DNA binding and oligomerization of NtrC studied by fluorescence anisotropy and fluorescence correlation spectroscopy.

abstract：:Cytokines are cell-to-cell signaling proteins that play a central role in immune development, pathogen responses, and diseases. Cytokines are highly regulated at the transcriptional level by combinations of transcription factors (TFs) that recruit cofactors and the transcriptional machinery. Here, we mined through thr...

journal_title：Nucleic acids research

authors： Carrasco Pro S,Dafonte Imedio A,Santoso CS,Gan KA,Sewell JA,Martinez M,Sereda R,Mehta S,Fuxman Bass JI

更新日期：2018-10-12 00:00:00

abstract：:Arabidopsis microRNA (miRNA) genes (MIR) give rise to 20- to 22-nt miRNAs that are generated predominantly by the type III endoribonuclease Dicer-like 1 (DCL1) but do not require any RNA-dependent RNA Polymerases (RDRs) or RNA Polymerase IV (Pol IV). Here, we identify a novel class of non-conserved MIR genes that give...

journal_title：Nucleic acids research

authors： Chellappan P,Xia J,Zhou X,Gao S,Zhang X,Coutino G,Vazquez F,Zhang W,Jin H

更新日期：2010-11-01 00:00:00

abstract：:Retinoic acid-inducible gene I (RIG-I) is a pattern recognition receptor expressed in metazoan cells that is responsible for eliciting the production of type I interferons and pro-inflammatory cytokines upon detection of intracellular, non-self RNA. Structural studies of RIG-I have identified a novel Pincer domain com...

journal_title：Nucleic acids research

authors： Rawling DC,Kohlway AS,Luo D,Ding SC,Pyle AM

更新日期：2014-10-01 00:00:00

abstract：:Helicase loading at a DNA replication origin often requires the dynamic interactions between the DNA helicase and an accessory protein. In E. coli, the DNA helicase is DnaB and DnaC is its loading partner. We used the method of hydrogen/deuterium exchange mass spectrometry to address the importance of DnaB-DnaC comple...

journal_title：Nucleic acids research

authors： Chodavarapu S,Jones AD,Feig M,Kaguni JM

更新日期：2016-01-08 00:00:00

abstract：:TropGeneDB (http://tropgenedb.cirad.fr) was created to store genetic, molecular and phenotypic data on tropical crop species. The most common data stored in TropGeneDB are molecular markers, quantitative trait loci, genetic and physical maps, genetic diversity, phenotypic diversity studies and information on genetic r...

journal_title：Nucleic acids research

authors： Hamelin C,Sempere G,Jouffe V,Ruiz M

更新日期：2013-01-01 00:00:00

abstract：:Understanding interactions between proteins and RNA is key to deciphering the mechanisms of many important biological processes. Here we describe RNABindR, a web-based server that identifies and displays RNA-binding residues in known protein-RNA complexes and predicts RNA-binding residues in proteins of unknown struct...

journal_title：Nucleic acids research

authors： Terribilini M,Sander JD,Lee JH,Zaback P,Jernigan RL,Honavar V,Dobbs D

更新日期：2007-07-01 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：:A 12 bp long GCN4-binding, self-complementary duplex DNA d(CATGACGTCATG)(2) has been investigated by NMR spectroscopy to study the structure and dynamics of the molecule in aqueous solution. The NMR structure of the DNA obtained using simulated annealing and iterative relaxation matrix calculations compares quite clos...

journal_title：Nucleic acids research

authors： Khandelwal P,Panchal SC,Radha PK,Hosur RV

更新日期：2001-01-15 00:00:00

abstract：:Sets of genes expressed in the same tissue are believed to be under the regulation of a similar set of transcription factors, and can thus be assumed to contain similar structural patterns in their regulatory regions. Here we present a study of the structural patterns in promoters of genes expressed specifically in 26...

journal_title：Nucleic acids research

authors： Vandenbon A,Nakai K

更新日期：2010-01-01 00:00:00

abstract：:A type II restriction endonuclease, DraI, isolated from Deinococcus radiophilus ATCC 27603 recognises the palindromic hexanucleotide sequence (formula; see text) and cleaves it, as indicated by the arrows, to produce blunt-ended fragments. The yield of enzyme is 100 to 1000 times that of the only other known type II r...

