The ConsensusPathDB interaction database: 2013 update.

abstract：:A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formation, but seem flexibl...

journal_title：Nucleic acids research

authors： Dršata T,Špačková N,Jurečka P,Zgarbová M,Šponer J,Lankaš F

更新日期：2014-06-01 00:00:00

abstract：:A straightforward enzymatic protocol for converting regular DNA into pseudo-complementary DNA could improve the performance of oligonucleotide microarrays by generating readily hybridizable structure-free targets. Here we screened several highly destabilizing analogs of G and C for one that could be used with 2-aminoa...

journal_title：Nucleic acids research

authors： Lahoud G,Timoshchuk V,Lebedev A,Arar K,Hou YM,Gamper H

更新日期：2008-12-01 00:00:00

abstract：:With read lengths of currently up to 2 × 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targete...

journal_title：Nucleic acids research

authors： Schirmer M,Ijaz UZ,D'Amore R,Hall N,Sloan WT,Quince C

更新日期：2015-03-31 00:00:00

abstract：:New linker phosphoramidite reagents containing a cleavable 3'-ester linkage are used for attaching the first nucleoside to the surface of a solid- phase support. Inexpensive, underivatized amino supports, such as long chain alkylamine controlled-pore glass, can serve as universal supports. No modifications to phosphor...

journal_title：Nucleic acids research

authors： Pon RT,Yu S

更新日期：2004-01-29 00:00:00

abstract：:Using a combination of bioinformatic and molecular biology approaches a Drosophila melanogaster protein, DmTTF, has been identified, which exhibits sequence and structural similarity with two mitochondrial transcription termination factors, mTERF (human) and mtDBP (sea urchin). Import/processing assays indicate that D...

journal_title：Nucleic acids research

authors： Roberti M,Polosa PL,Bruni F,Musicco C,Gadaleta MN,Cantatore P

更新日期：2003-03-15 00:00:00

abstract：:Transcription and mRNA export are linked processes. However, the molecular mechanisms of this coordination are not clear. Sus1 (hENY2) participates in this coordination as part of two protein complexes: SAGA, a transcriptional co-activator; TREX-2, which functions in mRNA biogenesis and export. Here, we investigate th...

journal_title：Nucleic acids research

authors： García-Oliver E,Pascual-García P,García-Molinero V,Lenstra TL,Holstege FC,Rodríguez-Navarro S

更新日期：2013-06-01 00:00:00

abstract：:The nucleotide sequence of the faeD gene of Escherichia coli and the amino acid sequence of its product is presented. The faeD product is an outer membrane protein required for transport of K88ab fimbrial subunits across the outer membrane. The protein is synthesized as a precursor containing a signal peptide, and the...

journal_title：Nucleic acids research

authors： Mooi FR,Claassen I,Bakker D,Kuipers H,de Graaf FK

更新日期：1986-03-25 00:00:00

abstract：:Brome mosaic virus (BMV) is a tripartite genome, positive-sense RNA virus of plants. Previously it was demonstrated that local hybridization between BMV RNAs (RNA-RNA heteroduplex formation) efficiently promotes non-homologous RNA recombination. In addition, studies on the role of the BMV polymerase in RNA recombinati...

journal_title：Nucleic acids research

authors： Figlerowicz M

更新日期：2000-04-15 00:00:00

abstract：:The anaerobically-regulated nirB promoter was used to express heterologous genes in Escherichia coli. Under anaerobic conditions the promoter was able to express tetanus toxin fragment C at approximately 20% total cell protein (tcp) and the Bordetella pertussis antigen pertactin at greater than 30% tcp. These levels a...

journal_title：Nucleic acids research

authors： Oxer MD,Bentley CM,Doyle JG,Peakman TC,Charles IG,Makoff AJ

更新日期：1991-06-11 00:00:00

abstract：:Gene expression circuitries, which enable cells to detect precise levels within a morphogen concentration gradient, have a pivotal impact on biological processes such as embryonic pattern formation, paracrine and autocrine signalling, and cellular migration. We present the rational synthesis of a synthetic genetic cir...

journal_title：Nucleic acids research

authors： Greber D,Fussenegger M

更新日期：2010-10-01 00:00:00

abstract：:Synthetic DNA fragments were constructed to determine the effect of G tracts, in conjunction with periodically spaced A tracts, on DNA bends. Relative length measurements showed that the G tracts spaced at the half helical turn enhanced the DNA bend. When the G tract was interrupted with a thymine or shortened to one ...

