Salt-and histone H1-induced structural changes of reconstituted minichromosomes.

abstract：:The 5'- and 3'-untranslated regions (5'- and 3'-UTRs) of eukaryotic mRNAs are known to play a crucial role in post-transcriptional regulation of gene expression modulating nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and stability. UTRdb is a specialized database of 5' and 3' unt...

journal_title：Nucleic acids research

authors： Pesole G,Liuni S,Grillo G,Licciulli F,Mignone F,Gissi C,Saccone C

更新日期：2002-01-01 00:00:00

abstract：:Periodically repeating DNA and protein elements are involved in various important biological events including genomic evolution, gene regulation, protein complex formation, and immunity. Notably, the currently used genome editing tools such as ZFNs, TALENs, and CRISPRs are also all associated with periodically repeati...

journal_title：Nucleic acids research

authors： Mori H,Evans-Yamamoto D,Ishiguro S,Tomita M,Yachie N

更新日期：2019-01-25 00:00:00

abstract：:The cDNA-chip technology is a highly versatile tool for the comprehensive analysis of gene expression at the transcript level. Although it has been applied successfully in expression profiling projects, there is an ongoing dispute concerning the quality of such expression data. The latter critically depends on the spe...

journal_title：Nucleic acids research

authors： Drobyshev AL,Machka C,Horsch M,Seltmann M,Liebscher V,Hrabé de Angelis M,Beckers J

更新日期：2003-01-15 00:00:00

abstract：:Sodium is one of the most abundant metals in the environment and in biology, playing critical ecological and physiological roles. Na+ is also the most common buffer salt for nucleic acids research, while its specific interaction with DNA has yet to be fully studied. Herein, we probe a highly selective and robust Na+ a...

journal_title：Nucleic acids research

authors： Zhou W,Ding J,Liu J

更新日期：2016-12-01 00:00:00

abstract：:Single-stranded DNA-binding proteins (SSBs) support DNA replication by protecting single-stranded DNA from nucleolytic attack, preventing intra-strand pairing events and playing many other regulatory roles within the replisome. Recent developments in single-molecule approaches have led to a revised picture of the repl...

journal_title：Nucleic acids research

authors： Spenkelink LM,Lewis JS,Jergic S,Xu ZQ,Robinson A,Dixon NE,van Oijen AM

更新日期：2019-05-07 00:00:00

abstract：:RNA editing by adensosine deaminases is a widespread mechanism to alter genetic information in metazoa. In addition to modifications in non-coding regions, editing contributes to diversification of protein function, in analogy to alternative splicing. However, although splicing programs respond to external signals, fa...

journal_title：Nucleic acids research

authors： Balik A,Penn AC,Nemoda Z,Greger IH

更新日期：2013-01-01 00:00:00

abstract：:Besides the nicking-closing (topoisomerase I) activity, an ATP-dependent DNA topoisomerase is present in rat liver nuclei. The enzyme, partially purified, is able to catenate in vitro closed DNA circles in a magnesium-dependent, ATP-dependent, histone H1-dependent reaction, and to decatenate in vitro kinetoplast DNA n...

journal_title：Nucleic acids research

authors： Duguet M,Lavenot C,Harper F,Mirambeau G,De Recondo AM

更新日期：1983-02-25 00:00:00

abstract：:The human 5S rRNA genes are found in clusters of tandem repeated units. We have cloned and partially characterized six restriction fragments from two clusters of 2.3 kb and 1.6 kb repeats, respectively. Four fragments from the cluster of 2.3 kb repeats contain a 5S rRNA gene and one fragment contains a gene variant wi...

journal_title：Nucleic acids research

authors： Sørensen PD,Frederiksen S

更新日期：1991-08-11 00:00:00

abstract：:Trinucleotide exchange (TriNEx) is a method for generating novel molecular diversity during directed evolution by random substitution of one contiguous trinucleotide sequence for another. Single trinucleotide sequences were deleted at random positions in a target gene using the engineered transposon MuDel that were su...

journal_title：Nucleic acids research

authors： Baldwin AJ,Busse K,Simm AM,Jones DD

更新日期：2008-08-01 00:00:00

abstract：:We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities. Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered by uncertainty in model parameters. While several machine learning approaches could be proposed t...

