ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.

abstract：:Uridylation-dependent RNA decay is a widespread eukaryotic pathway modulating RNA homeostasis. Terminal uridylyltransferases (Tutases) add untemplated uridyl residues to RNA 3'-ends, marking them for degradation by the U-specific exonuclease Dis3L2. In Schizosaccharomyces pombe, Cid1 uridylates a variety of RNAs. In t...

journal_title：Nucleic acids research

authors： Chung CZ,Jaramillo JE,Ellis MJ,Bour DYN,Seidl LE,Jo DHS,Turk MA,Mann MR,Bi Y,Haniford DB,Duennwald ML,Heinemann IU

更新日期：2019-04-08 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：:Alternative splicing and polyadenylation were observed pervasively in eukaryotic messenger RNAs. These alternative isoforms could either be consequences of physiological regulation or stochastic noise of RNA processing. To quantify the extent of stochastic noise in splicing and polyadenylation, we analyzed the alterna...

journal_title：Nucleic acids research

authors： Hon CC,Weber C,Sismeiro O,Proux C,Koutero M,Deloger M,Das S,Agrahari M,Dillies MA,Jagla B,Coppee JY,Bhattacharya A,Guillen N

更新日期：2013-02-01 00:00:00

abstract：:Deamination of cytosine (C), 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) occurs spontaneously in mammalian DNA with several hundred deaminations occurring in each cell every day. The resulting potentially mutagenic mispairs of uracil (U), thymine (T) or 5-hydroxymethyluracil (hmU) with guanine (G) are subs...

journal_title：Nucleic acids research

authors： Kemmerich K,Dingler FA,Rada C,Neuberger MS

更新日期：2012-07-01 00:00:00

abstract：:The analysis of chromatin fine structure and transcription factor occupancy of differentially expressed genes by in vivo footprinting and ligation-mediated-PCR (LMPCR) is a powerful tool to understand the impact of chromatin on gene expression. However, as with all PCR-based techniques, the accuracy of the experiments...

journal_title：Nucleic acids research

authors： Ingram R,Gao C,Lebon J,Liu Q,Mayoral RJ,Sommer SS,Hoogenkamp M,Riggs AD,Bonifer C

更新日期：2008-02-01 00:00:00

abstract：:Aside from classical loops among G-quadruplexes, the unique leaped V-shape scaffold spans over three G-tetrads, without any intervening residues. This scaffold enables a sharp reversal of two adjacent strand directions and simultaneously participates in forming the G-tetrad core. These features make this scaffold itse...

journal_title：Nucleic acids research

authors： Wan C,Fu W,Jing H,Zhang N

更新日期：2019-02-20 00:00:00

abstract：:Cellular RNA labeling strategies based on bioorthogonal chemical reactions are much less developed in comparison to glycan, protein and DNA due to its inherent instability and lack of effective methods to introduce bioorthogonal reactive functionalities (e.g. azide) into RNA. Here we report the development of a simple...

journal_title：Nucleic acids research

authors： Sawant AA,Tanpure AA,Mukherjee PP,Athavale S,Kelkar A,Galande S,Srivatsan SG

更新日期：2016-01-29 00:00:00

abstract：:p16INK4a and p21WAF1, two major cyclin-dependent kinase inhibitors, are the products of two tumor suppressor genes that play important roles in various cellular metabolic pathways. p21WAF1 is up-regulated in response to different DNA damaging agents. While the activation of p21WAF1 is p53-dependent following -rays, th...

journal_title：Nucleic acids research

authors： Al-Mohanna MA,Al-Khalaf HH,Al-Yousef N,Aboussekhra A

更新日期：2007-01-01 00:00:00

abstract：:Ditercalinium, an antitumor bifunctional intercalator which forms a high affinity reversible complex with DNA, was found to be specifically cytotoxic for polA and lig7 E. coli strains. In the polA strain, the cytotoxic effect of ditercalinium was suppressed by the uvrA mutation. DNA single strand breaks accumulated in...

journal_title：Nucleic acids research

authors： Lambert B,Roques BP,Le Pecq JB

更新日期：1988-02-11 00:00:00

abstract：:Telomeric regions of the genome are inherently difficult-to-replicate due to their propensity to generate DNA secondary structures and form nucleoprotein complexes that can impede DNA replication fork progression. Precisely how cells respond to DNA replication stalling within a telomere remains poorly characterized, l...

