Circular dichroism studies of an oligodeoxyribonucleotide containing a hairpin loop made of a hexaethylene glycol chain: conformation and stability.

abstract：:Long Interspersed Element-1 (LINE-1) retrotransposition contributes to inter- and intra-individual genetic variation and occasionally can lead to human genetic disorders. Various strategies have been developed to identify human-specific LINE-1 (L1Hs) insertions from short-read whole genome sequencing (WGS) data; howev...

journal_title：Nucleic acids research

authors： Zhou W,Emery SB,Flasch DA,Wang Y,Kwan KY,Kidd JM,Moran JV,Mills RE

更新日期：2020-02-20 00:00:00

abstract：:Scalable multiplexed amplification technologies are needed for cost-effective large-scale genotyping of genetic markers such as single nucleotide polymorphisms (SNPs). We present SNPWave, a novel SNP genotyping technology to detect various subsets of sequences in a flexible fashion in a fixed detection format. SNPWave...

journal_title：Nucleic acids research

authors： van Eijk MJ,Broekhof JL,van der Poel HJ,Hogers RC,Schneiders H,Kamerbeek J,Verstege E,van Aart JW,Geerlings H,Buntjer JB,van Oeveren AJ,Vos P

更新日期：2004-03-05 00:00:00

abstract：:The PRISM web server enables fast and accurate prediction of protein-protein interactions (PPIs). The prediction algorithm is knowledge-based. It combines structural similarity and accounts for evolutionary conservation in the template interfaces. The predicted models are stored in its repository. Given two protein st...

journal_title：Nucleic acids research

authors： Baspinar A,Cukuroglu E,Nussinov R,Keskin O,Gursoy A

更新日期：2014-07-01 00:00:00

abstract：:DNA methylation plays a crucial role in the establishment of tissue-specific gene expression and the regulation of key biological processes. However, our present inability to predict the effect of genome sequence variation on DNA methylation precludes a comprehensive assessment of the consequences of non-coding variat...

journal_title：Nucleic acids research

authors： Zeng H,Gifford DK

更新日期：2017-06-20 00:00:00

abstract：:It has been proposed that phage lambda site-specific recombination proceeds via two independent strand exchanges: the first exchange forming a Holliday-structure which is then converted into complete recombinant products by the second strand exchange. If this hypothesis is correct, one should be able to trap the putat...

journal_title：Nucleic acids research

authors： Kitts PA,Nash HA

更新日期：1988-07-25 00:00:00

abstract：:Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the...

journal_title：Nucleic acids research

authors： Jha V,Roy B,Jahagirdar D,McNutt ZA,Shatoff EA,Boleratz BL,Watkins DE,Bundschuh R,Basu K,Ortega J,Fredrick K

更新日期：2021-01-11 00:00:00

abstract：:The solubility of adult beta-globin chromatin (beta A chromatin) from immature chicken red blood cells can be controlled by the presence or absence of n-butyrate in a cell incubation medium. In the absence of n-butyrate, only a small percentage (approximately 4%) of the total beta A chromatin is in a soluble chromatin...

journal_title：Nucleic acids research

authors： Ferenz CR,Nelson DA

更新日期：1985-03-25 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：:The homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. The protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a precursor protein and the religation of the flanking amino acid sequences (exteins) to a functional protein. Furthermore, domain I is i...

journal_title：Nucleic acids research

authors： Werner E,Wende W,Pingoud A,Heinemann U

更新日期：2002-09-15 00:00:00

abstract：:Mono- and polyclonal antibodies directed against different domains of the potato leafroll luteovirus (PLRV) P1 (ORF1) protein were applied to the analysis of P1 expression during PLRV replication in planta. Western analyses detected P1 and a protein of approximately 25 kDa (P1-C25) that accumulated to readily detectab...

journal_title：Nucleic acids research

authors： Prüfer D,Kawchuk L,Monecke2 M,Nowok S,Fischer R,Rohde W

更新日期：1999-01-15 00:00:00

abstract：:The advent of RNA-sequencing and microarray technologies has led to rapid growth of transcriptome data generated for a wide range of organisms, under various cellular, organ and individual conditions. Since the number of possible combinations of intercellular and extracellular conditions is almost unlimited, catalogin...

journal_title：Nucleic acids research

authors： Obayashi T,Kagaya Y,Aoki Y,Tadaka S,Kinoshita K

更新日期：2019-01-08 00:00:00

abstract：:MicroRNAs (miRNAs) are small non-coding RNAs of approximately 22 nucleotides, which negatively regulate the gene expression at the post-transcriptional level. This study describes an update of the miRTarBase (http://miRTarBase.mbc.nctu.edu.tw/) that provides information about experimentally validated miRNA-target inte...

