Actinomycin D induced DNase I cleavage enhancement caused by sequence specific propagation of an altered DNA structure.

abstract：:A previously elaborated technique for fixing a chosen partially melted state of DNA with glyoxal was used in a study of the melting process of the replicative form (RF III) of phi X174 DNA. Electron-microscopic maps corresponding to five points of the melting curve of RF III were obtained and compared with the theoret...

journal_title：Nucleic acids research

authors： Lyubchenko YuL,Kalambet YuA,Lyamichev VI,Borovik AS

更新日期：1982-03-25 00:00:00

abstract：:Measuring minimal residual disease in cancer has applications for prognosis, monitoring treatment and detection of recurrence. Simple sequence-based methods to detect nucleotide substitution variants have error rates (about 10-3) that limit sensitive detection. We developed and characterized the performance of MASQ (m...

journal_title：Nucleic acids research

authors： Moffitt AB,Spector MS,Andrews P,Kendall J,Alexander J,Stepansky A,Ma B,Kolitz J,Chiorazzi N,Allen SL,Krasnitz A,Wigler M,Levy D,Wang Z

更新日期：2020-04-17 00:00:00

abstract：:Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized Pseudomonas aeruginosa and Pseudomonas putida. Unlike these bacteria, the Acinetobacter ADP1 is highly competent for natural transformation which affords extraordinary convenience for ...

journal_title：Nucleic acids research

authors： Barbe V,Vallenet D,Fonknechten N,Kreimeyer A,Oztas S,Labarre L,Cruveiller S,Robert C,Duprat S,Wincker P,Ornston LN,Weissenbach J,Marlière P,Cohen GN,Médigue C

更新日期：2004-10-28 00:00:00

abstract：:A comprehensive listing is made of posttranscriptionally modified nucleosides from RNA reported in the literature through mid-1994. Included are chemical structures, common names, symbols, Chemical Abstracts registry numbers (for ribonucleoside and corresponding base), Chemical Abstracts Index Name, phylogenetic sourc...

journal_title：Nucleic acids research

authors： Limbach PA,Crain PF,McCloskey JA

更新日期：1994-06-25 00:00:00

abstract：:Identification of common sub-sequences for a group of functionally related DNA sequences can shed light on the role of such elements in cell-specific gene expression. In the megakaryocytic lineage, no one single unique transcription factor was described as linage specific, raising the possibility that a cluster of gen...

journal_title：Nucleic acids research

authors： Hazony Y,Lu J,St Hilaire C,Ravid K

更新日期：2006-01-01 00:00:00

abstract：:Here we describe the application of a novel combinatorial method, restriction endonuclease protection selection and amplification (REPSA), to identification of a consensus DNA binding site for the TATA binding subunit (hTBP) of the human general transcription factor TFIID. Unlike most combinatorial methods, REPSA is b...

journal_title：Nucleic acids research

authors： Hardenbol P,Wang JC,Van Dyke MW

更新日期：1997-08-15 00:00:00

abstract：:Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid-liquid phase separation (LLPS), a process that relies on multivalent weak interactions of the constituent proteins and other macromole...

journal_title：Nucleic acids research

authors： Mészáros B,Erdős G,Szabó B,Schád É,Tantos Á,Abukhairan R,Horváth T,Murvai N,Kovács OP,Kovács M,Tosatto SCE,Tompa P,Dosztányi Z,Pancsa R

更新日期：2020-01-08 00:00:00

abstract：:Nucleosomes are the most abundant protein-DNA complexes in eukaryotes that provide compaction of genomic DNA and are implicated in regulation of transcription, DNA replication and repair. The details of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory signals. Hydroxyl-radical foot...

journal_title：Nucleic acids research

authors： Shaytan AK,Xiao H,Armeev GA,Wu C,Landsman D,Panchenko AR

更新日期：2017-09-19 00:00:00

abstract：:The genetic etiology of premature ovarian insufficiency (POI) has been well established to date, however, the role of long noncoding RNAs (lncRNAs) in POI is largely unknown. In this study, we identified a down-expressed lncRNA HCP5 in granulosa cells (GCs) from biochemical POI (bPOI) patients, which impaired DNA dama...

journal_title：Nucleic acids research

authors： Wang X,Zhang X,Dang Y,Li D,Lu G,Chan WY,Leung PCK,Zhao S,Qin Y,Chen ZJ

更新日期：2020-05-07 00:00:00

abstract：:Chromatin immunoprecipitation (ChIP) has been used to detect binding of DNA-binding proteins to sites in nuclear and mitochondrial genomes. Here, we describe a method for detecting protein-binding sites on chloroplast DNA, using modifications to the nuclear ChIP procedures. The method was developed using the lac opera...