journal_title：Nucleic acids research

authors： Zhu W,Lomsadze A,Borodovsky M

更新日期：2010-07-01 00:00:00

abstract：:Poly(ADP-ribosyl)ation is involved in numerous bio-logical processes including DNA repair, transcription and cell death. Cellular levels of poly(ADP-ribose) (PAR) are regulated by PAR polymerases (PARPs) and the degrading enzyme PAR glycohydrolase (PARG), controlling the cell fate decision between life and death in re...

journal_title：Nucleic acids research

authors： Illuzzi G,Fouquerel E,Amé JC,Noll A,Rehmet K,Nasheuer HP,Dantzer F,Schreiber V

更新日期：2014-07-01 00:00:00

abstract：:Human lung epithelioid cells were treated with Benzo (a) pyrene diol epoxide (anti) in order to establish the binding and removal of covalent adducts in chromosomal components. Isolating two different classes of mononucleosomes, it was found that their DNA contained different concentrations of B(a)PDE-DNA adducts, whi...

journal_title：Nucleic acids research

authors： Kootstra A

更新日期：1986-12-22 00:00:00

abstract：:Recognition of genomic binding sites by transcription factors can occur through base-specific recognition, or by recognition of variations within the structure of the DNA macromolecule. In this article, we investigate what information can be retrieved from local DNA structural properties that is relevant to transcript...

journal_title：Nucleic acids research

authors： Meysman P,Dang TH,Laukens K,De Smet R,Wu Y,Marchal K,Engelen K

更新日期：2011-01-01 00:00:00

abstract：:Sequence-specific interactions between aminoacyl-tRNA synthetases and their cognate tRNAs ensure both accurate RNA recognition and the efficient catalysis of aminoacylation. The effects of tRNA(Trp)variants on the aminoacylation reaction catalyzed by wild-type Escherichia coli tryptophanyl-tRNA synthe-tase (TrpRS) hav...

journal_title：Nucleic acids research

authors： Ibba M,Sever S,Praetorius-Ibba M,Söll D

更新日期：1999-09-15 00:00:00

abstract：:Because of their high nucleotide sequence homology, the specific detection of mRNA transcripts of individual members of a gene family presents certain problems. Here we apply and defend the single nucleotide primer extension (SNuPE) as a simple, specific, and highly quantitative assay for this purpose. The method dist...

journal_title：Nucleic acids research

authors： Lombardo AJ,Brown GB

更新日期：1996-12-01 00:00:00

abstract：:A new method which predicts internal exon sequences in human DNA has been developed. The method is based on a splice site prediction algorithm that uses the linear discriminant function to combine information about significant triplet frequencies of various functional parts of splice site regions and preferences of ol...

journal_title：Nucleic acids research

authors： Solovyev VV,Salamov AA,Lawrence CB

更新日期：1994-12-11 00:00:00

abstract：:Long non-coding RNAs (lncRNAs) that have no protein-coding capacity make up a large proportion of the transcriptome of various species. Many lncRNAs are expressed within the animal central nervous system in spatial- and temporal-specific patterns, indicating that lncRNAs play important roles in cellular processes, neu...

journal_title：Nucleic acids research

authors： Li M,Wen S,Guo X,Bai B,Gong Z,Liu X,Wang Y,Zhou Y,Chen X,Liu L,Chen R

更新日期：2012-12-01 00:00:00

abstract：:The genome of the cell is often exposed to DNA damaging agents and therefore requires an intricate well-regulated DNA damage response (DDR) to overcome its deleterious effects. The DDR needs proper regulation for its timely activation, repression, as well as appropriate choice of repair pathway. Studies in Saccharomyc...

journal_title：Nucleic acids research

authors： Jalal D,Chalissery J,Hassan AH

更新日期：2017-03-17 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：:We have sequenced the 0.7-kb-long fragment of Drosophila DNA which ensures the autonomous replication of plasmids in yeast. Deletion mapping has shown the ARS element to consist of at least two domains: the core having the consensus 11-bp sequence TAAATATAAAT and the enhancer which is no more than 90 bp long and is lo...

journal_title：Nucleic acids research

authors： Gragerov AI,Danilevskaya ON,Didichenko SA,Kaverina EN

更新日期：1988-02-11 00:00:00

abstract：:Laser microirradiation is a powerful tool for real-time single-cell analysis of the DNA damage response (DDR). It is often found, however, that factor recruitment or modification profiles vary depending on the laser system employed. This is likely due to an incomplete understanding of how laser conditions/dosages affe...

