Identification of the CTAG-recognizing restriction-modification systems MthZI and MthFI from Methanobacterium thermoformicicum and characterization of the plasmid-encoded mthZIM gene.

abstract：:Transcriptional regulatory networks specify regulatory proteins controlling the context-specific expression levels of genes. Inference of genome-wide regulatory networks is central to understanding gene regulation, but remains an open challenge. Expression-based network inference is among the most popular methods to i...

journal_title：Nucleic acids research

authors： Siahpirani AF,Roy S

更新日期：2017-02-28 00:00:00

abstract：:A novel method of determining the number of superhelical turns of a covalently-closed plasmid DNA is described. It relies on the determination of the hyperchromicity, and hence the proportion of unstacked basepairs, of a partially heat-denatured sample which co-migrates during electrophoresis with nicked circular dupl...

journal_title：Nucleic acids research

authors： Dougherty G,Koller T

更新日期：1982-01-22 00:00:00

abstract：:In order to characterize structure-function relationships, the kinetic behavior of chimeric RNA/DNA ribozyme was compared with that of all RNA ribozyme. Determined kcat values were proven to represent the chemical-cleavage step and not the product-dissociation step. In agreement with the finding by Dahm and Uhlenbeck ...

journal_title：Nucleic acids research

authors： Sawata S,Shimayama T,Komiyama M,Kumar PK,Nishikawa S,Taira K

更新日期：1993-12-11 00:00:00

abstract：:DNA adenine methyltransferase (Dam) is widespread and conserved among the γ-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. Dam also controls virulence in many pathogenic Gram-negative bacteria. ...

journal_title：Nucleic acids research

authors： Horton JR,Zhang X,Blumenthal RM,Cheng X

更新日期：2015-04-30 00:00:00

abstract：:The nucleotide sequence of the control region of the divergent argECBH operon has been established in the wild type and in mutants affecting expression of these genes. The argE and argCBH promoters face each other and overlap with an operator region containing two domains which may act as distinct repressor binding si...

journal_title：Nucleic acids research

authors： Piette J,Cunin R,Boyen A,Charlier D,Crabeel M,Van Vliet F,Glansdorff N,Squires C,Squires CL

更新日期：1982-12-20 00:00:00

abstract：:Synthesis of (p)ppRNA-DNA chains by purified HeLa cell DNA primase-DNA polymerase alpha (pol alpha-primase) was compared with those synthesized by a multiprotein form of DNA polymerase alpha (pol alpha 2) using unique single-stranded DNA templates containing the origin of replication for simian virus 40 (SV40) DNA. Th...

journal_title：Nucleic acids research

authors： Vishwanatha JK,Yamaguchi M,DePamphilis ML,Baril EF

更新日期：1986-09-25 00:00:00

abstract：:MPromDb (Mammalian Promoter Database) is a curated database that strives to annotate gene promoters identified from ChIP-seq results with the goal of providing an integrated resource for mammalian transcriptional regulation and epigenetics. We analyzed 507 million uniquely aligned RNAP-II ChIP-seq reads from 26 differ...

journal_title：Nucleic acids research

authors： Gupta R,Bhattacharyya A,Agosto-Perez FJ,Wickramasinghe P,Davuluri RV

更新日期：2011-01-01 00:00:00

abstract：:A computer program package has been made available which contains five compound programs written in FORTRAN 10 (for DECsystem-10). Program DATBAS is for storing and improving DNA sequence data, especially those obtained by the sequencing method using M13 phages. Programs NUCDAT and PROTEN are for analyzing DNA/RNA and...

journal_title：Nucleic acids research

authors： Isono K

更新日期：1984-01-11 00:00:00

abstract：:To address how eukaryotic replication forks respond to fork stalling caused by strong non-covalent protein-DNA barriers, we engineered the controllable Fob-block system in Saccharomyces cerevisiae. This system allows us to strongly induce and control replication fork barriers (RFB) at their natural location within the...

journal_title：Nucleic acids research

authors： Bentsen IB,Nielsen I,Lisby M,Nielsen HB,Gupta SS,Mundbjerg K,Andersen AH,Bjergbaek L

