Two non-histone proteins are associated with the promoter region and histone HI with the transcribed region of active hsp-70 genes as revealed by UV-induced DNA-protein crosslinking in vivo.

abstract：:We present a study of how substituent groups of naturally occurring and modified nucleotide bases affect the degree of hydration of right-handed B-DNA and left-handed Z-DNA. A comparison of poly(dG-dC) and poly(dG-dm5C) titrations with the lipotropic salts of the Hofmeister series infers that the methyl stabilization ...

journal_title：Nucleic acids research

authors： Kagawa TF,Howell ML,Tseng K,Ho PS

更新日期：1993-12-25 00:00:00

abstract：:The Fos and Jun family of transcription factors contain an invariant sequence motif lysine-cysteine-arginine (KCR) in the highly conserved DNA-binding region. Reduction of the cysteine residue is necessary to facilitate DNA-binding. Here, we examined the potential dual roles of the flanking lysine and arginine residue...

journal_title：Nucleic acids research

authors： Ng L,Forrest D,Curran T

更新日期：1993-12-25 00:00:00

abstract：:Accurate mapping of spliced RNA-Seq reads to genomic DNA has been known as a challenging problem. Despite significant efforts invested in developing efficient algorithms, with the human genome as a primary focus, the best solution is still not known. A recently introduced tool, TrueSight, has demonstrated better perfo...

journal_title：Nucleic acids research

authors： Burns PD,Li Y,Ma J,Borodovsky M

更新日期：2014-02-01 00:00:00

abstract：:The role of TATA elements in the expression of a mammalian promoter was investigated in the fission yeast Schizosaccharomyces pombe, by studying the human adenovirus E2-early promoter. This is a unique dual promoter with two nonconsensus TATA elements directing transcription from two cap sites, +1 and -26. A sequence ...

journal_title：Nucleic acids research

authors： Swaminathan S,Malhotra P,Manohar CF,Dhar R,Thimmapaya B

更新日期：1993-06-11 00:00:00

abstract：:ATF4 is a pro-oncogenic transcription factor whose translation is activated by eIF2 phosphorylation through delayed re-initiation involving two uORFs in the mRNA leader. However, in yeast, the effect of eIF2 phosphorylation can be mimicked by eIF5 overexpression, which turns eIF5 into translational inhibitor, thereby ...

journal_title：Nucleic acids research

authors： Kozel C,Thompson B,Hustak S,Moore C,Nakashima A,Singh CR,Reid M,Cox C,Papadopoulos E,Luna RE,Anderson A,Tagami H,Hiraishi H,Slone EA,Yoshino KI,Asano M,Gillaspie S,Nietfeld J,Perchellet JP,Rothenburg S,Masai H,W

更新日期：2016-10-14 00:00:00

abstract：:Gene promoters are enriched in guanine clusters that potentially fold into quadruplex structures. Such quadruplexes were implicated in the regulation of gene expression, plausibly by interacting with transcription factors. We showed previously that homodimers of the myogenic transcription factor MyoD bound in vitro mo...

journal_title：Nucleic acids research

authors： Shklover J,Weisman-Shomer P,Yafe A,Fry M

更新日期：2010-04-01 00:00:00

abstract：:Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data. Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene locus length (the length of the gene body and its surrounding non-coding sequence). Adjustment for gene locus length is necessary because ...

journal_title：Nucleic acids research

authors： Welch RP,Lee C,Imbriano PM,Patil S,Weymouth TE,Smith RA,Scott LJ,Sartor MA

更新日期：2014-07-01 00:00:00

abstract：:Natural transformation is a major mechanism of horizontal gene transfer in bacteria that depends on DNA recombination. RecA is central to the homologous recombination pathway, catalyzing DNA strand invasion and homology search. DprA was shown to be a key binding partner of RecA acting as a specific mediator for its lo...

journal_title：Nucleic acids research

authors： Lisboa J,Andreani J,Sanchez D,Boudes M,Collinet B,Liger D,van Tilbeurgh H,Guérois R,Quevillon-Cheruel S

更新日期：2014-06-01 00:00:00

abstract：:The continuing threat of infectious disease and future pandemics, coupled to the continuous increase of drug-resistant pathogens, makes the discovery of new and better vaccines imperative. For effective vaccine development, antigen discovery and validation is a prerequisite. The compilation of information concerning p...

