Crystal structure of trioxacarcin A covalently bound to DNA.

abstract：:Phylogenetic analysis and examination of protein domains allow accurate genome annotation and are invaluable to study proteins and protein complex evolution. However, two sequences can be homologous without sharing statistically significant amino acid or nucleotide identity, presenting a challenging bioinformatics pro...

journal_title：Nucleic acids research

authors： Alako BT,Rainey D,Nijveen H,Leunissen JA

更新日期：2006-07-01 00:00:00

abstract：:Immunoglobulin (Ig) diversification by somatic hypermutation in germinal center B cells is instrumental for maturation of the humoral immune response, but also bears the risk of excessive or aberrant genetic changes. Thus, introduction of DNA damage by activation-induced cytidine deaminase as well as DNA repair by mul...

journal_title：Nucleic acids research

authors： Frankenberger S,Davari K,Fischer-Burkart S,Böttcher K,Tomi NS,Zimber-Strobl U,Jungnickel B

更新日期：2014-04-01 00:00:00

abstract：:The MyHits web site (http://myhits.isb-sib.ch) is an integrated service dedicated to the analysis of protein sequences. Since its first description in 2004, both the user interface and the back end of the server were improved. A number of tools (e.g. MAFFT, Jacop, Dotlet, Jalview, ESTScan) were added or updated to imp...

journal_title：Nucleic acids research

authors： Pagni M,Ioannidis V,Cerutti L,Zahn-Zabal M,Jongeneel CV,Hau J,Martin O,Kuznetsov D,Falquet L

更新日期：2007-07-01 00:00:00

abstract：:Labeling of a covalently closed circular double-stranded DNA was achieved using a so-called 'padlock oligonucleotide'. The oligonucleotide was targeted to a sequence which is present in the replication origin of phage f1 and thus in numerous commonly used plasmids. After winding around the double-stranded target DNA s...

journal_title：Nucleic acids research

authors： Roulon T,Coulaud D,Delain E,Le Cam E,Hélène C,Escudé C

更新日期：2002-02-01 00:00:00

abstract：:Homozygosity for a natural deletion variant of the HIV-coreceptor molecule CCR5, CCR5Δ32, confers resistance toward HIV infection. Allogeneic stem cell transplantation from a CCR5Δ32-homozygous donor has resulted in the first cure from HIV ('Berlin patient'). Based thereon, genetic disruption of CCR5 using designer nu...

journal_title：Nucleic acids research

authors： Mock U,Machowicz R,Hauber I,Horn S,Abramowski P,Berdien B,Hauber J,Fehse B

更新日期：2015-06-23 00:00:00

abstract：:In Saccharomyces cerevisiae, the DNA damage response (DDR) is activated by the spatio-temporal colocalization of Mec1-Ddc2 kinase and the 9-1-1 clamp. In the absence of direct means to monitor Mec1 kinase activation in vivo, activation of the checkpoint kinase Rad53 has been taken as a proxy for DDR activation. Here, ...

journal_title：Nucleic acids research

authors： Janke R,Herzberg K,Rolfsmeier M,Mar J,Bashkirov VI,Haghnazari E,Cantin G,Yates JR 3rd,Heyer WD

更新日期：2010-04-01 00:00:00

abstract：:Characterization of the ability of human interferons (IFNs) to rapidly induce genes led to the identification of the first two members of the STAT (signal transducers and activators of transcription) family, Stat1 and Stat2. To study the unique role of this transcription factor in IFN signaling under more physiologica...

journal_title：Nucleic acids research

authors： Park C,Lecomte MJ,Schindler C

更新日期：1999-11-01 00:00:00

abstract：:We have determined the complete nucleotide sequence of the hormonally regulated yolk protein 1 (YP1) gene of Drosophila melanogaster. We have also determined the sequence location of the 5' and 3' ends of both the mature mRNA and the gene's only intron. The YP1 gene contains sequences similar to those found in many ot...

journal_title：Nucleic acids research

authors： Hung MC,Wensink PC

更新日期：1981-12-11 00:00:00

abstract：:Chromosome stability is primarily determined by telomere length. TRF1 is the core subunit of shelterin that plays a critical role in telomere organization and replication. However, the dynamics of TRF1 in scenarios of telomere-processing activities remain elusive. Using single-molecule magnetic tweezers, we here inves...

