：:Deletion of Hop2 in mice eliminates homologous chromosome synapsis and disrupts double-strand break (DSB) repair through homologous recombination. HOP2 in vitro shows two distinctive activities: when it is incorporated into a HOP2-MND1 complex it stimulates DMC1 and RAD51 recombination activities and the purified HOP2...

journal_title：Nucleic acids research

authors： Pezza RJ,Voloshin ON,Volodin AA,Boateng KA,Bellani MA,Mazin AV,Camerini-Otero RD

更新日期：2014-02-01 00:00:00

abstract：:Double-stranded DNA viruses use ATP-powered molecular motors to package their genomic DNA. To ensure efficient genome encapsidation, these motors regulate functional transitions between initiation, translocation, and termination modes. Here, we report structural and biophysical analyses of the C-terminal domain of the...

journal_title：Nucleic acids research

authors： Mahler BP,Bujalowski PJ,Mao H,Dill EA,Jardine PJ,Choi KH,Morais MC

更新日期：2020-11-18 00:00:00

abstract：:Given the inherent limitations of in silico studies relying solely on DNA sequence analysis, the functional characterization of mammalian promoters and associated cis-regulatory elements requires experimental support, which demands cloning and analysis of putative promoter regions. Focusing on human chromosome 21, we ...

journal_title：Nucleic acids research

authors： Warnatz HJ,Querfurth R,Guerasimova A,Cheng X,Haas SA,Hufton AL,Manke T,Vanhecke D,Nietfeld W,Vingron M,Janitz M,Lehrach H,Yaspo ML

更新日期：2010-10-01 00:00:00

abstract：:We report the first isolation and characterisation of a human Ig V lambda gene. The gene was isolated from a recombinant phage library of human chromosome 22 using a mouse Ig lambda cDNA as probe. DNA sequence analysis predicts a short leader peptide interrupted by an intron of 88 nucleotides, and a mature polypeptide...

journal_title：Nucleic acids research

authors： Anderson ML,Szajnert MF,Kaplan JC,McColl L,Young BD

更新日期：1984-09-11 00:00:00

abstract：:A cDNA clone which expresses a protein that cross-reacts immunologically with the human C1 and C2 hnRNP core proteins has been isolated. The clone was selected by a sensitive immunochemical assay employing an avidin-biotin complex for detection, and identified as a clone for the hnRNP C proteins by a highly sensitive ...

journal_title：Nucleic acids research

authors： Lahiri DK,Thomas JO

更新日期：1986-05-27 00:00:00

abstract：:S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold. The data are mainly extracted from original publications, but a World Wide Web interface for direct...

journal_title：Nucleic acids research

authors： Liebich I,Bode J,Frisch M,Wingender E

更新日期：2002-01-01 00:00:00

abstract：:Adenine, thymine and cytosine PNA monomers have been prepared using 3-amino-1,2-propanediol as a starting material. The benzoyl group was used to protect the exocyclic amines of the heterocyclic bases of A and C PNA monomers and the backbone primary amine was protected with the monomethoxytrityl group. The thymine and...

journal_title：Nucleic acids research

authors： Finn PJ,Gibson NJ,Fallon R,Hamilton A,Brown T

更新日期：1996-09-01 00:00:00

abstract：:Selenocysteine (Sec), the 21(st) amino acid in translation, uses its specific tRNA (tRNA(Sec)) to recognize the UGA codon. The Sec-specific elongation factor SelB brings the selenocysteinyl-tRNA(Sec) (Sec-tRNA(Sec)) to the ribosome, dependent on both an in-frame UGA and a Sec-insertion sequence (SECIS) in the mRNA. Th...

journal_title：Nucleic acids research

authors： Itoh Y,Sekine S,Yokoyama S

更新日期：2015-10-15 00:00:00

abstract：:Studies of bacterial chromosomes and plasmids indicate that their replication initiator proteins bind to origins of replication at many double-stranded sites and also at AT-rich regions where single-stranded DNA is exposed during origin opening. Single-strand binding apparently promotes origin opening by stabilizing a...

journal_title：Nucleic acids research

authors： Chatterjee S,Jha JK,Ciaccia P,Venkova T,Chattoraj DK

更新日期：2020-11-04 00:00:00

abstract：:The comprehensive multiplatform genomics data generated by The Cancer Genome Atlas (TCGA) Research Network is an enabling resource for cancer research. It includes an unprecedented amount of microRNA sequence data: ~11 000 libraries across 33 cancer types. Combined with initiatives like the National Cancer Institute G...