journal_title：Nucleic acids research

authors： Jørgensen SW,Liberti SE,Larsen NB,Lisby M,Mankouri HW,Hickson ID

更新日期：2019-05-21 00:00:00

abstract：:The products of many bacterial non-ribosomal peptide synthetases (NRPS) are highly important secondary metabolites, including vancomycin and other antibiotics. The ability to predict substrate specificity of newly detected NRPS Adenylation (A-) domains by genome sequencing efforts is of great importance to identify an...

journal_title：Nucleic acids research

authors： Röttig M,Medema MH,Blin K,Weber T,Rausch C,Kohlbacher O

更新日期：2011-07-01 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：:Recent data showed that p53 stimulates the expression of genes encoding not only pro- but also antioxidant enzymes. It was suggested that antioxidant genes could be induced under physiologic levels of stress while the prooxidant ones respond to higher level of stress. Results presented in this article illustrate an ad...

journal_title：Nucleic acids research

authors： Meiller A,Alvarez S,Drané P,Lallemand C,Blanchard B,Tovey M,May E

更新日期：2007-01-01 00:00:00

abstract：:Developmental stage-specific expression of the β-type globin genes is regulated by many cis- and trans-acting components. The adult β-globin gene contains an E-box located 60 bp downstream of the transcription start site that has been shown to bind transcription factor upstream stimulatory factor (USF) and to contribu...

journal_title：Nucleic acids research

authors： Barrow JJ,Li Y,Hossain M,Huang S,Bungert J

更新日期：2014-04-01 00:00:00

abstract：:DNA synthesis of broad host-range plasmid R1162 is initiated from two positions, flanking a large (40 bp stem, 40 bp loop) inverted repeat. Each start-point is located within a highly conserved, but oppositely oriented, 10 base-pair sequence. Synthesis from the two positions converges within the intervening inverted r...

journal_title：Nucleic acids research

authors： Lin LS,Meyer RJ

更新日期：1987-10-26 00:00:00

abstract：:A gene bank of Staphylococcus aureus strain Cowan I was established using an E. coli HB101/pBR327 host-vector system. Recombinants expressing staphylococcal protein A (SPA) were detected using an IgG-binding assay. A 3.2 Kb DNA fragment directing the synthesis of SPA in E. coli was identified. SPA produced by E. coli ...

journal_title：Nucleic acids research

authors： Duggleby CJ,Jones SA

更新日期：1983-05-25 00:00:00

abstract：:Knowledge of the various interactions between molecules in the cell is crucial for understanding cellular processes in health and disease. Currently available interaction databases, being largely complementary to each other, must be integrated to obtain a comprehensive global map of the different types of interactions...

journal_title：Nucleic acids research

authors： Kamburov A,Stelzl U,Lehrach H,Herwig R

更新日期：2013-01-01 00:00:00

abstract：:The speed of the new DNA sequencing techniques has created a need for computer programs to handle the data produced. This paper describes simple programs designed specifically for use by people with little or no computer experience. The programs are for use on small computers and provide facilities for storage, editin...

journal_title：Nucleic acids research

authors： Staden R

更新日期：1977-11-01 00:00:00

abstract：:The 1.7 Å X-ray crystal structure of the B-DNA dodecamer, [d(CGCGAATTCGCG)]₂ (DDD)-bound non-covalently to a platinum(II) complex, [{Pt(NH₃)₃}₂-µ-{trans-Pt(NH₃)₂(NH₂(CH₂)₆NH₂)₂}](NO₃)₆ (1, TriplatinNC-A,) shows the trinuclear cation extended along the phosphate backbone and bridging the minor groove. The square planar...

journal_title：Nucleic acids research

authors： Komeda S,Moulaei T,Chikuma M,Odani A,Kipping R,Farrell NP,Williams LD

更新日期：2011-01-01 00:00:00

abstract：:G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that form within guanine-rich strands of regulatory genomic regions. G4s have been extensively described in the human genome, especially in telomeres and oncogene promoters; in recent years the presence of G4s in viruses has attracted increasing...

journal_title：Nucleic acids research

authors： Ruggiero E,Richter SN

更新日期：2018-04-20 00:00:00

abstract：:A mutation in a gene dicA of Escherichia coli leads to temperature-sensitive cell division, by allowing expression of a nearby division inhibition gene dicB (1). We have now established the sequence of the DicA region and identified DicA as a 15.5 KD protein. A second gene dicC transcribed divergently from dicA and co...

