Supercoiling energy and nucleosome formation: the role of the arginine-rich histone kernel.

abstract：:DNA circuit is a versatile and highly-programmable toolbox which can potentially be used for the autonomous sensing of dynamic events, such as biomolecular interactions. However, the experimental implementation of in silico circuit designs has been hindered by the problem of circuit leakage. Here, we systematically an...

journal_title：Nucleic acids research

authors： Ang YS,Tong R,Yung LY

更新日期：2016-08-19 00:00:00

abstract：:Several restriction endonuclease fragments isolated from highly repetitive satellite DNA of the chromatin eliminating nematode Ascaris lumbricoides var. suum have been cloned. Each type of restriction fragment corresponds to a different variant of the same related ancestral sequence. These variants differ by small del...

journal_title：Nucleic acids research

authors： Müller F,Walker P,Aeby P,Neuhaus H,Felder H,Back E,Tobler H

更新日期：1982-12-11 00:00:00

abstract：:MicroRNAs (miRNAs) can group together along the human genome to form stable secondary structures made of several hairpins hosting miRNAs in their stems. The few known examples of such structures are all involved in cancer development. A large scale computational analysis of human chromosomes crossing sequence analysis...

journal_title：Nucleic acids research

authors： Mathelier A,Carbone A

更新日期：2013-04-01 00:00:00

abstract：:Epigenetic regulation of gene expression is tightly controlled by the dynamic modification of histones by chemical groups, the diversity of which has largely expanded over the past decade with the discovery of lysine acylations, catalyzed from acyl-coenzymes A. We investigated the dynamics of lysine acetylation and cr...

journal_title：Nucleic acids research

authors： Crespo M,Damont A,Blanco M,Lastrucci E,Kennani SE,Ialy-Radio C,Khattabi LE,Terrier S,Louwagie M,Kieffer-Jaquinod S,Hesse AM,Bruley C,Chantalat S,Govin J,Fenaille F,Battail C,Cocquet J,Pflieger D

更新日期：2020-05-07 00:00:00

abstract：:Prokaryotic genomic DNA is generally negatively supercoiled in vivo. Many regulatory processes, including the initiation of transcription, are known to depend on the superhelical state of the DNA substrate. The stresses induced within DNA by negative superhelicity can destabilize the DNA duplex at specific sites. Vari...

journal_title：Nucleic acids research

authors： Wang H,Kaloper M,Benham CJ

更新日期：2006-01-01 00:00:00

abstract：:The chromatin structure of a germ-line specific gene, the TPG-3 gene, one of the rainbow trout protamine genes was analyzed in various tissues. The protamine genes are expressed in early stage testis but not in late stage testis, liver or erythrocyte. Five potential CpG methylation sites in the coding and flanking reg...

journal_title：Nucleic acids research

authors： Delcuve GP,Davie JR

更新日期：1987-04-24 00:00:00

abstract：:The FlyRNAi database at the Drosophila RNAi Screening Center and Transgenic RNAi Project (DRSC/TRiP) provides a suite of online resources that facilitate functional genomics studies with a special emphasis on Drosophila melanogaster. Currently, the database provides: gene-centric resources that facilitate ortholog map...

journal_title：Nucleic acids research

authors： Hu Y,Comjean A,Rodiger J,Liu Y,Gao Y,Chung V,Zirin J,Perrimon N,Mohr SE

更新日期：2021-01-08 00:00:00

abstract：:KpnI restriction of DNAs from all anthropoid primates studied releases a conspicuous series of segments representing families of long, interspersed repetitive DNAs termed here the KpnI 1.2, 1.5, 1.8 and 1.9 kb families. Human KpnI 1.2 to 1.9 kb segments representative of these families were isolated and separately clo...

journal_title：Nucleic acids research

authors： Shafit-Zagardo B,Maio JJ,Brown FL

更新日期：1982-05-25 00:00:00

abstract：:A method is described which allows selection of sequences which can substitute for the normal AATAAA hexanucleotide involved in polyadenylation of SV40 late mRNAs. Plaques were generated from viral DNA lacking the motif, forcing acquisition of substitute sequences. Four variants were characterized. All displayed wild-...

journal_title：Nucleic acids research

authors： Swimmer C,Shenk T

更新日期：1985-11-25 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：:Transcription of tRNA-encoding genes by RNA polymerase (Pol) III requires the six-subunit general transcription factor IIIC that uses subcomplexes τA and τB to recognize two gene-internal promoter elements named A- and B-box. The Schizosaccharomyces pombe τA subcomplex comprises subunits Sfc1, Sfc4 and Sfc7. The cryst...

