Interaction of dimeric intercalating dyes with single-stranded DNA.

abstract：:Increasing numbers of proteins, nucleic acids and other molecular entities have been explored as therapeutic targets, hundreds of which are targets of approved and clinical trial drugs. Knowledge of these targets and corresponding drugs, particularly those in clinical uses and trials, is highly useful for facilitating...

journal_title：Nucleic acids research

authors： Zhu F,Han B,Kumar P,Liu X,Ma X,Wei X,Huang L,Guo Y,Han L,Zheng C,Chen Y

更新日期：2010-01-01 00:00:00

abstract：:In eukaryotic ribosome, the N domain of polypeptide release factor eRF1 is involved in decoding stop signals in mRNAs. However, structure of the decoding site remains obscure. Here, we specifically altered the stop codon recognition pattern of human eRF1 by point mutagenesis of the invariant Glu55 and Tyr125 residues ...

journal_title：Nucleic acids research

authors： Kolosov P,Frolova L,Seit-Nebi A,Dubovaya V,Kononenko A,Oparina N,Justesen J,Efimov A,Kisselev L

更新日期：2005-11-10 00:00:00

abstract：:A refined map for the linear arrangement of histones along DNA in nucleosomal core particles has been determined by DNA-protein crosslinking. On one strand of 145-bp core DNA, histones are aligned in the following order: (5') H2B25,35-H455,65-H375,85,95/H488-H2B105,11 5-H2A118-H3135,145/H2A145 (3') (the subscripts giv...

journal_title：Nucleic acids research

authors： Bavykin SG,Usachenko SI,Lishanskaya AI,Shick VV,Belyavsky AV,Undritsov IM,Strokov AA,Zalenskaya IA,Mirzabekov AD

更新日期：1985-05-24 00:00:00

abstract：:The leaf senescence database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. Through manual curation and extensive annotation, we updated the LSD to a new version LSD 3.0, which contains 5853 genes and 617 mutants from 68 species. To provide sustainable and reli...

journal_title：Nucleic acids research

authors： Li Z,Zhang Y,Zou D,Zhao Y,Wang HL,Zhang Y,Xia X,Luo J,Guo H,Zhang Z

更新日期：2020-01-08 00:00:00

abstract：:One surprisingly common element of RNA secondary structure consists of a hairpin capped by a four-base loop (or the tetraloop). Recently the 3-D structures of two RNA-tetraloops have been determined by NMR-studies. Both structures have a similar architecture: the first and the last bases of the loop form a hydrogen bo...

journal_title：Nucleic acids research

authors： Kajava A,Rüterjans H

更新日期：1993-09-25 00:00:00

abstract：:Several electrophoretic and chromatographic systems have been investigated and compared for sequence analysis of oligodeoxyribonucleotides. Three systems were found to be useful for the separation of a series of sequential degradation products resulting from a labeled oligonucleotide: (I) 2-D electrophoresisdagger; (I...

journal_title：Nucleic acids research

authors： Jay E,Bambara R,Padmanabhan R,Wu R

更新日期：1974-03-01 00:00:00

abstract：:RNase D was recently reported as a new enzymatic activity associated with HIV-1 reverse transcriptase (RT), cleaving RNA at two positions within the double-stranded region of the tRNA primer-viral RNA template complex (Ben-Artzi et al., Proc. Natl. Acad. Sci. USA 89 (1992) 927-931). This would make RNase D a fourth di...

journal_title：Nucleic acids research

authors： Hostomsky Z,Hudson GO,Rahmati S,Hostomska Z

更新日期：1992-11-11 00:00:00

abstract：:Post-translational modifications (PTMs) play a key role in numerous cellular processes by directly affecting structure, dynamics and interaction networks of target proteins. Despite their importance, our understanding of protein PTMs at the atomistic level is still largely incomplete. Molecular dynamics (MD) simulatio...

journal_title：Nucleic acids research

authors： Margreitter C,Petrov D,Zagrovic B

更新日期：2013-07-01 00:00:00

abstract：:In order to examine the nature of the complex formation between the ribosomal protein S1 and nucleic acids three methods were used: Inhibition of the reaction of n-ethyl[2.3 14C]-maleimide with S1 by the addition of oligonucleotides; adsorption of the complexes to nitrocellulose filters; and equilibrium dialysis. The ...

journal_title：Nucleic acids research

authors： Lipecky R,Kohlschein J,Gassen HG

更新日期：1977-10-01 00:00:00

abstract：:The behaviour of highly purified bacterial expressed rat O6-methylguanine-DNA methyltransferase (MGMT) towards the repair of CGCm6GAGCTCGCG and CGCe6GAGCTCGCG (km6G/ke6G = 1.45, where k is the second order repair rate constant determined, m6G and e6G are O6-methyl and O6-ethylguanine) is similar to that of E. coli 39k...