journal_title：Nucleic acids research

authors： Chou CH,Chang NW,Shrestha S,Hsu SD,Lin YL,Lee WH,Yang CD,Hong HC,Wei TY,Tu SJ,Tsai TR,Ho SY,Jian TY,Wu HY,Chen PR,Lin NC,Huang HT,Yang TL,Pai CY,Tai CS,Chen WL,Huang CY,Liu CC,Weng SL,Liao KW,Hsu WL,Hu

更新日期：2016-01-04 00:00:00

abstract：:We examined the 3'-flanking regions required for accurate 3'-end formation of wheat histone H3 mRNA using gene expression in transformed sunflower cells. The introduction of mutations into the conserved sequence AATGGAAATG in the 3'-flanking region of plant histone genes, located 22 bp upstream from the polyadenylatio...

journal_title：Nucleic acids research

authors： Ohtsubo N,Iwabuchi M

更新日期：1994-03-25 00:00:00

abstract：:For sophisticated gene targeting procedures requiring two sequential selective steps to operate efficiently it is essential that the marker genes used are not prone to position effects. The double replacement gene targeting procedure, to produce mice with subtle gene alterations, is based on the use of hypoxanthine ph...

journal_title：Nucleic acids research

authors： Melton DW,Ketchen AM,Selfridge J

更新日期：1997-10-01 00:00:00

abstract：:Mammalian DNA (cytosine-5) methyltransferase 1 (DNMT1) is essential for maintenance methylation. Phosphorylation of Ser143 (pSer143) stabilizes DNMT1 during DNA replication. Here, we show 14-3-3 is a reader protein of DNMT1pSer143. In mammalian cells 14-3-3 colocalizes and binds DNMT1pSer143 post-DNA replication. The ...

journal_title：Nucleic acids research

authors： Estève PO,Zhang G,Ponnaluri VK,Deepti K,Chin HG,Dai N,Sagum C,Black K,Corrêa IR Jr,Bedford MT,Cheng X,Pradhan S

更新日期：2016-02-29 00:00:00

abstract：:Bacterial small RNAs (sRNAs) are a heterogeneous group of post-transcriptional regulators that often act at the heart of large networks. Hundreds of sRNAs have been discovered by genome-wide screens and most of these sRNAs exert their functions by base-pairing with target mRNAs. However, studies addressing the molecul...

journal_title：Nucleic acids research

authors： Fröhlich KS,Förstner KU,Gitai Z

更新日期：2018-11-16 00:00:00

abstract：:Nuclear extracts prepared from growth hormone-secreting (GC) and prolactin-secreting (235-1) rat anterior pituitary cell lines were compared for their ability to bind to the DNA sequences conferring tissue-specificity to the expression of the rat growth hormone (rGH) gene promoter. Cell-specific differences in the int...

journal_title：Nucleic acids research

authors： Schaufele F,West BL,Reudelhuber T

更新日期：1990-09-11 00:00:00

abstract：:The multifunctional HCV core protein consists of a hydrophilic RNA interacting D1 domain and a hydrophobic D2 domain interacting with membranes and lipid droplets. The core D1 domain was found to possess nucleic acid annealing and strand transfer properties. To further understand these chaperone properties, we investi...

journal_title：Nucleic acids research

authors： Sharma Kk,Didier P,Darlix JL,de Rocquigny H,Bensikaddour H,Lavergne JP,Pénin F,Lessinger JM,Mély Y

更新日期：2010-06-01 00:00:00

abstract：:High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11-20 pairs of probes. In order to o...

journal_title：Nucleic acids research

authors： Irizarry RA,Bolstad BM,Collin F,Cope LM,Hobbs B,Speed TP

更新日期：2003-02-15 00:00:00

abstract：:The SRPDB (signal recognition particle database) provides aligned SRP RNA and protein sequences, annotated and phylogenetically ordered. This release includes 82 SRP RNAs (including 22 bacterial and 9 archaeal homologs) and a total of 20 protein sequences representing SRP9, SRP14, SRP19, SRP54, SRP68, and SRP72. The o...

journal_title：Nucleic acids research

authors： Zwieb C,Larsen N

更新日期：1994-09-01 00:00:00

abstract：:Revealing the clonal composition of a single tumor is essential for identifying cell subpopulations with metastatic potential in primary tumors or with resistance to therapies in metastatic tumors. Sequencing technologies provide only an overview of the aggregate of numerous cells. Computational approaches to de-mix a...