journal_title：Nucleic acids research

authors： Ansari HR,Flower DR,Raghava GP

更新日期：2010-01-01 00:00:00

abstract：:Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere binding patterns to nucleobase imine N1/N3/N7 atoms. Among those, purine N7 atoms are considered to be the best nucleobase binding sites for diva...

journal_title：Nucleic acids research

authors： Leonarski F,D'Ascenzo L,Auffinger P

更新日期：2017-01-25 00:00:00

abstract：:Retroviral particles contain a dimeric RNA genome, which serves as template for the generation of double-stranded DNA by reverse transcription. Transfer between RNA strands during DNA synthesis is governed by both sequence similarity between templates and structural features of the dimeric RNA. A kissing hairpin, beli...

journal_title：Nucleic acids research

authors： Mikkelsen JG,Rasmussen SV,Pedersen FS

更新日期：2004-01-09 00:00:00

abstract：:The cis-requirements for the first editing site in the atp9 mRNA from pea mitochondria were investigated in an in vitro RNA editing system. Template RNAs deleted 5' of -20 are edited correctly, but with decreased efficiency. Deletions between -20 and the edited nucleotide abolish editing activity. Substitution of the ...

journal_title：Nucleic acids research

authors： Takenaka M,Neuwirt J,Brennicke A

更新日期：2004-08-04 00:00:00

abstract：:PKR is a doubled-stranded RNA-dependent protein kinase which is implicated in the regulation of several cellular processes, including cell proliferation. PKR undergoes phosphorylation and activation in mouse embryonic 3T3-F442A cells in response to endogenous RNA(s). Activation of PKR is related to growth and differen...

journal_title：Nucleic acids research

authors： Petryshyn RA,Ferrenz AG,Li J

更新日期：1997-07-01 00:00:00

abstract：:Mammalian mitochondrial ribosomes evolved from bacterial ribosomes by reduction of ribosomal RNAs, increase of ribosomal protein content, and loss of guanine nucleotides. Guanine is the base most sensitive to oxidative damage. By systematically comparing high-quality, small ribosomal subunit RNA sequence alignments an...

journal_title：Nucleic acids research

authors： Hosseini M,Roy P,Sissler M,Zirbel CL,Westhof E,Leontis N

更新日期：2018-11-16 00:00:00

abstract：:Transcription of transfer RNA genes by RNA polymerase III (Pol III) is controlled by general factors, TFIIIB and TFIIIC, and a negative regulator, Maf1. Here we report the interplay between TFIIIC and Maf1 in controlling Pol III activity upon the physiological switch of yeast from fermentation to respiration. TFIIIC d...

journal_title：Nucleic acids research

authors： Ciesla M,Skowronek E,Boguta M

更新日期：2018-10-12 00:00:00

abstract：:Human stem cells are promising sources for regenerative therapy. To ensure safety of future therapeutic applications, the differentiation potency of stem cells has to be tested and be widely opened to the public. The potency is generally assessed by teratoma formation comprising differentiated cells from all three ger...

journal_title：Nucleic acids research

authors： Park SJ,Komiyama Y,Suemori H,Umezawa A,Nakai K

更新日期：2016-01-04 00:00:00

abstract：:Several different computational problems have been solved using DNA as a medium. However, the DNA computations that have so far been carried out have examined a relatively small number of possible sequence solutions in order to find correct sequence solutions. We have encoded a search algorithm in DNA that required th...

journal_title：Nucleic acids research

authors： James KD,Boles AR,Henckel D,Ellington AD

更新日期：1998-11-15 00:00:00

abstract：:Messenger RNA in eukaryotes is comprised of several abundance classes. Also, the decay of these unstable molecules shows at least two very different lifetimes. Two independent techniques are used here to examine the relation between message abundance and lifetime in cell lines from very different organisms. The method...

journal_title：Nucleic acids research

authors： Lenk R,Herman R,Penman S

更新日期：1978-08-01 00:00:00

abstract：:The extent of base pairing in Escherichia coli and Bacillus stearothermophilus 5S RNAs was determined by infrared spectroscopy. From the infrared spectra taken at 20 degrees and 52 degrees C it is concluded that E. coli and B. stearothermophlius 5S RNAs possess a large number of base pairs (Table I). Comparison of our...

journal_title：Nucleic acids research

authors： Appel B,Erdmann VA,Stulz J,Ackerman T

更新日期：1979-10-25 00:00:00

abstract：:We have studied the coil-to-helix transition of the DNA oligomer d(C4A4T4C4), using circular dichroism measurements to monitor the formation of A.T base pairs within the central self-complementary A4T4 region and the formation of protonated C.C+ base pairs at the ends of the oligomer. We found that both A.T and C.C+ b...