journal_title：Nucleic acids research

authors： Milton DL,Casper ML,Wills NM,Gesteland RF

更新日期：1990-02-25 00:00:00

abstract：:Fluorogenic RNAs that are based on the complex formed by 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) derivatives and the RNA aptamer named Spinach were used to engineer a new generation of in vitro and in vivo sensors for bioanalytics. With the resolved crystal structure of the RNA/small molecule complex, ...

journal_title：Nucleic acids research

authors： Ketterer S,Fuchs D,Weber W,Meier M

更新日期：2015-10-30 00:00:00

abstract：:High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such a...

journal_title：Nucleic acids research

authors： Hach F,Sarrafi I,Hormozdiari F,Alkan C,Eichler EE,Sahinalp SC

更新日期：2014-07-01 00:00:00

abstract：:A fluoride-cleavable phosphoramidite for biotinylation was designed, synthesized and coupled efficiently to the 5'-end of DNA on an automatic synthesizer. The diisopropylsilyl acetal functionality was used to link the biotin moiety through a tertiary hydroxide group to the 5'-end of DNA. This linkage proved to be comp...

journal_title：Nucleic acids research

authors： Fang S,Bergstrom DE

更新日期：2003-01-15 00:00:00

abstract：:Yeast two-hybrid (Y2H) screenings result in identification of many out-of-frame (OOF) clones that code for short (2-100 amino acids) peptides with no sequence homology to known proteins. We hypothesize that these peptides can reveal common short linear motifs (SLiMs) responsible for their selection. We present a new p...

journal_title：Nucleic acids research

authors： Liu Y,Woods NT,Kim D,Sweet M,Monteiro AN,Karchin R

更新日期：2011-10-01 00:00:00

abstract：:We have developed a PCR-based short interfering RNA (siRNA) quantification method based on competition between siRNA and a homologous DNA primer for annealing to template DNA, avoiding the requirement for prior conversion of RNA to cDNA. Primers and probe were designed to amplify regions of the human papillomavirus E6...

journal_title：Nucleic acids research

authors： Liu WL,Stevenson M,Seymour LW,Fisher KD

更新日期：2009-01-01 00:00:00

abstract：:To unravel the network of transcription factors established during development it is important to understand how genes specifically expressed during embryogenesis are regulated. Oct-4 is a transcription factor whose expression is associated with an undifferentiated cell phenotype in the early mouse embryo and is downr...

journal_title：Nucleic acids research

authors： Sylvester I,Schöler HR

更新日期：1994-03-25 00:00:00

abstract：:A direct correlation exists between the level of histone H4 hyperacetylation induced by sodium butyrate and the extent to which nucleosomes lose their compact shape and become elongated (62.0% of the particles have a length/width ratio over 1.6; overall mean in the length/width ratio = 1.83 +/- 0.48) when bound to ele...

journal_title：Nucleic acids research

authors： Oliva R,Bazett-Jones DP,Locklear L,Dixon GH

更新日期：1990-05-11 00:00:00

abstract：:The DEAH-box NTPase Prp43 disassembles spliceosomes in co-operation with the cofactors Ntr1/Spp382 and Ntr2, forming the NTR complex. How Prp43 is regulated by its cofactors to discard selectively only intron-lariat spliceosomes (ILS) and defective spliceosomes and to prevent disassembly of earlier and properly assemb...

journal_title：Nucleic acids research

authors： Fourmann JB,Tauchert MJ,Ficner R,Fabrizio P,Lührmann R

更新日期：2017-04-20 00:00:00

abstract：:Sensitive detection of microsatellite instability (MSI) in tissue or liquid biopsies using next generation sequencing (NGS) has growing prognostic and predictive applications in cancer. However, the complexities of NGS make it cumbersome as compared to established multiplex-PCR detection of MSI. We present a new appro...

journal_title：Nucleic acids research

authors： Yu F,Leong KW,Makrigiorgos A,Adalsteinsson VA,Ladas I,Ng K,Mamon H,Makrigiorgos GM

更新日期：2020-12-08 00:00:00

abstract：:Base compositions were examined at every position in codons of more than 50 genes from taxonomically different bacteria and of the corresponding antisense sequences on the bacterial genes. We propose that the nonstop frame on antisense strand [NSF(a)] of GC-rich bacterial genes is the most promising sequence for newly...