journal_title：Nucleic acids research

authors： Taylor NM,Baudin F,von Scheven G,Müller CW

更新日期：2013-10-01 00:00:00

abstract：:Here we describe a method of labelling short oligonucleotide probes with enzyme without purification or chemical modifications. Biotinylated oligonucleotides as short as 10 nt are coupled with streptavidin-conjugated enzyme, hybridised and detected with enzyme-triggered chemiluminescence. The detection of hybridisatio...

journal_title：Nucleic acids research

authors： Guerasimova A,Ivanov I,Lehrach H

更新日期：1999-01-15 00:00:00

abstract：:The repeating nucleotide sequence of 68 base pairs in the mtDNA from an ethidium-induced cytoplasmic petite mutant of yeast has been determined. For sequence analysis specifically primed and terminated RNA copies, obtained by in vitro transcription of the separated strands, were use. The sequence consists of 66 consec...

journal_title：Nucleic acids research

authors： Van Kreijl CF,Bos JL

更新日期：1977-07-01 00:00:00

abstract：:The hybridization of complementary strands of DNA is the underlying principle of all microarray-based techniques for the analysis of DNA variation. In this paper, we study how probe immobilization at surfaces, specifically probe density, influences the kinetics of target capture using surface plasmon resonance (SPR) s...

journal_title：Nucleic acids research

authors： Peterson AW,Heaton RJ,Georgiadis RM

更新日期：2001-12-15 00:00:00

abstract：:In prokaryotes and archaea transfer ribonucleic acid (tRNA) stability as well as cellular UV protection relies on the post-transcriptional modification of uracil at position 8 (U8) of tRNAs by the 4-thiouridine synthetase ThiI. Here, we report three crystal structures of ThiI from Thermotoga maritima in complex with a...

journal_title：Nucleic acids research

authors： Neumann P,Lakomek K,Naumann PT,Erwin WM,Lauhon CT,Ficner R

更新日期：2014-06-01 00:00:00

abstract：:The accumulation of somatic mitochondrial DNA (mtDNA) mutations contributes to the pathogenesis of human disease. Currently, mitochondrial mutations are largely considered results of inaccurate processing of its heavily damaged genome. However, mainly from a lack of methods to monitor mtDNA mutations with sufficient s...

journal_title：Nucleic acids research

authors： Valente WJ,Ericson NG,Long AS,White PA,Marchetti F,Bielas JH

更新日期：2016-10-14 00:00:00

abstract：:The Metabolic Pathway Collection from EMP is an extraction of data from the larger Enzymes and Metabolic Pathways database (EMP). This extraction has been made publicly available in the hope that others will find it useful for a variety of purposes. The original release in October 1995 contained 1814 distinct pathways...

journal_title：Nucleic acids research

authors： Selkov E,Galimova M,Goryanin I,Gretchkin Y,Ivanova N,Komarov Y,Maltsev N,Mikhailova N,Nenashev V,Overbeek R,Panyushkina E,Pronevitch L,Selkov E Jr

更新日期：1997-01-01 00:00:00

abstract：:Non-coding genetic variants/mutations can play functional roles in the cell by disrupting regulatory interactions between transcription factors (TFs) and their genomic target sites. For most human TFs, a myriad of DNA-binding models are available and could be used to predict the effects of DNA mutations on TF binding....

journal_title：Nucleic acids research

authors： Martin V,Zhao J,Afek A,Mielko Z,Gordân R

更新日期：2019-07-02 00:00:00

abstract：:Drosophila tissue culture cells have been important in the study of homologous promoters and more recently in the study of mammalian transcriptional factors such as CTF and SP1 which bind and stimulate transcription from transfected genes. In this paper we show that a Drosophila melanogaster haploid cell line (1182-4)...

journal_title：Nucleic acids research

authors： Saunders SE,Rawls JM,Wardle CJ,Burke JF

更新日期：1989-08-11 00:00:00

abstract：:Loss-of-function in melanocortin 1 receptor (MC1R), a GS protein-coupled receptor that regulates signal transduction through cAMP and protein kinase A (PKA) in melanocytes, is a major inherited melanoma risk factor. Herein, we report a novel cAMP-mediated response for sensing and responding to UV-induced DNA damage re...