journal_title：Nucleic acids research

authors： Purvis IJ,Moseley BE

更新日期：1983-08-25 00:00:00

abstract：:Adjustable transgene expression is considered key for next-generation molecular interventions in gene therapy scenarios, therapeutic reprogramming of clinical cell phenotypes for tissue engineering and sophisticated gene-function analyses in the post-genomic era. We have designed a portfolio of latest generation self-...

journal_title：Nucleic acids research

authors： Mitta B,Weber CC,Rimann M,Fussenegger M

更新日期：2004-07-16 00:00:00

abstract：:The widespread applications of various 'omics' technologies in biomedical research together with the emergence of public data repositories have resulted in a plethora of data sets for almost any given physiological state or disease condition. Properly combining or integrating these data sets with similar basic hypothe...

journal_title：Nucleic acids research

authors： Xia J,Fjell CD,Mayer ML,Pena OM,Wishart DS,Hancock RE

更新日期：2013-07-01 00:00:00

abstract：:A highly sensitive method to detect traces of aldehyde-containing apurinic/apyrimidinic (AP) sites in nucleic acids has been developed. Based on this method, a novel approach to detect DNA base mismatches recognized by the mismatch repair glycosylase MutY is demonstrated. Open chain aldehydes generated in nucleic acid...

journal_title：Nucleic acids research

authors： Maulik G,Botchway S,Chakrabarti S,Tetradis S,Price B,Makrigiorgos GM

更新日期：1999-03-01 00:00:00

abstract：:Restriction fragments containing established curved regions, such as the pBR322 tn3 region, the phage lambda attP region and the SV40 T-antigen and terminus of replication regions, exhibit systematically retarded elution upon anion exchange based HPLC. Using this method, we were able to detect readily other SV40 curve...

journal_title：Nucleic acids research

authors： Fack F,Sarantoglou V

更新日期：1991-08-11 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：:It is a routine task in metabolic engineering to introduce multicomponent pathways into a heterologous host for production of metabolites. However, this process sometimes may take weeks to months due to the lack of standardized genetic tools. Here, we present a method for the design and construction of biological part...

journal_title：Nucleic acids research

authors： Guo Y,Dong J,Zhou T,Auxillos J,Li T,Zhang W,Wang L,Shen Y,Luo Y,Zheng Y,Lin J,Chen GQ,Wu Q,Cai Y,Dai J

更新日期：2015-07-27 00:00:00

abstract：:The human immunodeficiency virus (HIV) and other retroviruses show extensive genomic variation, which is primarily due to error-prone replication by the viral reverse transcriptase (RT) enzymes. RT errors include misincorporation with subsequent extension of the mismatched terminal base, and extension of realigned pri...

journal_title：Nucleic acids research

authors： Das AT,Berkhout B

更新日期：1995-04-25 00:00:00

abstract：:We report the molecular cloning and characterization of a cDNA derived from a zebrafish gene (ZF-21) related to the mouse homeobox containing gene Hox2.1. Interesting information about the differential conservation of various domains was gained from comparisons between the putative protein sequences from ZF-21 (275 am...

journal_title：Nucleic acids research

authors： Njølstad PR,Molven A,Hordvik I,Apold J,Fjose A

更新日期：1988-10-11 00:00:00

abstract：:Here we describe a novel endonuclease IV (Endo IV) based assay utilizing a substrate that mimics the abasic lesions that normally occur in double-stranded DNA. The three component substrate is characterized by single-stranded DNA target, an oligonucleotide probe, separated from a helper oligonucleotide by a one base g...

journal_title：Nucleic acids research

authors： Kutyavin IV,Milesi D,Belousov Y,Podyminogin M,Vorobiev A,Gorn V,Lukhtanov EA,Vermeulen NM,Mahoney W

更新日期：2006-01-01 00:00:00

abstract：:The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and r...

journal_title：Nucleic acids research

authors： De Nicola B,Lech CJ,Heddi B,Regmi S,Frasson I,Perrone R,Richter SN,Phan AT

更新日期：2016-07-27 00:00:00

abstract：:Analysis of haplotypes is an important tool in population genetics, familial heredity and gene mapping. Determination of haplotypes of multiple single nucleotide polymorphisms (SNPs) or other simple mutations is time consuming and expensive when analyzing large populations, and often requires the help of computational...

journal_title：Nucleic acids research

authors： Eitan Y,Kashi Y

更新日期：2002-06-15 00:00:00

abstract：:The laboratory mouse is the premier animal model for studying human biology because all life stages can be accessed experimentally, a completely sequenced reference genome is publicly available and there exists a myriad of genomic tools for comparative and experimental research. In the current era of genome scale, dat...

journal_title：Nucleic acids research

authors： Bult CJ,Eppig JT,Blake JA,Kadin JA,Richardson JE,Mouse Genome Database Group.

