The COG database: new developments in phylogenetic classification of proteins from complete genomes.

abstract：:We have established a sensitive, monoclonal antibody (Mab)-based procedure permitting the selective enrichment of sequences containing the miscoding alkylation product O6-ethylguanine (O6-EtGua) from mammalian DNA. H5 rat hepatoma cells were reacted with the N-nitroso carcinogen N-ethyl-N-nitrosourea in vitro, to give...

journal_title：Nucleic acids research

authors： Hochleitner K,Thomale J,Nikitin AYu,Rajewsky MF

更新日期：1991-08-25 00:00:00

abstract：:Proper cytokine gene expression is essential in development, homeostasis and immune responses. Studies on the transcriptional control of cytokine genes have mostly focused on highly researched transcription factors (TFs) and cytokines, resulting in an incomplete portrait of cytokine gene regulation. Here, we used enha...

journal_title：Nucleic acids research

authors： Santoso CS,Li Z,Lal S,Yuan S,Gan KA,Agosto LM,Liu X,Pro SC,Sewell JA,Henderson A,Atianand MK,Fuxman Bass JI

更新日期：2020-12-02 00:00:00

abstract：:The eukaryotic mismatch repair protein Msh6 shares five domains in common with other MutS members. However, it also contains several hundred additional residues at its N-terminus. A few of these residues bind to PCNA, but the functions of the other amino acids in the N-terminal region (NTR) are unknown. Here we demons...

journal_title：Nucleic acids research

authors： Clark AB,Deterding L,Tomer KB,Kunkel TA

更新日期：2007-01-01 00:00:00

abstract：:Copy number variants (CNVs) are currently defined as genomic sequences that are polymorphic in copy number and range in length from 1000 to several million base pairs. Among current array-based CNV detection platforms, long-oligonucleotide arrays promise the highest resolution. However, the performance of currently av...

journal_title：Nucleic acids research

authors： Cahan P,Godfrey LE,Eis PS,Richmond TA,Selzer RR,Brent M,McLeod HL,Ley TJ,Graubert TA

更新日期：2008-04-01 00:00:00

abstract：:Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database (http://merops.sanger.ac.uk) aims to fulfil the need for an integrated source of information about these. The database has hierarchical classifications in which homologous sets of peptidases a...

journal_title：Nucleic acids research

authors： Rawlings ND,Barrett AJ,Bateman A

更新日期：2012-01-01 00:00:00

abstract：:Phosphorylation of the easily accessible 3',5'-diesters 1a-d with diphenyl phosphorochloridate, followed by selective 5'-deacylation, affords the phosphotriester derivatives 2a-d in good yields. Alkaline treatment of 2a-d results in the formation of the 2',3'-cyclic phosphates (3a-d). The usefulness of the phosphotrie...

journal_title：Nucleic acids research

authors： van Boom JH,Burgers PM,Haasnoot CA

更新日期：1976-10-01 00:00:00

abstract：:A differential effect is found of various bivalent cations (Ba2+, Ca2+, Mg2+, Cd2+, Co2+, Mn2+, Ni2+, Zn2+ and Hg2+) on stability of intermolecular Py-Pu-Pu triplex with different sequence of base triads. Ca2+, Mg2+, Cd2+, Co2+, Mn2+, Ni2+ and Zn2+ do stabilize the d(C)n d(G)n d(G)n triplex whereas Ba2+ and Hg2+ do no...

journal_title：Nucleic acids research

authors： Malkov VA,Voloshin ON,Soyfer VN,Frank-Kamenetskii MD

更新日期：1993-02-11 00:00:00

abstract：:A method for quantifying the proportion of supercoiled circular (SC) forms in DNA solutions is described. The method (SCFluo) takes advantage of the reversible denaturation property of SC forms and the high specificity of the PicoGreen fluorochrome for double-stranded (ds)DNA. Fluorescence values of forms capable of r...

journal_title：Nucleic acids research

authors： Levy MS,Lotfian P,O'Kennedy R,Lo-Yim MY,Shamlou PA

更新日期：2000-06-15 00:00:00

abstract：:Decay of (125)I produces a shower of low energy electrons (Auger electrons) that cause strand breaks in DNA in a distance-dependent manner with 90% of the breaks located within 10 bp from the decay site. We studied strand breaks in RNA molecules produced by decay of (125)I incorporated into complementary DNA oligonucl...

journal_title：Nucleic acids research

authors： Gaidamakova EK,Neumann RD,Panyutin IG

更新日期：2002-11-15 00:00:00

abstract：:Patterns in biological sequences frequently signify interesting features in the underlying molecule. Many tools exist to search for well-known patterns. Less support is available for exploratory analysis, where no well-defined patterns are known yet. PatScanUI (https://patscan.secondarymetabolites.org/) provides a hig...