journal_title：Nucleic acids research

authors： Jarrett SG,Wolf Horrell EM,D'Orazio JA

更新日期：2016-12-15 00:00:00

abstract：:HT1080 cells stably expressing green fluorescent protein (GFP) linked to a 3' terminal AU-rich element (ARE) proved to be a convenient system to study the dynamics of mRNA stability, as changes in mRNA levels are reflected in increased or decreased fluorescence intensity. This study examined whether mRNA stability can...

journal_title：Nucleic acids research

authors： Raineri I,Wegmueller D,Gross B,Certa U,Moroni C

更新日期：2004-02-19 00:00:00

abstract：:Segments of SV40 DNA having homologous overlapping termini recombine to produce viable genomes in monkey cells. Frequencies of recombination on either side of a deletion marker are non-random; replication and palindromes do not appear to be essential. Since recombination involves host enzymes, a suitable system has be...

journal_title：Nucleic acids research

authors： Upcroft P,Carter B,Kidson C

更新日期：1980-06-25 00:00:00

abstract：:We have overproduced and purified wild type regA protein, a translational repressor encoded by bacteriophage T4. The repressor activity of the cloned regA protein has been tested on four known regA target genes (T4 genes: 44, 45, rpbA and regA) using in vitro coupled transcription-translation reactions. We have demons...

journal_title：Nucleic acids research

authors： Webster KR,Adari HY,Spicer EK

更新日期：1989-12-11 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：:Bacteria adapt to changes in their environment via differential gene expression mediated by DNA binding transcriptional regulators. The PRODORIC2 database hosts one of the largest collections of DNA binding sites for prokaryotic transcription factors. It is the result of the thoroughly redesigned PRODORIC database. PR...

journal_title：Nucleic acids research

authors： Eckweiler D,Dudek CA,Hartlich J,Brötje D,Jahn D

更新日期：2018-01-04 00:00:00

abstract：:Loss-of-function (LOF) methods such as RNA interference (RNAi), antisense oligonucleotides or CRISPR-based genome editing provide unparalleled power for studying the biological function of genes of interest. However, a major concern is non-specific targeting, which involves depletion of transcripts other than those in...

journal_title：Nucleic acids research

authors： Stojic L,Lun ATL,Mangei J,Mascalchi P,Quarantotti V,Barr AR,Bakal C,Marioni JC,Gergely F,Odom DT

更新日期：2018-07-06 00:00:00

abstract：:CRISPR/Cas9 is a powerful genome editing system but uncontrolled Cas9 nuclease expression triggers off-target effects and even in vivo immune responses. Inspired by synthetic biology, here we built a synthetic switch that self-regulates Cas9 expression not only in the transcription step by guide RNA-aided self-cleavag...

journal_title：Nucleic acids research

authors： Shen CC,Hsu MN,Chang CW,Lin MW,Hwu JR,Tu Y,Hu YC

更新日期：2019-02-20 00:00:00

abstract：:MiR-210 is up-regulated in multiple cancer types but its function is disputable and further investigation is necessary. Using a bioinformatics approach, we identified the putative target genes of miR-210 in hypoxia-induced CNE cells from genome-wide scale. Two functional gene groups related to cell cycle and RNA proce...

journal_title：Nucleic acids research

authors： He J,Wu J,Xu N,Xie W,Li M,Li J,Jiang Y,Yang BB,Zhang Y

更新日期：2013-01-07 00:00:00

abstract：:The three CD3 genes on human chromosome 11q23 encode proteins (gamma, delta and epsilon) which form part of the antigen receptor on T lymphocytes. All three genes are clustered within 50 kb and are activated approximately contemporaneously during the early stages of T cell ontogeny. In order to pinpoint potential regu...

journal_title：Nucleic acids research

authors： Tunnacliffe A

更新日期：1990-02-11 00:00:00

abstract：:Chemically modified siRNAs are expected to have resistance toward nuclease degradation and good thermal stability in duplex formation for in vivo applications. We have recently found that 2'-OMe-4'-thioRNA, a hybrid chemical modification based on 2'-OMeRNA and 4'-thioRNA, has high hybridization affinity for complement...

journal_title：Nucleic acids research

authors： Takahashi M,Nagai C,Hatakeyama H,Minakawa N,Harashima H,Matsuda A

更新日期：2012-07-01 00:00:00