journal_title：Nucleic acids research

authors： Li X,Wang M,Zheng W,Huang W,Wang Z,Jin K,Liu L,Yu Z

更新日期：2021-01-25 00:00:00

abstract：:Nucleotide excision repair (NER) is a major DNA repair pathway for a variety of DNA lesions. XPB plays a key role in DNA opening at damage sites and coordinating damage incision by nucleases. XPB is conserved from archaea to human. In archaea, XPB is associated with a nuclease Bax1. Here we report crystal structures o...

journal_title：Nucleic acids research

authors： DuPrez K,He F,Chen Z,Hilario E,Fan L

更新日期：2020-06-19 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：:Restriction endonucleases HindII and TaqI, but not SalI, were found to efficiently cleave synthetic hexadecanucleotide duplexes which contained either an A/C or a G/T mismatch within their respective restriction sites. Double-stranded M13 DNAs with identical mismatches were also cleaved under the assay conditions. The...

journal_title：Nucleic acids research

authors： Jiricny J,Martin D

更新日期：1986-03-11 00:00:00

abstract：:Murine embryonic stem (ES) cells are commonly cultured on feeder layers of primary murine embryonic fibroblasts (MEFs). Because gene targeting experiments often involve sequential selection for multiple-drug resistance in single ES cell lines, we have developed a new mouse strain which represents an economical donor f...

journal_title：Nucleic acids research

authors： Tucker KL,Wang Y,Dausman J,Jaenisch R

更新日期：1997-09-15 00:00:00

abstract：:The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a premier public resource for literature-based, manually curated associations between chemicals, gene products, phenotypes, diseases, and environmental exposures. In this biennial update, we present our new chemical-phenotype module that codes chemi...

journal_title：Nucleic acids research

authors： Davis AP,Grondin CJ,Johnson RJ,Sciaky D,McMorran R,Wiegers J,Wiegers TC,Mattingly CJ

更新日期：2019-01-08 00:00:00

abstract：:The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration wi...

journal_title：Nucleic acids research

authors： Mashima J,Kodama Y,Fujisawa T,Katayama T,Okuda Y,Kaminuma E,Ogasawara O,Okubo K,Nakamura Y,Takagi T

更新日期：2017-01-04 00:00:00

abstract：:The pac1+ gene of the fission yeast Schizosaccharomyces pombe is essential for viability and its overexpression induces sterility and suppresses mutations in the pat1+ and snm1+ genes. The pac1+ gene encodes a protein that is structurally similar to RNase III from Escherichia coli, but its normal function is unknown. ...

journal_title：Nucleic acids research

authors： Rotondo G,Frendewey D

更新日期：1996-06-15 00:00:00

abstract：:RNA structural complexity and flexibility present a challenge for computational modeling efforts. Experimental information and bioinformatics data can be used as restraints to improve the accuracy of RNA tertiary structure prediction. Regarding utilization of restraints, the fundamental questions are: (i) What is the ...

journal_title：Nucleic acids research

authors： Wang J,Williams B,Chirasani VR,Krokhotin A,Das R,Dokholyan NV

更新日期：2019-06-20 00:00:00

abstract：:We have developed a simple method to measure RNA synthesis in real time. In this technique, transcription reactions are performed in the presence of molecular beacons that possess a 2'-O-methylribonucleotide backbone. These probes become fluorescent as they hybridize to nascent RNA during the course of synthesis. We f...

journal_title：Nucleic acids research

authors： Marras SA,Gold B,Kramer FR,Smith I,Tyagi S

更新日期：2004-05-20 00:00:00

abstract：:The chemical reactivity of matched T and C bases to osmium tetroxide and hydroxylamine near mismatched and unmatched bases in a heteroduplex between two strands of DNA with multiple differences was examined. Data was available for matched bases one or two positions away from 24 mismatches. Reactive bases were found ne...

journal_title：Nucleic acids research

authors： Cotton RG,Campbell RD

更新日期：1989-06-12 00:00:00

abstract：:Poly(ADP-ribosyl)ation regulates numerous cellular processes like genome maintenance and cell death, thus providing protective functions but also contributing to several pathological conditions. Poly(ADP-ribose) (PAR) molecules exhibit a remarkable heterogeneity in chain lengths and branching frequencies, but the biol...