更新日期：2013-03-01 00:00:00

abstract：:Molecules of single-stranded ribosomal RNA and double-stranded replicative form of phage f2 RNA (dsRNA) adopt a compact form in solutions, containing sufficiently high concentrations of salt (NaCl) and polymer (PEG). However, only in the cases of native dsRNA molecules the compact particles are characterized by a regu...

journal_title：Nucleic acids research

authors： Evdokimov YM,Pyatigorskaya TL,Kadikov VA,Polyvtsev OF,Doskocil J,Koudelka J,Varshavsky YM

更新日期：1976-06-01 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：:We identify a novel activity of the RarA (also MgsA) protein of Escherichia coli, demonstrating that this protein functions at DNA ends to generate flaps. A AAA+ ATPase in the clamp loader clade, RarA protein is part of a highly conserved family of DNA metabolism proteins. We demonstrate that RarA binds to double-stra...

journal_title：Nucleic acids research

authors： Stanage TH,Page AN,Cox MM

更新日期：2017-03-17 00:00:00

abstract：:Carbohydrate-binding proteins play crucial roles across all organisms and viruses. The complexity of carbohydrate structures, together with inconsistencies in how their 3D structures are reported, has led to difficulties in characterizing the protein-carbohydrate interfaces. In order to better understand protein-carbo...

journal_title：Nucleic acids research

authors： Copoiu L,Torres PHM,Ascher DB,Blundell TL,Malhotra S

更新日期：2020-01-08 00:00:00

abstract：:We define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions. Therefore, a comparison of phosphovariants between individuals or be...

journal_title：Nucleic acids research

authors： Ryu GM,Song P,Kim KW,Oh KS,Park KJ,Kim JH

更新日期：2009-03-01 00:00:00

abstract：:Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding g...

journal_title：Nucleic acids research

authors： Winter S,Jahn K,Wehner S,Kuchenbecker L,Marz M,Stoye J,Böcker S

更新日期：2016-11-16 00:00:00

abstract：:Synthetic biology seeks to envision living cells as a matter of engineering. However, increasing evidence suggests that the genetic load imposed by the incorporation of synthetic devices in a living organism introduces a sort of unpredictability in the design process. As a result, individual part characterization is n...

journal_title：Nucleic acids research

authors： Carbonell-Ballestero M,Garcia-Ramallo E,Montañez R,Rodriguez-Caso C,Macía J

更新日期：2016-01-08 00:00:00

abstract：:Aberrant CpG methylation changes occurring during tumour progression include the loss (hypomethylation) and gain (hypermethylation) of methyl groups. Techniques currently available for examining such changes either require selection of a region, then examination of methylation changes, or utilise methylation-sensitive...

journal_title：Nucleic acids research

authors： Brock GJ,Huang TH,Chen CM,Johnson KJ

更新日期：2001-12-15 00:00:00

abstract：:Neph et al. (2012) (Circuitry and dynamics of human transcription factor regulatory networks. Cell, 150: 1274-1286) reported the transcription factor (TF) regulatory networks of 41 human cell types using the DNaseI footprinting technique. This provides a valuable resource for uncovering regulation principles in differ...

journal_title：Nucleic acids research

authors： Zhang S,Tian D,Tran NH,Choi KP,Zhang L

更新日期：2014-11-10 00:00:00

abstract：:The National Center for Biotechnology Information (NCBI) Clone DB (http://www.ncbi.nlm.nih.gov/clone/) is an integrated resource providing information about and facilitating access to clones, which serve as valuable research reagents in many fields, including genome sequencing and variation analysis. Clone DB represen...

journal_title：Nucleic acids research

authors： Schneider VA,Chen HC,Clausen C,Meric PA,Zhou Z,Bouk N,Husain N,Maglott DR,Church DM

更新日期：2013-01-01 00:00:00

abstract：:With an increased emphasis on genotyping of single nucleotide polymorphisms (SNPs) in disease association studies, the genotyping platform of choice is constantly evolving. In addition, the development of more specific SNP assays and appropriate genotype validation applications is becoming increasingly critical to elu...

journal_title：Nucleic acids research

authors： Johnson MP,Haupt LM,Griffiths LR

更新日期：2004-03-26 00:00:00

abstract：:The estrogen receptor (ER) contains two nonacidic transcriptional activation functions, AF-1 and AF-2 (formerly TAF-1 and TAF-2). In this study we show that AF-1 and AF-2 are able to stimulate transcription in vitro in a HeLa cell system when fused to the DNA binding domain of the yeast activator GAL4. We also demonst...