journal_title：Nucleic acids research

authors： Blin K,Wohlleben W,Weber T

更新日期：2018-07-02 00:00:00

abstract：:Gene expression circuitries, which enable cells to detect precise levels within a morphogen concentration gradient, have a pivotal impact on biological processes such as embryonic pattern formation, paracrine and autocrine signalling, and cellular migration. We present the rational synthesis of a synthetic genetic cir...

journal_title：Nucleic acids research

authors： Greber D,Fussenegger M

更新日期：2010-10-01 00:00:00

abstract：:A novel expression system was established that allows expression and propagation of the human hepatitis B virus (HBV) genome in cultured animal cells. An overlength HBV genome encoding the viral pregenomic RNA was put under transcriptional control of the human metallothionein IIA promoter thereby replacing the endogen...

journal_title：Nucleic acids research

authors： Junker M,Galle P,Schaller H

更新日期：1987-12-23 00:00:00

abstract：:Cellular RNAs that do not function as messenger RNAs (mRNAs), transfer RNAs (tRNAs) or ribosomal RNAs (rRNAs) comprise a diverse class of molecules that are commonly referred to as non-protein-coding RNAs (ncRNAs). These molecules have been known for quite a while, but their importance was not fully appreciated until ...

journal_title：Nucleic acids research

authors： Hüttenhofer A,Vogel J

更新日期：2006-01-25 00:00:00

abstract：:We described here an approach for mapping proteins on any sequence of genomic DNA. UV-induced DNA-protein crosslinking within whole cells and the 'protein image' hybridization technique (1) were applied to test the proteins bound to different regions of the D. melanogaster hsp-70 gene. The histone H1-DNA association w...

journal_title：Nucleic acids research

authors： Belikov SV,Belgovsky AI,Preobrazhenskaya OV,Karpov VL,Mirzabekov AD

更新日期：1993-02-25 00:00:00

abstract：:Initiation of bacterial DNA replication at oriC is mediated by primosomal proteins that act cooperatively to melt an AT-rich region where the replicative helicase is loaded prior to the assembly of the replication fork. In Bacillus subtilis, the dnaD, dnaB and dnaI genes are essential for initiation of DNA replication...

journal_title：Nucleic acids research

authors： Grainger WH,Machón C,Scott DJ,Soultanas P

更新日期：2010-05-01 00:00:00

abstract：:OGG1 initiated base excision repair (BER) is the major pathway for repair of oxidative DNA base damage 8-oxoguanine (8-oxoG). Here, we report that RECQL4 DNA helicase, deficient in the cancer-prone and premature aging Rothmund-Thomson syndrome, physically and functionally interacts with OGG1. RECQL4 promotes catalytic...

journal_title：Nucleic acids research

authors： Duan S,Han X,Akbari M,Croteau DL,Rasmussen LJ,Bohr VA

更新日期：2020-07-09 00:00:00

abstract：:Spirochetes of the genus Borrelia possess unusual genomes that consist in a linear chromosome and multiple linear and circular plasmids. The linear replicons are terminated by covalently closed hairpin ends, referred to as hairpin telomeres. The hairpin telomeres represent a simple solution to the end-replication prob...

journal_title：Nucleic acids research

authors： Huang SH,Kobryn K

更新日期：2016-06-20 00:00:00

abstract：:We have investigated the mechanism of the electrophoresis-driven chromatin aggregation which had been described by Weintraub (1984, Cell 38, 17-27) as a putative mean for propagation of genetic repression in eukaryotes. We show that the oligonucleosome aggregates are assembled de novo at the starting zone of DNP elect...

journal_title：Nucleic acids research

authors： Grigoryev SA,Spirin KS,Krasheninnikov IA

更新日期：1990-12-25 00:00:00

abstract：:The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes,...

journal_title：Nucleic acids research

authors： Howe DG,Ramachandran S,Bradford YM,Fashena D,Toro S,Eagle A,Frazer K,Kalita P,Mani P,Martin R,Moxon ST,Paddock H,Pich C,Ruzicka L,Schaper K,Shao X,Singer A,Van Slyke CE,Westerfield M

更新日期：2021-01-08 00:00:00

abstract：:We have explored the functional relationships between spliceosome and Microprocessor complex activities in a novel class of microRNAs (miRNAs), named Splice site Overlapping (SO) miRNAs, whose pri-miRNA hairpins overlap splice sites. We focused on the evolutionarily conserved SO miR-34b, and we identified two indispen...

journal_title：Nucleic acids research

authors： Mattioli C,Pianigiani G,Pagani F

更新日期：2013-10-01 00:00:00

abstract：:The DNA unwinding element (DUE) is a sequence rich in adenine and thymine residues present within the origin region of both prokaryotic and eukaryotic replicons. Recently, it has been shown that this is the site where bacterial DnaA proteins, the chromosomal replication initiators, form a specific nucleoprotein filame...