journal_title：Nucleic acids research

authors： Aberle L,Krüger A,Reber JM,Lippmann M,Hufnagel M,Schmalz M,Trussina IREA,Schlesiger S,Zubel T,Schütz K,Marx A,Hartwig A,Ferrando-May E,Bürkle A,Mangerich A

更新日期：2020-10-09 00:00:00

abstract：:Complex carbohydrates of plants are the main food sources of animals and microbes, and serve as promising renewable feedstock for biofuel and biomaterial production. Carbohydrate active enzymes (CAZymes) are the most important enzymes for complex carbohydrate metabolism. With an increasing number of plant and plant-as...

journal_title：Nucleic acids research

authors： Zhang H,Yohe T,Huang L,Entwistle S,Wu P,Yang Z,Busk PK,Xu Y,Yin Y

更新日期：2018-07-02 00:00:00

abstract：:Bacteria core RNA polymerase (RNAP) must associate with a sigma factor to recognize promoter sequences. Promoters recognized by the sigma(54) (or sigma(N)) associated RNA polymerase are unique in having conserved positions around -24 and -12 nucleotides upstream from the transcriptional start site. Using DNA microarra...

journal_title：Nucleic acids research

authors： Zhao K,Liu M,Burgess RR

更新日期：2010-03-01 00:00:00

abstract：:RNA interference represents a potent intervention for cancer treatment but requires a robust delivery agent for transporting gene-modulating molecules, such as small interfering RNAs (siRNAs). Although numerous molecular approaches for siRNA delivery are adequate in vitro, delivery to therapeutic targets in vivo is li...

journal_title：Nucleic acids research

authors： Alonso-Valenteen F,Pacheco S,Srinivas D,Rentsendorj A,Chu D,Lubow J,Sims J,Miao T,Mikhael S,Hwang JY,Abrol R,Medina Kauwe LK

更新日期：2019-12-02 00:00:00

abstract：:Post-translational modifications (PTMs) regulate many aspects of protein function and are indispensable for the spatio-temporal regulation of cellular processes. The proteome-wide identification of PTM targets has made significant progress in recent years, as has the characterization of their writers, readers, modifie...

journal_title：Nucleic acids research

authors： Teloni F,Altmeyer M

更新日期：2016-02-18 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

abstract：:DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polym...

journal_title：Nucleic acids research

authors： Satange R,Chuang CY,Neidle S,Hou MH

更新日期：2019-09-19 00:00:00

abstract：:The fine structure of the melting curve for the linear colE1 DNA has been obtained. To find the ColE1 DNA regions corresponding to peaks in the melting curve's fine structure, we fixed the melted DNA regions with glyoxal /12/. Electron-microscopic denaturation maps were obtained for nine temperature points within the ...

journal_title：Nucleic acids research

authors： Borovik AS,Kalambet YA,Lyubchenko YL,Shitov VT,Golovanov EI

更新日期：1980-09-25 00:00:00

abstract：:Since its discovery in 1979, left-handed Z-DNA has evolved from an in vitro curiosity to a challenging DNA structure with crucial roles in gene expression, regulation and recombination. A fundamental question that has puzzled researchers for decades is how the transition from B-DNA, the prevalent right-handed form of ...

journal_title：Nucleic acids research

authors： Moradi M,Babin V,Roland C,Sagui C

更新日期：2013-01-07 00:00:00

abstract：:Two models have been proposed for triggering release of the lagging strand polymerase at the replication fork, enabling cycling to the primer for the next Okazaki fragment--either collision with the 5'-end of the preceding fragment (collision model) or synthesis of a new primer by primase (signaling model). Specific p...

journal_title：Nucleic acids research

authors： Yuan Q,McHenry CS

更新日期：2014-02-01 00:00:00

abstract：:The chromatographic profiles of isoaccepting tRNAs were analyzed at five time points during the 96 hr, dimethylsulfoxide induced, erythroid-like differentiation of Friend leukemia cells. Sixty-four isoaccepting species of tRNA for 16 amino acids were resolved by RPC-5 chromatography. The relative amounts of tRNAphe, t...

journal_title：Nucleic acids research

authors： Lin VK,Agris PF

更新日期：1980-08-11 00:00:00