journal_title：Nucleic acids research

authors： Saquilabon Cruz GM,Kong X,Silva BA,Khatibzadeh N,Thai R,Berns MW,Yokomori K

更新日期：2016-02-18 00:00:00

abstract：:Adaptation to the host cell environment to efficiently take-over the host cell's machinery is crucial in particular for small RNA viruses like picornaviruses that come with only small RNA genomes and replicate exclusively in the cytosol. Their Internal Ribosome Entry Site (IRES) elements are specific RNA structures th...

journal_title：Nucleic acids research

authors： Andreev DE,Hirnet J,Terenin IM,Dmitriev SE,Niepmann M,Shatsky IN

更新日期：2012-07-01 00:00:00

abstract：:With the improved rapid sequencing techniques, the earlier sequence of U2 RNA of Novikoff hepatoma (Shibata et al, J. Biol. Chem. 250, 3909-3920, 1975) was reanalyzed and modified. The improved sequence of U2 RNA is 188 (or 189) nucleotides long and is in register with a characterized U2 RNA pseudogene (Denison et al,...

journal_title：Nucleic acids research

authors： Reddy R,Henning D,Epstein P,Busch H

更新日期：1981-11-11 00:00:00

abstract：:A study of the activity of deoxyribonucleotide-substituted analogs of the hammerhead domain of RNA catalysis has led to the design of a 14mer oligomer composed entirely of deoxyribonucleotides that promotes the cleavage of an RNA substrate. Characterization of this reaction with sequence variants and mixed DNA/RNA oli...

journal_title：Nucleic acids research

authors： Chartrand P,Harvey SC,Ferbeyre G,Usman N,Cedergren R

更新日期：1995-10-25 00:00:00

abstract：:Sequences from -3500 to +1365 of the chicken histone H5 gene have been analyzed for the presence of cis-acting elements in H5 expressing (transformed CFU-E) and non-expressing cells (fibroblasts). The region from -3500 to -115 had little effect on transcription. Proximal upstream sequences contain a negative element (...

journal_title：Nucleic acids research

authors： Rousseau S,Renaud J,Ruiz-Carrillo A

更新日期：1989-09-25 00:00:00

abstract：:Various environmental oxidative stresses are sensed by redox-sensitive regulators through cysteine thiol oxidation or modification. A few zinc-containing anti-sigma (ZAS) factors in actinomycetes have been reported to respond sensitively to thiol oxidation, among which RsrA from Streptomyces coelicolor is best charact...

journal_title：Nucleic acids research

authors： Jung YG,Cho YB,Kim MS,Yoo JS,Hong SH,Roe JH

更新日期：2011-09-01 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：:Methylation of the 2'-hydroxyl-group of ribonucleotides is found in all major classes of RNA in eukaryotes and is one of the most abundant posttranscriptional modifications of stable RNAs. In spite of intense studies, the multiple functions of RNA 2'-O-methylation are still not understood. One major obstacle in the fi...

journal_title：Nucleic acids research

authors： Aschenbrenner J,Marx A

更新日期：2016-05-05 00:00:00

abstract：:Oligodeoxyribonucleotides incorporating non-hydrolyzable dialkyl sulfide linked thymidine dimers (TsT) were synthesized chemically by the solid-phase approach. The sulfide dimer TsT was stable to degradation by snake-venom phosphodiesterase, calf spleen phosphodiesterase, Nuclease P1 and Nuclease S1. Thermal denaturat...

journal_title：Nucleic acids research

authors： Kawai SH,Wang D,Giannaris PA,Damha MJ,Just G

更新日期：1993-03-25 00:00:00

abstract：:Thermally induced structural transition in the d(TTTTATAATAAA) d(TTTATTATAAAA) heteroduplex is characterized by UV-spectroscopy and differential scanning calorimetry. At low salt (less than 0.1 M) the occurrence of a cooperative transition in the lower temperature range, followed by a broad transition connected with s...

journal_title：Nucleic acids research

authors： Bolewska K,Zielenkiewicz A,Wierzchowski KL

更新日期：1984-04-11 00:00:00