journal_title：Nucleic acids research

authors： Wegrzyn K,Fuentes-Perez ME,Bury K,Rajewska M,Moreno-Herrero F,Konieczny I

更新日期：2014-07-01 00:00:00

abstract：:We report the use of an engineered ribozyme to produce a circular human exon in vitro. Specifically, we have designed a derivative of a yeast self-splicing group II intron that is able to catalyze the formation of a circular exon encoding the first kringle domain (K1) of the human tissue plasminogen activator protein....

journal_title：Nucleic acids research

authors： Mikheeva S,Hakim-Zargar M,Carlson D,Jarrell K

更新日期：1997-12-15 00:00:00

abstract：:Daunomycin is one of the most important agents used in anticancer chemotherapy. It interacts with DNA through intercalation of its planar chromophore between successive base pairs. The effect of intercalation on structure, dynamics and energetics is the topic of a wealth of scientific studies. In the present study, we...

journal_title：Nucleic acids research

authors： Trieb M,Rauch C,Wibowo FR,Wellenzohn B,Liedl KR

更新日期：2004-09-01 00:00:00

abstract：:A method for the facile preparation of oligoribonucleotide analogues containing beta-d-allofuranosyl nucleosides with additional functional groups tethered to the 6'-O positions is presented. It is based on the synthesis of two protected nucleosides carrying a 6'-O -bromopentyl and a 6'-O -methylaminopentyl substituen...

journal_title：Nucleic acids research

authors： Wu X,Pitsch S

更新日期：1998-10-01 00:00:00

abstract：:Gene losses provide an insightful route for studying the morphological and physiological adaptations of species, but their discovery is challenging. Existing genome annotation tools focus on annotating intact genes and do not attempt to distinguish nonfunctional genes from genes missing annotation due to sequencing an...

journal_title：Nucleic acids research

authors： Turakhia Y,Chen HI,Marcovitz A,Bejerano G

更新日期：2020-09-18 00:00:00

abstract：:ZFP57 is necessary for maintaining repressive epigenetic modifications at Imprinting control regions (ICRs). In mouse embryonic stem cells (ESCs), ZFP57 binds ICRs (ICRBS) and many other loci (non-ICRBS). To address the role of ZFP57 on all its target sites, we performed high-throughput and multi-locus analyses of inb...

journal_title：Nucleic acids research

authors： Riso V,Cammisa M,Kukreja H,Anvar Z,Verde G,Sparago A,Acurzio B,Lad S,Lonardo E,Sankar A,Helin K,Feil R,Fico A,Angelini C,Grimaldi G,Riccio A

更新日期：2016-09-30 00:00:00

abstract：:Post-translational modifications (such as ubiquitination) of clock proteins are critical in maintaining the precision and robustness of the evolutionarily conserved circadian clock. Ubiquitination of the core clock transcription factor BMAL1 (brain and muscle Arnt-like 1) has recently been reported. However, it remain...

journal_title：Nucleic acids research

authors： Gossan NC,Zhang F,Guo B,Jin D,Yoshitane H,Yao A,Glossop N,Zhang YQ,Fukada Y,Meng QJ

更新日期：2014-05-01 00:00:00

abstract：:Among a collection of 74 aprt mutations induced by treatment of plateau phase Chinese hamster ovary CHO cells with the radiomimetic DNA double-strand cleaving agent neocarzinostatin, nine were large-scale rearrangements. Molecular analysis indicated that all nine were highly conservative, non-homologous reciprocal exc...

journal_title：Nucleic acids research

authors： Wang P,Lee JW,Yu Y,Turner K,Zou Y,Jackson-Cook CK,Povirk LF

更新日期：2002-06-15 00:00:00

abstract：:We have located and sequenced the murine homologue of the hst/k-FGF oncogene in genomic DNA clones that extend 3' from int-2 on mouse chromosome 7. The two genes are in the same transcriptional orientation, less than 20 kilobase pairs (kb) apart, and presumably evolved by tandem duplication of a common ancestral gene....

journal_title：Nucleic acids research

authors： Brookes S,Smith R,Thurlow J,Dickson C,Peters G

更新日期：1989-06-12 00:00:00

abstract：:Next-generation sequencing allows now the sequencing of small RNA molecules and the estimation of their expression levels. Consequently, there will be a high demand of bioinformatics tools to cope with the several gigabytes of sequence data generated in each single deep-sequencing experiment. Given this scene, we deve...

journal_title：Nucleic acids research

authors： Hackenberg M,Sturm M,Langenberger D,Falcón-Pérez JM,Aransay AM

更新日期：2009-07-01 00:00:00