journal_title：Nucleic acids research

authors： Newell CA,Gray JC

更新日期：2010-08-01 00:00:00

abstract：:Since 1992, FlyBase (flybase.org) has been an essential online resource for the Drosophila research community. Concentrating on the most extensively studied species, Drosophila melanogaster, FlyBase includes information on genes (molecular and genetic), transgenic constructs, phenotypes, genetic and physical interacti...

journal_title：Nucleic acids research

authors： Gramates LS,Marygold SJ,Santos GD,Urbano JM,Antonazzo G,Matthews BB,Rey AJ,Tabone CJ,Crosby MA,Emmert DB,Falls K,Goodman JL,Hu Y,Ponting L,Schroeder AJ,Strelets VB,Thurmond J,Zhou P,the FlyBase Consortium.

更新日期：2017-01-04 00:00:00

abstract：:The nucleotide sequence of 5.8S rRNA from the Chinese silkworm Philosamia cynthia ricini has been determined by gel sequencing and mobility shift methods. The complete primary structure is (sequence in text). This is one of the largest known 5.8S rRNAs. As compared to Bombyx 5.8S rRNA, it is two nucleotides longer; t...

journal_title：Nucleic acids research

authors： Feng YX,Krupp G,Gross HJ

更新日期：1982-10-25 00:00:00

abstract：:The goal of the present study is to identify genes that respond to iron availability. Suppression subtraction hybridization (SSH) was used to generate cDNA libraries from iron loaded and control human astrocytoma cells (SW1088). The cDNA libraries were screened with antisense cDNA probes obtained from mRNA isolated fr...

journal_title：Nucleic acids research

authors： Ye Z,Connor JR

更新日期：2000-04-15 00:00:00

abstract：:Detection of cell-free DNA in liquid biopsies offers great potential for use in non-invasive prenatal testing and as a cancer biomarker. Fetal and tumor DNA fractions however can be extremely low in these samples and ultra-sensitive methods are required for their detection. Here, we report an extremely simple and fast...

journal_title：Nucleic acids research

authors： Ståhlberg A,Krzyzanowski PM,Jackson JB,Egyud M,Stein L,Godfrey TE

更新日期：2016-06-20 00:00:00

abstract：:The bHLH transcription factor MyoD, the prototypical master regulator of differentiation, directs a complex program of gene expression during skeletal myogenesis. The up-regulation of the cdk inhibitor p57kip2 plays a critical role in coordinating differentiation and growth arrest during muscle development, as well as...

journal_title：Nucleic acids research

authors： Busanello A,Battistelli C,Carbone M,Mostocotto C,Maione R

更新日期：2012-09-01 00:00:00

abstract：:Multiple regulatory modules contribute to the complex expression programs realized by many loci. Although long thought of as isolated components, recent studies demonstrate that such regulatory sequences can physically associate with promoters and with each other and may localize to specific sub-nuclear transcription ...

journal_title：Nucleic acids research

authors： Dib S,Denarier E,Dionne N,Beaudoin M,Friedman HH,Peterson AC

更新日期：2011-04-01 00:00:00

abstract：:Structural changes of reconstituted SV 40 minichromosomes have been studied in relation to the salt concentration and addition of histone H1 by sedimentation and electron microscopy. Sedimentation data are represented as functions of the NaCl concentration and the Debye-Hückel electrostatic screening radius 1/alpha. T...

journal_title：Nucleic acids research

authors： Böttger M,Scherneck S,von Mickwitz CU,Fenske H,Lindigkeit R

更新日期：1979-08-10 00:00:00

abstract：:Bovine mitochondrial (mt) phenylalanine tRNA (tRNA(Phe)), which lacks the 'conserved' GG and T psi YCG sequences, was efficiently purified by the selective hybridization method using a solid phase DNA probe. The entire nucleotide sequence of the tRNA, including modified nucleotides, was determined and its higher-order...

journal_title：Nucleic acids research

authors： Wakita K,Watanabe Y,Yokogawa T,Kumazawa Y,Nakamura S,Ueda T,Watanabe K,Nishikawa K

更新日期：1994-02-11 00:00:00

abstract：:Mutator-like transposable elements (MULEs) are widespread across fungal, plant and animal species. Despite their abundance and importance as genetic tools in plants, the transposition mechanism of the MULE superfamily was previously unknown. Discovery of the Muta1 element from Aedes aegypti and its successful transpos...

