Highly efficient preparation of single-stranded DNA rings by T4 ligase at abnormally low Mg(II) concentration.

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：:The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (approximately 913,000) and chloroplast-encoded sequences (approximately 250,000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, exons, introns, gene...

journal_title：Nucleic acids research

authors： O'Brien EA,Zhang Y,Wang E,Marie V,Badejoko W,Lang BF,Burger G

更新日期：2009-01-01 00:00:00

abstract：:Upon HIV-1 infection of a target cell, the viral reverse transcriptase (RT) copies the genomic RNA to synthesize the viral DNA. The genomic RNA is within the incoming HIV-1 core where it is coated by molecules of nucleocapsid (NC) protein that chaperones the reverse transcription process. Indeed, the RT chaperoning pr...

journal_title：Nucleic acids research

authors： Grigorov B,Bocquin A,Gabus C,Avilov S,Mély Y,Agopian A,Divita G,Gottikh M,Witvrouw M,Darlix JL

更新日期：2011-07-01 00:00:00

abstract：:To synchronize SV40 replicons, simian cells infected with a tsA mutant were restricted at 40 degrees, to complete ongoing replication and returned to 32 degrees, to activate new replicons in the presence of the DNA chain elongation inhibitor aphidicolin. Upon further incubation at 40 degrees without the drug, 3H-dT wa...

journal_title：Nucleic acids research

authors： Dinter-Gottlieb G,Kaufmann G

更新日期：1982-01-22 00:00:00

abstract：:Reversible methylation of the N6 or N1 position of adenine in RNA has recently been shown to play significant roles in regulating the functions of RNA. RNA can also be alkylated upon exposure to endogenous and exogenous alkylating agents. Here we examined how regio-specific methylation at the hydrogen bonding edge of ...

journal_title：Nucleic acids research

authors： You C,Dai X,Wang Y

更新日期：2017-09-06 00:00:00

abstract：:Pds5 is required for sister chromatid cohesion, and somewhat paradoxically, to remove cohesin from chromosomes. We found that Pds5 plays a critical role during DNA replication that is distinct from its previously known functions. Loss of Pds5 hinders replication fork progression in unperturbed human and mouse cells. I...

journal_title：Nucleic acids research

authors： Carvajal-Maldonado D,Byrum AK,Jackson J,Wessel S,Lemaçon D,Guitton-Sert L,Quinet A,Tirman S,Graziano S,Masson JY,Cortez D,Gonzalo S,Mosammaparast N,Vindigni A

更新日期：2019-02-20 00:00:00

abstract：:PRINTS is a database of protein family 'fingerprints' offering a diagnostic resource for newly-determined sequences. By contrast with PROSITE, which uses single consensus expressions to characterise particular families, PRINTS exploits groups of motifs to build characteristic signatures. These signatures offer improve...

journal_title：Nucleic acids research

authors： Attwood TK,Beck ME,Flower DR,Scordis P,Selley JN

更新日期：1998-01-01 00:00:00

abstract：:A synthetic gene encoding the Schizophyllum commune xylanase XynA was constructed by a novel PCR-based procedure. Three long oligonucleotides were synthesized and used in combination with flanking PCR primers to generate a 607 base pair gene which contained 31 unique locations for restriction enzyme cleavage. The amin...

journal_title：Nucleic acids research

authors： Graham RW,Atkinson T,Kilburn DG,Miller RC Jr,Warren RA

更新日期：1993-10-25 00:00:00

abstract：:Trinucleotide repeat (TNR) expansions cause at least 17 heritable neurological diseases, including Huntington's disease. Expansions are thought to arise from abnormal processing of TNR DNA by specific trans-acting proteins. For example, the DNA repair complex MutSβ (MSH2-MSH3 heterodimer) is required in mice for on-go...

journal_title：Nucleic acids research

authors： Gannon AM,Frizzell A,Healy E,Lahue RS

更新日期：2012-11-01 00:00:00

abstract：:Virtually the whole region of the mobile dispersed genetic element mdg1 including the direct repeats that frame mdg1 /1/ is transcribed. The end of the transcriptional unit is located within the direct repeat. Although the transcription of mdg1 is symmetric, one direction is transcribed preferentially and is a full-le...