journal_title：Nucleic acids research

authors： Chu A,Robertson G,Brooks D,Mungall AJ,Birol I,Coope R,Ma Y,Jones S,Marra MA

更新日期：2016-01-08 00:00:00

abstract：:The numerous genomic sequences and ESTs released by the Arabidopsis thaliana Genome Initiative (AGI) have allowed a systematic and functional study of the DEAD box RNA helicase family. Sequencing and in silico analysis led to the characterization of 28 novel A. thaliana DEAD box RNA helicases forming a family of 32 me...

journal_title：Nucleic acids research

authors： Aubourg S,Kreis M,Lecharny A

更新日期：1999-01-15 00:00:00

abstract：:A feature of Haemophilus influenzae genomes is the presence of several loci containing tracts of six or more identical tetranucleotide repeat units. These repeat tracts are unstable and mediate high frequency, reversible alterations in the expression of surface antigens. This process, termed phase variation (PV), enab...

journal_title：Nucleic acids research

authors： Bayliss CD,Sweetman WA,Moxon ER

更新日期：2005-01-14 00:00:00

abstract：:Mollusca represents the second largest animal phylum but remains poorly explored from a genomic perspective. While the recent increase in genomic resources holds great promise for a deep understanding of molluscan biology and evolution, access and utilization of these resources still pose a challenge. Here, we present...

journal_title：Nucleic acids research

authors： Liu F,Li Y,Yu H,Zhang L,Hu J,Bao Z,Wang S

更新日期：2021-01-08 00:00:00

abstract：:Synthetic genetic sensors and circuits enable programmable control over timing and conditions of gene expression and, as a result, are increasingly incorporated into the control of complex and multi-gene pathways. Size and complexity of genetic circuits are growing, but stay limited by a shortage of regulatory parts t...

journal_title：Nucleic acids research

authors： Bervoets I,Van Brempt M,Van Nerom K,Van Hove B,Maertens J,De Mey M,Charlier D

更新日期：2018-02-28 00:00:00

abstract：:Treatment of the ciliated protozoan Tetrahymena thermophila with 8-methoxypsoralen combined with long wavelength ultraviolet irradiation (UVA, lambda approximately 360 nm) resulted in a dose dependent equal inhibition of the synthesis of rRNA, 5.8S, 5S and tRNA. Similar results were obtained with 3-carbethoxy-8-methox...

journal_title：Nucleic acids research

authors： Nielsen PE

更新日期：1987-02-11 00:00:00

abstract：:The Cox protein from bacteriophage P2 forms oligomeric filaments and it has been proposed that DNA can be wound up around these filaments, similar to how histones condense DNA. We here use fluorescence microscopy to study single DNA-Cox complexes in nanofluidic channels and compare how the Cox homologs from phages P2 ...

journal_title：Nucleic acids research

authors： Frykholm K,Berntsson RP,Claesson M,de Battice L,Odegrip R,Stenmark P,Westerlund F

更新日期：2016-09-06 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：:More than one-third of the RAG1 protein can be truncated from the N-terminus with only subtle effects on the products of V(D)J recombination in vitro or in a mouse. What, then, is the function of the N-terminal domain? We believe it to be regulatory. We determined, several years ago, that an included RING motif could ...

journal_title：Nucleic acids research

authors： Maitra R,Sadofsky MJ

更新日期：2009-06-01 00:00:00

abstract：:Non-selenocysteine-containing phospholipid hydroperoxide glutathione peroxidase (NPGPx or GPx7) is an oxidative stress sensor that modulates the antioxidative activity of its target proteins through intermolecular disulfide bond formation. Given NPGPx's role in protecting cells from oxidative damage, identification of...

journal_title：Nucleic acids research

authors： Chen PJ,Weng JY,Hsu PH,Shew JY,Huang YS,Lee WH

更新日期：2015-10-30 00:00:00

abstract：:We studied in vivo transcription and gene expression directed by a series of synthetic sequences, bearing the consensus hexamer (CH) pair of E.coli promoters in various contexts. The results demonstrate that, for the contexts tested, the CH pair supports transcription activity and gene expression, whether the spacer l...

journal_title：Nucleic acids research

authors： Jacquet MA,Reiss C

更新日期：1990-03-11 00:00:00