journal_title：Nucleic acids research

authors： Ikehara K,Amada F,Yoshida S,Mikata Y,Tanaka A

更新日期：1996-11-01 00:00:00

abstract：:KU is a heterodimer, consisting of approximately 70 and approximately 80 kDa subunits (KU70 and KU80, respectively), which is involved in a variety of nuclear functions. We generated tbKU80-deficient trypanosomes to explore the potential role of the tbKU complex in telomere maintenance and transcriptional regulation o...

journal_title：Nucleic acids research

authors： Janzen CJ,Lander F,Dreesen O,Cross GA

更新日期：2004-12-15 00:00:00

abstract：:HIV-1 reverse transcriptase (RT) is a primary target for anti-AIDS drugs. Structures of HIV-1 RT, usually determined at approximately 2.5-3.0 A resolution, are important for understanding enzyme function and mechanisms of drug resistance in addition to being helpful in the design of RT inhibitors. Despite hundreds of ...

journal_title：Nucleic acids research

authors： Bauman JD,Das K,Ho WC,Baweja M,Himmel DM,Clark AD Jr,Oren DA,Boyer PL,Hughes SH,Shatkin AJ,Arnold E

更新日期：2008-09-01 00:00:00

abstract：:The Genotyping tool at the National Center for Biotechnology Information is a web-based program that identifies the genotype (or subtype) of recombinant or non-recombinant viral nucleotide sequences. It works by using BLAST to compare a query sequence to a set of reference sequences for known genotypes. Predefined ref...

journal_title：Nucleic acids research

authors： Rozanov M,Plikat U,Chappey C,Kochergin A,Tatusova T

更新日期：2004-07-01 00:00:00

abstract：:Mild ultraviolet irradiation of E. coli ribosomal subunits leads to the formation of a number of intra-RNA cross-links, in addition to the RNA-protein cross-links already reported (see refs. 9, 10). After partial ribonuclease digestion of the RNA from irradiated subunits, complexes containing these intra-RNA cross-lin...

journal_title：Nucleic acids research

authors： Zwieb C,Brimacombe R

更新日期：1980-06-11 00:00:00

abstract：:The 3'-untranslated region (UTR) of tobacco mosaic virus (TMV), which terminates in a tRNA-like structure, functionally substitutes for a poly(A) tail in both plant and animal cells. The addition of the TMV 3'-UTR to chimeric mRNA constructs increases their expression up to 100-fold, increasing both translational effi...

journal_title：Nucleic acids research

authors： Gallie DR,Feder JN,Schimke RT,Walbot V

更新日期：1991-09-25 00:00:00

abstract：:The universal L-shaped tertiary structure of tRNAs is maintained with the help of nucleotide modifications within the D- and T-loops, and these modifications are most extensive within hyperthermophilic species. The obligate-commensal Nanoarchaeum equitans and its phylogenetically-distinct host Ignicoccus hospitalis gr...

journal_title：Nucleic acids research

authors： Rose S,Auxilien S,Havelund JF,Kirpekar F,Huber H,Grosjean H,Douthwaite S

更新日期：2020-07-09 00:00:00

abstract：:Replacement of alpha-, beta- and gamma-phosphate groups in 2'-deoxynucleoside 5'-triphosphates (dNTP) with phosphonate groups yields a new set of dNTP mimics with potential biological and therapeutic applications. Here, we describe the synthesis of 15 new dNTPs modified at alpha-, beta- and gamma-phosphates containing...

journal_title：Nucleic acids research

authors： Alexandrova LA,Skoblov AY,Jasko MV,Victorova LS,Krayevsky AA

更新日期：1998-02-01 00:00:00

abstract：:The use of the ammonia deprotection step to introduce (15)N labels at specific exocyclic amino positions of adenine, cytosine, guanine or 2-aminopurine of oligodeoxynucleotides is described. ...

journal_title：Nucleic acids research

authors： Acedo M,Fàbrega C,Aviño A,Goodman M,Fagan P,Wemmer D,Eritja R

更新日期：1994-08-11 00:00:00

abstract：:The purpose of this work was to analyse at the molecular level the DNA recognized by the antibodies to Z-DNA in in situ experiments. Antibodies to Z-DNA interact strongly with R-band positive heterochromatic segments of fixed metaphase chromosomes of Cebus (Viegas-Pequignot et al., 1983). These segments are constitute...

journal_title：Nucleic acids research

authors： Malfoy B,Rousseau N,Vogt N,Viegas-Pequignot E,Dutrillaux B,Leng M

更新日期：1986-04-25 00:00:00