更新日期：2013-01-01 00:00:00

abstract：:Investigation of biological processes using selective chemical interventions is generally applied in biomedical research and drug discovery. Many studies of this kind make use of gene expression experiments to explore cellular responses to chemical interventions. Recently, some research groups constructed libraries of...

journal_title：Nucleic acids research

authors： Li Y,Hao P,Zheng S,Tu K,Fan H,Zhu R,Ding G,Dong C,Wang C,Li X,Thiesen HJ,Chen YE,Jiang H,Liu L,Li Y

更新日期：2008-11-01 00:00:00

abstract：:Natural oligopeptides may regulate nearly all vital processes. To date, the chemical structures of nearly 6000 oligopeptides have been identified from >1000 organisms representing all the biological kingdoms. We have compiled the known physical, chemical and biological properties of these oligopeptides--whether synthe...

journal_title：Nucleic acids research

authors： Zamyatnin AA,Borchikov AS,Vladimirov MG,Voronina OL

更新日期：2006-01-01 00:00:00

abstract：:Human transcription factor IIIC contains a 55 kDa polypeptide which specifically interacts with the Adenovirus 2 VAI gene promoter and which mimics most of the DNA binding properties of the entire factor. The specificity and affinity of this protein:DNA interaction was demonstrated by: (i) Separation of purified fract...

journal_title：Nucleic acids research

authors： Schneider HR,Waldschmidt R,Seifart KH

更新日期：1990-08-25 00:00:00

abstract：:PRED(BALB/c) is a computational system that predicts peptides binding to the major histocompatibility complex-2 (H2(d)) of the BALB/c mouse, an important laboratory model organism. The predictions include the complete set of H2(d) class I (H2-K(d), H2-L(d) and H2-D(d)) and class II (I-E(d) and I-A(d)) molecules. The p...

journal_title：Nucleic acids research

authors： Zhang GL,Srinivasan KN,Veeramani A,August JT,Brusic V

更新日期：2005-07-01 00:00:00

abstract：:The large terminase subunit is a central component of the genome packaging motor from tailed bacteriophages and herpes viruses. This two-domain enzyme has an N-terminal ATPase activity that fuels DNA translocation during packaging and a C-terminal nuclease activity required for initiation and termination of the packag...

journal_title：Nucleic acids research

authors： Cornilleau C,Atmane N,Jacquet E,Smits C,Alonso JC,Tavares P,Oliveira L

更新日期：2013-01-07 00:00:00

abstract：:Selection for amino acid affinity by elution of RNAs from tryptophan-Sepharose using free L-tryptophan evokes one sequence predominantly (K(D) = 12 microM), a symmetrical internal loop of 3 nt per side. Though we have also isolated larger sequences with affinity for tryptophan, successively squeezed selection in rando...

journal_title：Nucleic acids research

authors： Majerfeld I,Yarus M

更新日期：2005-09-25 00:00:00

abstract：:HSP90, found in all kingdoms of life, is a major chaperone protein regulating many client proteins. We demonstrated that HSP90α, one of two paralogs duplicated in vertebrates, plays an important role in the biogenesis of fetal PIWI-interacting RNAs (piRNA), which act against the transposon activities, in mouse male ge...

journal_title：Nucleic acids research

authors： Ichiyanagi T,Ichiyanagi K,Ogawa A,Kuramochi-Miyagawa S,Nakano T,Chuma S,Sasaki H,Udono H

更新日期：2014-10-29 00:00:00

abstract：:Spirochetes of the genus Borrelia include the tick-transmitted causative agents of Lyme disease and relapsing fever. They possess unusual genomes composed mainly of linear replicons terminated by closed DNA hairpin telomeres. Hairpin telomeres present an uninterrupted DNA chain to the replication machinery overcoming ...

journal_title：Nucleic acids research

authors： Mir T,Huang SH,Kobryn K

更新日期：2013-12-01 00:00:00