journal_title：Nucleic acids research

authors： Liem LK,Lim A,Li BF

更新日期：1994-05-11 00:00:00

abstract：:Two novel fluorescent cyanine-AMP conjugates, F550/570 and F650/670, have been synthesized to serve as transcription initiators under the T7 phi2.5 promoter. Efficient fluorophore labeling of 5' RNA is achieved in a single transcription step by including F550/570 and F650/670 in the transcription solution. The current...

journal_title：Nucleic acids research

authors： Li N,Yu C,Huang F

更新日期：2005-02-24 00:00:00

abstract：:We describe a method for the formation of hybrid genes by in vivo recombination between two genes with partial sequence homology. DNA structures consisting of plasmid vector sequences, flanked by the alpha 2 interferon gene on the one side and a portion of the alpha 1 interferon gene (homology about 80%) on the other,...

journal_title：Nucleic acids research

authors： Weber H,Weissmann C

更新日期：1983-08-25 00:00:00

abstract：:Although the promoters of both the Bax and p21 genes are activated by p53, they differ in the effect on this activation of the POU family transcription factor Brn-3a. Thus, Brn-3a inhibits activation of the Bax promoter by p53 but enhances the ability of p53 to activate the p21 promoter. We demonstrate that repression...

journal_title：Nucleic acids research

authors： Perez-Sanchez C,Budhram-Mahadeo VS,Latchman DS

更新日期：2002-11-15 00:00:00

abstract：:The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130,000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77,000 Thalassiosira pseudonana ESTs from seven libraries...

journal_title：Nucleic acids research

authors： Maheswari U,Mock T,Armbrust EV,Bowler C

更新日期：2009-01-01 00:00:00

abstract：:Type II restriction endonuclease BsaWI recognizes a degenerated sequence 5'-W/CCGGW-3' (W stands for A or T, '/' denotes the cleavage site). It belongs to a large family of restriction enzymes that contain a conserved CCGG tetranucleotide in their target sites. These enzymes are arranged as dimers or tetramers, and re...

journal_title：Nucleic acids research

authors： Tamulaitis G,Rutkauskas M,Zaremba M,Grazulis S,Tamulaitiene G,Siksnys V

更新日期：2015-09-18 00:00:00

abstract：:Site-specific DNA double-strand breaks have been used to generate knock-in through the homology-dependent or -independent pathway. However, low efficiency and accompanying negative impacts such as undesirable indels or tumorigenic potential remain problematic. In this study, we present an enhanced reduced-risk genome ...

journal_title：Nucleic acids research

authors： He X,Chen W,Liu Z,Yu G,Chen Y,Cai YJ,Sun L,Xu W,Zhong L,Gao C,Chen J,Zhang M,Yang S,Yao Y,Zhang Z,Ma F,Zhang CC,Lu HP,Yu B,Cheng TL,Qiu J,Sheng Q,Zhou HM,Lv ZR,Yan J,Zhou Y,Qiu Z,Cui Z,Zhang X,Me

更新日期：2020-06-04 00:00:00

abstract：:Differential melting profiles and denaturation maps are calculated for fdDNA whose sequence of nucleotides has been determined recently. The melting profiles for the total DNA and a number of its restriction fragments are compared with experimental data taken from literature. The comparison enables one to correlate a ...

journal_title：Nucleic acids research

authors： Vologodskii AV,Frank-Kamenetskii MD

更新日期：1978-07-01 00:00:00

abstract：:Conserved in a variety of evolutionarily divergent plant species, LOB DOMAIN (LBD) genes define a large, plant-specific family of largely unknown function. LBD genes have been implicated in a variety of developmental processes in plants, although to date, relatively few members have been assigned functions. LBD protei...

journal_title：Nucleic acids research

authors： Husbands A,Bell EM,Shuai B,Smith HM,Springer PS

更新日期：2007-01-01 00:00:00

abstract：:Human adenovirus mutants that carry a large deletion in early region 4 (E4) are severely defective in the synthesis of viral late proteins. Plasmids that carry intact E4 sequences can complement the late protein synthetic defect of such mutants when introduced into infected cells by transfection, presumably due to the...

journal_title：Nucleic acids research

authors： Ketner G,Bridge E,Virtanen A,Hemström C,Pettersson U

更新日期：1989-04-25 00:00:00

abstract：:RNA polymerase (RNAP) is a major target of gene regulation. Thermus thermophilus bacteriophage P23-45 encodes two RNAP binding proteins, gp39 and gp76, which shut off host gene transcription while allowing orderly transcription of phage genes. We previously reported the structure of the T. thermophilus RNAP•σA holoenz...