journal_title：Nucleic acids research

authors： Brou C,Wu J,Ali S,Scheer E,Lang C,Davidson I,Chambon P,Tora L

更新日期：1993-01-11 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：:Mitochondrial DNA (mtDNA) is entirely dependent on nuclear genes for its transcription and replication. One of these genes is TOP1MT, which encodes the mitochondrial DNA topoisomerase IB, involved in mtDNA relaxation. To elucidate TOP1MT regulation, we performed genome-wide profiling across the 60-cell line panel (the...

journal_title：Nucleic acids research

authors： Zoppoli G,Douarre C,Dalla Rosa I,Liu H,Reinhold W,Pommier Y

更新日期：2011-08-01 00:00:00

abstract：:Oligonucleotide-mediated multiplex genome engineering is an important tool for bacterial genome editing. The efficient application of this technique requires the inactivation of the endogenous methyl-directed mismatch repair system that in turn leads to a drastically elevated genomic mutation rate and the consequent a...

journal_title：Nucleic acids research

authors： Nyerges Á,Csorgő B,Nagy I,Latinovics D,Szamecz B,Pósfai G,Pál C

更新日期：2014-04-01 00:00:00

abstract：:Genome-wide transcriptome profiling has enabled non-supervised classification of tumours, revealing different sub-groups characterized by specific gene expression features. However, the biological significance of these subtypes remains for the most part unclear. We describe herein an interactive platform, Minimum Span...

journal_title：Nucleic acids research

authors： Lemieux S,Sargeant T,Laperrière D,Ismail H,Boucher G,Rozendaal M,Lavallée VP,Ashton-Beaucage D,Wilhelm B,Hébert J,Hilton DJ,Mader S,Sauvageau G

更新日期：2017-07-27 00:00:00

abstract：:Genetic screens in Saccharomyces cerevisiae have identified the roles of ribosome components, tRNAs and translation factors in translational fidelity. These screens rely on the suppression of altered start codons, nonsense codons or frameshift mutations in genes involved in amino acid or nucleotide metabolism. Many of...

journal_title：Nucleic acids research

authors： Magazinnik T,Anand M,Sattlegger E,Hinnebusch AG,Kinzy TG

更新日期：2005-08-12 00:00:00

abstract：:Two similar, but not identical, models have been proposed for the amino acid-base pair contacts in the CAP-DNA complex ('Model I,' Weber, I. and Steitz, T., Proc. Natl. Acad. Sci. USA, 81, 3973-3977, 1984; 'Model II,' Ebright, et al., Proc. Natl. Acad. Sci. USA, 81, 7274-7278, 1984). One difference between the two mod...

journal_title：Nucleic acids research

authors： Gunasekera A,Ebright YW,Ebright RH

更新日期：1990-12-11 00:00:00

abstract：:Nucleotide excision repair (NER) mechanism is the major pathway responsible for the removal of a large variety of bulky lesions from the genome. Two different NER subpathways have been identified, i.e. the transcription-coupled and the global genome repair pathways. For DNA-damage induced by ultraviolet light both tra...

journal_title：Nucleic acids research

authors： van Oosterwijk MF,Filon R,Kalle WH,Mullenders LH,van Zeeland AA

更新日期：1996-12-01 00:00:00

abstract：:This review takes a second look at a set of mRNAs that purportedly employ an alternative mechanism of initiation when cap-dependent translation is reduced during mitosis or stress conditions. A closer look is necessary because evidence cited in support of the internal initiation hypothesis is often flawed. When putati...

journal_title：Nucleic acids research

authors： Kozak M

更新日期：2005-11-28 00:00:00

abstract：:Preparation of the two nonanucleotides, d(pG-G-A-G-G-A-G-A-A) and d(pT-T-C-T-G-T-T-G-A), and the octanucleotide, d(pT-G-G-C-C-C-A-T) is described by a rapid solid-phase method on a polyamide support. The syntheses were carried out using a modified solid-phase peptide synthesiser and required one day for each nucleotid...

journal_title：Nucleic acids research

authors： Gait MJ,Sheppard RC

更新日期：1977-12-01 00:00:00