journal_title：Nucleic acids research

authors： Ilyin Y,Chmeliauskaite VG,Kulguskin VV,Georgiev GP

更新日期：1980-11-25 00:00:00

abstract：:Treatment of the ciliated protozoan Tetrahymena thermophila with 8-methoxypsoralen combined with long wavelength ultraviolet irradiation (UVA, lambda approximately 360 nm) resulted in a dose dependent equal inhibition of the synthesis of rRNA, 5.8S, 5S and tRNA. Similar results were obtained with 3-carbethoxy-8-methox...

journal_title：Nucleic acids research

authors： Nielsen PE

更新日期：1987-02-11 00:00:00

abstract：:Topoisomerase II is an essential enzyme that is required for virtually every process that requires movement of DNA within the nucleus or the opening of the double helix. This enzyme helps to regulate DNA under- and overwinding and removes knots and tangles from the genetic material. In order to carry out its critical ...

journal_title：Nucleic acids research

authors： Deweese JE,Osheroff N

更新日期：2009-02-01 00:00:00

abstract：:Pluripotency, the ability of embryonic stem cells to differentiate into specialized cell types, is determined by ESC-specific gene regulators such as transcription factors and chromatin modification factors. It is not well understood how ESCs are poised for differentiation, however, and methods are needed for prognosi...

journal_title：Nucleic acids research

authors： Ha M,Hong S

更新日期：2017-10-13 00:00:00

abstract：:A class of heterogeneous nuclear RNA (hnRNA) molecules contain an internal transcribed poly A sequence of close to 25 uninterrupted AMP residues. HnRNA molecules containing this sequence are separable from those containing the large 3' terminal poly A sequence on the basis of their differential affinity for oligo dT c...

journal_title：Nucleic acids research

authors： Venkatesan S,Nakazato H,Kopp DW,Edmonds M

更新日期：1979-03-01 00:00:00

abstract：:One of the greatest challenges that modern molecular biology is facing is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of regulatory motifs playing key roles in the regulation of gene expression at transcriptional and post-tran...

journal_title：Nucleic acids research

authors： Pavesi G,Mereghetti P,Mauri G,Pesole G

更新日期：2004-07-01 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：:Cell-free extracts employed as chromatin assembly systems contain a myriad of proteins, polyanions and nucleic acids. The roles of ATP, MgCl2 and other cofactors in the catalysis of nucleosome formation by the Xenopus laevis oocyte S-150 have yet to be established unequivocally. In this study we examine the influence ...

journal_title：Nucleic acids research

authors： Sekiguchi JM,Kmiec EB

更新日期：1992-02-25 00:00:00

abstract：:Little is known about the function of most non-coding RNAs (ncRNAs). The majority of long ncRNAs (lncRNAs) is expressed at very low levels and it is a matter of intense debate whether these can be of functional relevance. Here, we identified lncRNAs regulating the viability of lung cancer cells in a high-throughput RN...

journal_title：Nucleic acids research

authors： Seiler J,Breinig M,Caudron-Herger M,Polycarpou-Schwarz M,Boutros M,Diederichs S

更新日期：2017-05-19 00:00:00

abstract：:The mRNA encoding repressor cI of phage lambda is the only known E. coli message which starts directly with the initiation AUG codon. The ability of in vitro synthesized cI mRNA fragments (150 or 400 nts) to form ternary initiation complexes has been studied using the toeprint method. In the presence of tRNA(Met)f, th...

journal_title：Nucleic acids research

authors： Balakin AG,Skripkin EA,Shatsky IN,Bogdanov AA

更新日期：1992-02-11 00:00:00

abstract：:The Rice Proteome Database is the first detailed database to describe the proteome of rice. The current release contains 21 reference maps based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of proteins from rice tissues and subcellular compartments. These reference maps comprise 11 941 identified pr...

journal_title：Nucleic acids research

authors： Komatsu S,Kojima K,Suzuki K,Ozaki K,Higo K

更新日期：2004-01-01 00:00:00

abstract：:Search of interrelationships between the structural-functional protein organization and exon structure of encoding gene provides insights into issues concerned with the function, origin and evolution of genes and proteins. The functions of proteins and their domains are defined mostly by functional sites. The relation...