journal_title：Nucleic acids research

authors： Béjar S,Cam K,Bouché JP

更新日期：1986-09-11 00:00:00

abstract：:Ribosome biogenesis is fundamental for cellular life, but surprisingly little is known about the underlying pathway. In eukaryotes a comprehensive collection of experimentally verified ribosome biogenesis factors (RBFs) exists only for Saccharomyces cerevisiae. Far less is known for other fungi, animals or plants, and...

journal_title：Nucleic acids research

authors： Ebersberger I,Simm S,Leisegang MS,Schmitzberger P,Mirus O,von Haeseler A,Bohnsack MT,Schleiff E

更新日期：2014-02-01 00:00:00

abstract：:DNA target recognizing domains of different multispecific DNA-cytosine-methyltransferases can be rearranged through engineering of the corresponding genes to generate enzymes with novel combinations of target recognition. ...

journal_title：Nucleic acids research

authors： Trautner TA,Balganesh TS,Pawlek B

更新日期：1988-07-25 00:00:00

abstract：:Tomato golden mosaic geminivirus has a genome of two single-stranded (ss) DNA components, A and B. An almost identical 'common' region in DNA A and DNA B is thought to contain sequence elements controlling replication and transcription. Hence investigation of sequences important for DNA replication by in vitro mutagen...

journal_title：Nucleic acids research

authors： Hayes RJ,Buck KW

更新日期：1989-12-25 00:00:00

abstract：:The frequencies of occurrence of four bases in the first, second and third codon positions and in the total coding sequences have been calculated by the codon usage table published in 1990 by Ikemura et al. The distribution of frequencies are further analysed in detail by a graphic technique presented recently by us. ...

journal_title：Nucleic acids research

authors： Zhang CT,Zhang R

更新日期：1991-11-25 00:00:00

abstract：:VL30 genetic elements constitute a murine multicopy gene family that is retrovirus-like, despite the lack of sequence homology with any known retrovirus. Over one hundred copies of VL30 units are dispersed throughout the mouse genome. We report here that the mouse genome also contains 'solo' VL30 long terminal repeats...

journal_title：Nucleic acids research

authors： Rotman G,Itin A,Keshet E

更新日期：1984-03-12 00:00:00

abstract：:Sgs1 is a member of the RecQ family of DNA helicases, which have been implicated in genomic stability, cancer and ageing. Srs2 is another DNA helicase that shares several phenotypic features with Sgs1 and double sgs1srs2 mutants have a severe synthetic growth phenotype. This suggests that there may be functional overl...

journal_title：Nucleic acids research

authors： Mankouri HW,Craig TJ,Morgan A

更新日期：2002-03-01 00:00:00

abstract：:DNA was purified from double minutes isolated from MTX-resistant EL4/8 mouse lymphoma cells, digested to completion with Bam H1 restriction endonuclease and cloned in lambda-1059. The properties of the library suggest that the DNA from which it was made was not detectably contaminated with non-dm chromosome material, ...

journal_title：Nucleic acids research

authors： Caizzi R,Bostock CJ

更新日期：1982-11-11 00:00:00

abstract：:Signal Transducers and Activators of Transcription (STAT) 5A/B regulate cytokine-inducible genes upon binding to GAS motifs. It is not known what percentage of genes with GAS motifs bind to and are regulated by STAT5. Moreover, it is not clear whether genome-wide STAT5 binding is modulated by its concentration. To cla...

journal_title：Nucleic acids research

authors： Zhu BM,Kang K,Yu JH,Chen W,Smith HE,Lee D,Sun HW,Wei L,Hennighausen L

更新日期：2012-05-01 00:00:00

abstract：:Chicken-erythrocyte inner histone tetramer has been complexed with several natural and synthetic DNA duplexes by salt-gradient dialysis at various protein/DNA ratios. The resulting complexes, in low-ionic-strength buffer, have been examined by electron microscopy, circular dichroism, and thermal denaturation. Electron...

journal_title：Nucleic acids research

authors： Bryan PN,Wright EB,Hsie MH,Olins AL,Olins DE

更新日期：1978-10-01 00:00:00