journal_title：Nucleic acids research

authors： Ooi WY,Murayama Y,Mekler V,Minakhin L,Severinov K,Yokoyama S,Sekine SI

更新日期：2018-01-09 00:00:00

abstract：:A tetradecanucleotide U-A-G-C(U-C-G)2G-G-C-Up corresponding to bases 21-34 of a nascent sequence of formylmethionyl tRNA of E. coli has been synthesized by the joining of two combinations of chemically synthesized oligonucleotides: 1) U-A-G-C + U-C-G-U-C-G + G-G-C-Up and 2) U-A-G-C + U-C-G-U + C-G-G-G-C-Up. In reactio...

journal_title：Nucleic acids research

authors： Ohtsuka E,Doi T,Uemura H,Taniyama Y,Ikehara M

更新日期：1980-09-11 00:00:00

abstract：:R spider is a web-based tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions in human biology accumulated in the Reactome and KEGG databases. R spider implements a network-based statistical framework, which provides a global understanding of gene relations in the supplied ...

journal_title：Nucleic acids research

authors： Antonov AV,Schmidt EE,Dietmann S,Krestyaninova M,Hermjakob H

更新日期：2010-07-01 00:00:00

abstract：:A novel program suite was implemented for the functional interpretation of high-throughput gene expression data based on the identification of Gene Ontology (GO) nodes. The focus of the analysis lies on the interpretation of microarray data from prokaryotes. The three well established statistical methods of the thresh...

journal_title：Nucleic acids research

authors： Scheer M,Klawonn F,Münch R,Grote A,Hiller K,Choi C,Koch I,Schobert M,Härtig E,Klages U,Jahn D

更新日期：2006-07-01 00:00:00

abstract：:The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provide...

journal_title：Nucleic acids research

authors： Markowitz VM,Chen IM,Palaniappan K,Chu K,Szeto E,Grechkin Y,Ratner A,Jacob B,Huang J,Williams P,Huntemann M,Anderson I,Mavromatis K,Ivanova NN,Kyrpides NC

更新日期：2012-01-01 00:00:00

abstract：:A fundamental problem with applying Consensus, Weight-Matrix or hidden Markov models as search tools for biosequences is that there is no way to know, from the model, if the modeled sequences display any dependencies between positional identities. In some instances, these dependencies are crucial in correctly acceptin...

journal_title：Nucleic acids research

authors： Ray WC

更新日期：2005-07-01 00:00:00

abstract：:Point mutations in mitochondrial tRNA genes are responsible for individual subgroups of mitochondrial encephalomyopathies. We have recently reported that point mutations in the tRNA(Leu)(UUR) and tRNA(Lys) genes cause a defect in the normal modification at the first nucleotide of the anticodon. As part of a systematic...

journal_title：Nucleic acids research

authors： Yasukawa T,Hino N,Suzuki T,Watanabe K,Ueda T,Ohta S

更新日期：2000-10-01 00:00:00

abstract：:The nucleotide sequence of Neurospora crassa 5.8 S rDNA and adjacent regions has been determined. The deduced 5.8 S rRNA sequence of Neurospora differs from the 5.8 S rRNA sequence of Saccharomyces cerevisiae at 13 of 158 residues. Nine of these differences are clustered in a segment capable of forming a short hairpin...

journal_title：Nucleic acids research

authors： Selker E,Yanofsky C

更新日期：1979-06-11 00:00:00

abstract：:Defined DNA substrates containing discrete abasic sites or paired abasic sites set 1, 3, 5 and 7 bases apart on opposite strands were constructed to examine the reactivity of S1, mung bean and P1 nucleases towards abasic sites. None of the enzymes acted on the substrate containing discrete abasic sites. Under conditio...

journal_title：Nucleic acids research

authors： Chaudhry MA,Weinfeld M

更新日期：1995-10-11 00:00:00

abstract：:Plant specialized metabolites are chemically highly diverse, play key roles in host-microbe interactions, have important nutritional value in crops and are frequently applied as medicines. It has recently become clear that plant biosynthetic pathway-encoding genes are sometimes densely clustered in specific genomic lo...

journal_title：Nucleic acids research

authors： Kautsar SA,Suarez Duran HG,Blin K,Osbourn A,Medema MH

更新日期：2017-07-03 00:00:00

abstract：:N7-Methyl-2'-deoxyguanosine (m7dG) is the predominant lesion formed by methylating agents. A systematic investigation on the effect of m7dG on DNA replication has been difficult due to the chemical instability of m7dG. To gain insights into the m7dG effect, we employed a 2'-fluorine-mediated transition-state destabilz...

journal_title：Nucleic acids research

authors： Koag MC,Kou Y,Ouzon-Shubeita H,Lee S

更新日期：2014-07-01 00:00:00