journal_title：Nucleic acids research

authors： Gray DM,Cui T,Ratliff RL

更新日期：1984-10-11 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 side chains of the 20 types of amino acids, owing to a large extent to their different physical properties, have characteristic distributions in interior/surface regions of individual proteins and in interface/non-interface portions of protein surfaces that bind proteins or nucleic acids. These distributions have ...

journal_title：Nucleic acids research

authors： Tjong H,Qin S,Zhou HX

更新日期：2007-07-01 00:00:00

abstract：:Here, we describe two freely available web servers for molecular docking. The PatchDock method performs structure prediction of protein-protein and protein-small molecule complexes. The SymmDock method predicts the structure of a homomultimer with cyclic symmetry given the structure of the monomeric unit. The inputs t...

journal_title：Nucleic acids research

authors： Schneidman-Duhovny D,Inbar Y,Nussinov R,Wolfson HJ

更新日期：2005-07-01 00:00:00

abstract：:We have isolated from a single human liver cDNA library two clones which are highly homologous (78% over the coding region) to the major phenobarbital-inducible P450 from rat (P450IIB1). This is the first direct demonstration of the presence of the P450IIB gene subfamily in humans. This subfamily is much less extensiv...

journal_title：Nucleic acids research

authors： Miles JS,Spurr NK,Gough AC,Jowett T,McLaren AW,Brook JD,Wolf CR

更新日期：1988-07-11 00:00:00

abstract：:The activation of a telomere maintenance mechanism is required for cancer development in humans. While most tumors achieve this by expressing the enzyme telomerase, a fraction (5-15%) employs a recombination-based mechanism termed alternative lengthening of telomeres (ALT). Here we show that loss of the single-strande...

journal_title：Nucleic acids research

authors： Grudic A,Jul-Larsen A,Haring SJ,Wold MS,Lønning PE,Bjerkvig R,Bøe SO

更新日期：2007-01-01 00:00:00

abstract：:Various antitumor drugs stabilize DNA topoisomerase II-DNA transient covalent complexes. The complexes distribution along pBR322 DNA was shown previously to depend upon the nature of the drug (Tewey et al. (1984) Science 226, 466-468). The position in pBR322 of DNA cleavage by calf DNA topoisomerase II for 115 such si...

journal_title：Nucleic acids research

authors： Fossé P,René B,Le Bret M,Paoletti C,Saucier JM

更新日期：1991-06-11 00:00:00

abstract：:Cells internalized synthetic oligonucleotides (oligos) in culture. The hybridization of these molecules to target RNA in the living cell was subsequently detected and characterized after fixation of the cells, with or without previous detergent extraction. Hybridized oligo was distinguished from free oligo in the cell...

journal_title：Nucleic acids research

authors： Politz JC,Taneja KL,Singer RH

更新日期：1995-12-25 00:00:00

abstract：:Nuclear actin-related proteins (Arps) are subunits of several chromatin remodelers, but their molecular functions within these complexes are unclear. We report the crystal structure of the INO80 complex subunit Arp8 in its ATP-bound form. Human Arp8 has several insertions in the conserved actin fold that explain its i...

journal_title：Nucleic acids research

authors： Gerhold CB,Winkler DD,Lakomek K,Seifert FU,Fenn S,Kessler B,Witte G,Luger K,Hopfner KP

更新日期：2012-11-01 00:00:00

abstract：:Oligodeoxyribonucleotides incorporating non-hydrolyzable dialkyl sulfide linked thymidine dimers (TsT) were synthesized chemically by the solid-phase approach. The sulfide dimer TsT was stable to degradation by snake-venom phosphodiesterase, calf spleen phosphodiesterase, Nuclease P1 and Nuclease S1. Thermal denaturat...

journal_title：Nucleic acids research

authors： Kawai SH,Wang D,Giannaris PA,Damha MJ,Just G

更新日期：1993-03-25 00:00:00

abstract：:Mutations in immunoglobulin µ-binding protein 2 (Ighmbp2) cause distal spinal muscular atrophy type 1 (DSMA1), an autosomal recessive disease that is clinically characterized by distal limb weakness and respiratory distress. However, despite extensive studies, the mechanism of disease-causing mutations remains elusive...

journal_title：Nucleic acids research

authors： Lim SC,Bowler MW,Lai TF,Song H

更新日期：2012-11-01 00:00:00