journal_title：Nucleic acids research

authors： Liu K,Wessler SR

更新日期：2017-06-20 00:00:00

abstract：:Anti-microRNA (miRNA) oligonucleotides (AMOs) with 2'-O-Methyl (2'OMe) residues are commonly used to study miRNA function and can achieve high potency, with low cytotoxicity. Not withstanding this, we demonstrate the sequence-dependent capacity of 2'OMe AMOs to inhibit Toll-like receptor (TLR) 7 and 8 sensing of immun...

journal_title：Nucleic acids research

authors： Sarvestani ST,Stunden HJ,Behlke MA,Forster SC,McCoy CE,Tate MD,Ferrand J,Lennox KA,Latz E,Williams BR,Gantier MP

更新日期：2015-01-01 00:00:00

abstract：:An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the map...

journal_title：Nucleic acids research

authors： Yamagata K,Yamanishi A,Kokubu C,Takeda J,Sese J

更新日期：2016-05-05 00:00:00

abstract：:The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the...

journal_title：Nucleic acids research

authors： Federhen S

更新日期：2012-01-01 00:00:00

abstract：:It is a central issue to elucidate the new type of molecular recognition accompanied by a global structural change of a molecule upon binding to its targets. Here we investigate the driving force for the binding of R12 (a ribonucleic acid aptamer) and P16 (a partial peptide of a prion protein) during which P16 exhibit...

journal_title：Nucleic acids research

authors： Hayashi T,Oshima H,Mashima T,Nagata T,Katahira M,Kinoshita M

更新日期：2014-06-01 00:00:00

abstract：:Bacillus subtilis plasmid pGR71 is a promoter-probe shuttle vector derived from pUB110. The expression of the cat gene on pGR71 in B. subtilis requires the insertion of a Bacillus promoter and a ribosomal binding site (RBS) into the HindIII cloning site immediately upstream from the cat gene. A recombinant plasmid of ...

journal_title：Nucleic acids research

authors： Fujiwara S,Tsubokura N,Kurusu Y,Minami K,Kobayashi Y

更新日期：1990-02-25 00:00:00

abstract：:The yeast two-hybrid system is frequently used to identify protein-protein interactions. Confirming the specificity of candidate clones requires separation and isolation of yeast plasmids, propagation in bacteria and testing combinations of DNA-binding and activation domain hybrids in yeast. In order to simplify this ...

journal_title：Nucleic acids research

authors： Petermann R,Mossier BM,Aryee DN,Kovar H

更新日期：1998-05-01 00:00:00

abstract：:Interactions between proteins bound to distant sites along a DNA molecule require bending and twisting deformations in the intervening DNA. In certain systems, the sterically allowed protein-DNA and protein-protein interactions are hypothesized to produce loops with distinct geometries that may also be thermodynamical...

journal_title：Nucleic acids research

authors： Lia G,Semsey S,Lewis DE,Adhya S,Bensimon D,Dunlap D,Finzi L

更新日期：2008-07-01 00:00:00

abstract：:Knowledge of subcellular localizations (SCLs) of plant proteins relates to their functions and aids in understanding the regulation of biological processes at the cellular level. We present PlantLoc, a highly accurate and fast webserver for predicting the multi-label SCLs of plant proteins. The PlantLoc server has two...

journal_title：Nucleic acids research

authors： Tang S,Li T,Cong P,Xiong W,Wang Z,Sun J

更新日期：2013-07-01 00:00:00

abstract：:The ciliate Tetrahymena thermophila is an important eukaryotic model organism that has been used in pioneering studies of general phenomena, such as ribozymes, telomeres, chromatin structure and genome reorganization. Recent work has shown that Tetrahymena has many classes of small RNA molecules expressed during veget...

journal_title：Nucleic acids research

authors： Andersen KL,Nielsen H

更新日期：2012-02-01 00:00:00

abstract：:Nucleotide excision DNA repair is mechanistically conserved across all kingdoms of life. In prokaryotes, this multi-enzyme process requires six proteins: UvrA-D, DNA polymerase I and DNA ligase. To examine how UvrC locates the UvrB-DNA pre-incision complex at a site of damage, we have labeled UvrB and UvrC with differ...

journal_title：Nucleic acids research

authors： Hughes CD,Wang H,Ghodke H,Simons M,Towheed A,Peng Y,Van Houten B,Kad NM

更新日期：2013-05-01 00:00:00

abstract：:A protein-DNA complex has less gel electrophoretic mobility than the free DNA fragment. One parameter for the degree of retardation of a linear DNA fragment in a protein-DNA complex is the molecular weight of the bound protein(s). The quotient of the migration distances of free DNA (m) and protein-DNA complex (m') is ...

journal_title：Nucleic acids research

authors： Bading H

更新日期：1988-06-24 00:00:00