journal_title：Nucleic acids research

authors： Medvedeva I,Demenkov P,Kolchanov N,Ivanisenko V

更新日期：2012-01-01 00:00:00

abstract：:High-throughput screening assays have been developed to rapidly identify small molecule inhibitors targeting catalytic group I introns. Biochemical reactions catalyzed by a self-splicing group I intron derived from Pneumocystis carinii or from bacteriophage T4 have been investigated. In vitro biochemical assays amenab...

journal_title：Nucleic acids research

authors： Mei HY,Cui M,Sutton ST,Truong HN,Chung FZ,Czarnik AW

更新日期：1996-12-15 00:00:00

abstract：:While RNA structures have been extensively characterized in vitro, very few techniques exist to probe RNA structures inside cells. Here, we have exploited mechanisms of post-transcriptional regulation to synthesize fluorescence-based probes that assay RNA structures in vivo. Our probing system involves the co-expressi...

journal_title：Nucleic acids research

authors： Sowa SW,Vazquez-Anderson J,Clark CA,De La Peña R,Dunn K,Fung EK,Khoury MJ,Contreras LM

更新日期：2015-01-01 00:00:00

abstract：:We have assessed the ability of nucleosomes to influence the formation of mammalian topoisomerase II-DNA complexes by mapping the sites of cleavage induced by four unrelated topoisomerase II inhibitors in naked versus nucleosome-reconstituted SV40 DNA. DNA fragments were reconstituted with histone octamers from HeLa c...

journal_title：Nucleic acids research

authors： Capranico G,Jaxel C,Roberge M,Kohn KW,Pommier Y

更新日期：1990-08-11 00:00:00

abstract：:We have investigated the substrate specificity of the Ogg1 protein of Saccharomyces cerevisiae (yOgg1 protein) for excision of modified DNA bases from oxidatively damaged DNA substrates using gas chromatography/isotope dilution mass spectrometry. Four DNA substrates prepared by treatment with H2O2/Fe(III)-EDTA/ascorbi...

journal_title：Nucleic acids research

authors： Karahalil B,Girard PM,Boiteux S,Dizdaroglu M

更新日期：1998-03-01 00:00:00

abstract：:Folding of group II introns is characterized by a first slow compaction of domain 1 (D1) followed by the rapid docking of other domains to this scaffold. D1 compaction initiates in a small subregion encompassing the κ and ζ elements. These two tertiary elements are also the major interaction sites with domain 5 to for...

journal_title：Nucleic acids research

authors： Donghi D,Pechlaner M,Finazzo C,Knobloch B,Sigel RK

更新日期：2013-02-01 00:00:00

abstract：:We present a general method for isolating molecular markers specific to any region of a chromosome using existing mapping populations. Two pools of DNA from individuals homozygous for opposing alleles for a targeted chromosomal interval, defined by two or more linked RFLP markers, are constructed from members of an ex...

journal_title：Nucleic acids research

authors： Giovannoni JJ,Wing RA,Ganal MW,Tanksley SD

更新日期：1991-12-11 00:00:00

abstract：:RNA secondary structures, e.g. stem-loops that are often found at the 5' and 3' ends of mRNAs, are in many cases known to be crucial for transcript stability but their role in prolonging the lifetime of transcripts remains elusive. In this study we show for an essential RNA-stabilizing stem-loop at the 5' end of rbcL ...

journal_title：Nucleic acids research

authors： Suay L,Salvador ML,Abesha E,Klein U

更新日期：2005-08-22 00:00:00

abstract：:Homo-oligomerization of proteins is abundant in nature, and is often intimately related with the physiological functions of proteins, such as in metabolism, signal transduction or immunity. Information on the homo-oligomer structure is therefore important to obtain a molecular-level understanding of protein functions ...

journal_title：Nucleic acids research

authors： Baek M,Park T,Heo L,Park C,Seok C

更新日期：2017-07-03 00:00:00

abstract：:Telomerase activity, not detectable in somatic cells but frequently activated during carcinogenesis, confers immortality to tumors. Mechanisms governing expression of the catalytic subunit hTERT, the limiting factor for telomerase activity, still remain unclear. We previously proposed a model in which the binding of t...

journal_title：Nucleic acids research

authors： Renaud S,Loukinov D,Alberti L,Vostrov A,Kwon YW,Bosman FT,Lobanenkov V,Benhattar J

更新日期：2011-02-01 00:00:00