journal_title：Nucleic acids research

authors： Strino F,Parisi F,Micsinai M,Kluger Y

更新日期：2013-09-01 00:00:00

abstract：:Proper DNA double-strand break (DSB) repair is essential for maintaining genome integrity. Microhomology-mediated end joining (MMEJ) is an error-prone repair mechanism, which introduces mutations at break sites and contributes to chromosomal translocations and telomere fusions, thus driving carcinogenesis. Mitotic kin...

journal_title：Nucleic acids research

authors： Wang H,Qiu Z,Liu B,Wu Y,Ren J,Liu Y,Zhao Y,Wang Y,Hao S,Li Z,Peng B,Xu X

更新日期：2018-11-16 00:00:00

abstract：:Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions. The current version 46 describes 7088 human proteins (34% of the predicted human proteome), participating in 6744 reactions based on data extracted from 15 107 research publications with PubMed link...

journal_title：Nucleic acids research

authors： Croft D,Mundo AF,Haw R,Milacic M,Weiser J,Wu G,Caudy M,Garapati P,Gillespie M,Kamdar MR,Jassal B,Jupe S,Matthews L,May B,Palatnik S,Rothfels K,Shamovsky V,Song H,Williams M,Birney E,Hermjakob H,Stein L,D'Eusta

更新日期：2014-01-01 00:00:00

abstract：:Scanning force microscopy was used to examine DNA condensates prepared with varying stoichiometries of lipospermine or polyethylenimine in physiological solution. For the first time, individual DNA strands were clearly visualized in incomplete condensates without drying. Using lipospermine at sub-saturating concentrat...

journal_title：Nucleic acids research

authors： Dunlap DD,Maggi A,Soria MR,Monaco L

更新日期：1997-08-01 00:00:00

abstract：:A hallmark of defense mechanisms based on clustered regularly interspaced short palindromic repeats (CRISPR) and associated sequences (Cas) are the crRNAs that guide these complexes in the destruction of invading DNA or RNA. Three separate CRISPR-Cas systems exist in the cyanobacterium Synechocystis sp. PCC 6803. Base...

journal_title：Nucleic acids research

authors： Reimann V,Alkhnbashi OS,Saunders SJ,Scholz I,Hein S,Backofen R,Hess WR

更新日期：2017-01-25 00:00:00

abstract：:Robust methods to detect DNA-binding proteins from structures of unknown function are important for structural biology. This paper describes a method for identifying such proteins that (i) have a solvent accessible structural motif necessary for DNA-binding and (ii) a positive electrostatic potential in the region of ...

journal_title：Nucleic acids research

authors： Shanahan HP,Garcia MA,Jones S,Thornton JM

更新日期：2004-09-08 00:00:00

abstract：:Ornithine decarboxylase (ODC) expression is important for proliferation and is elevated in many tumor cells. We previously showed that Sp1 is a major positive regulator of ODC transcription. In this paper we have investigated transcriptional regulation of rat ODC by the closely related factor Sp3. While over-expressio...

journal_title：Nucleic acids research

authors： Kumar AP,Butler AP

更新日期：1997-05-15 00:00:00

abstract：:NF-IL6beta regulates gene expression and plays function roles in many tissues. The EGF-regulated cyclooxygenase-2 (cox-2) expression is mediated through p38(MAPK) signaling pathway and positively correlates with NF-IL6beta expression in A431 cells. NF-IL6beta coordinated with c-Jun on cox-2 transcriptional activation ...

journal_title：Nucleic acids research

authors： Wang JM,Ko CY,Chen LC,Wang WL,Chang WC

更新日期：2006-01-05 00:00:00

abstract：:The RNA of a deleted strain (lacking Src gene) of an avian sarcoma virus (ASV) was examined by a newly developed immunoelectron microscopic procedure which uses anti-nucleotide antibodies as probes. After denaturation of the RNA and reaction with a high affinity, highly specific anti-7-methylguanosine-5'-phosphate (an...

journal_title：Nucleic acids research

authors： Castleman H,Meredith RD,Erlanger BF

更新日期：1980-10-10 00:00:00

abstract：:Single-strand specific endoribonuclease YbeY has been shown to play an important role in the processing of the 3' end of the 16S rRNA in Escherichia coli. Lack of YbeY results in the accumulation of the 17S rRNA precursor. In contrast to a previous report, we show that Sinorhizobium meliloti YbeY exhibits endoribonucl...

journal_title：Nucleic acids research

authors： Babu VMP,Sankari S,Budnick JA,Caswell CC,Walker GC

更新日期：2020-01-10 00:00:00