Abstract:
:The thermodynamics of 13 hybridization reactions between 10 base DNA sequences of design 5'-ATGCXYATGC-3' with X, Y = A, C, G, T and their complementary PNA and DNA sequences were determined from isothermal titration calorimetry (ITC) measurements at ambient temperature. For the PNA/DNA hybridization reactions, the binding constants range from 1.8 x 10(6)M(-1)for PNA(TT)/DNA to 4.15 x 10(7)M(-1)for PNA(GA)/DNA and the binding enthalpies range from -194 kJ mol(-1)for PNA(CG)/DNA to -77 kJ mol(-1)for PNA(GT)/DNA. For the corresponding DNA/DNA binding reactions, the binding constants range from 2.9 x 10(5)M(-1)for DNA(GT)/DNA to 1.9 x 10(7)M(-1)for DNA(CC)/DNA and the binding enthalpies range from -223 kJ mol(-1)for DNA(CG)/DNA to -124 kJ mol(-1)for DNA(TT)/DNA. Most of the PNA sequences exhibited tighter binding affinities than their corresponding DNA sequences resulting from smaller entropy changes in the PNA/DNA hybridization reactions. van't Hoff enthalpies and extrapolated Delta G values determined from UV melting studies on the duplexes exhibited closer agreement with the ITC binding enthalpies and Delta G values for the DNA/DNA duplexes than for the PNA/DNA duplexes.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Schwarz FP,Robinson S,Butler JMdoi
10.1093/nar/27.24.4792keywords:
subject
Has Abstractpub_date
1999-12-15 00:00:00pages
4792-800issue
24eissn
0305-1048issn
1362-4962pii
gkc688journal_volume
27pub_type
杂志文章abstract::The sequential arrangement of histones along DNA in nucleosome core particles was determined between 0.5 and 600 mM salt and from 0 to 8 M urea. These concentrations of salt and urea up to 6 M had no significant effect on the linear order of histones along DNA but 8 M urea caused the rearrangement of histones. Conform...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.5.1053
更新日期:1981-03-11 00:00:00
abstract::Exon trapping is a method to functionally clone expressed sequences from genomic DNA. We have previously developed the vector system pETV-SD2, which contains only a splice donor site (SD) followed by a LacZ gene, allowing trapping of internal exons of human genes by blue-white selection. We now describe the adaptation...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.20.4148
更新日期:1994-10-11 00:00:00
abstract::We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a ph...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx147
更新日期:2017-05-05 00:00:00
abstract::Spirochetes of the genus Borrelia include the tick-transmitted causative agents of Lyme disease and relapsing fever. They possess unusual genomes composed mainly of linear replicons terminated by closed DNA hairpin telomeres. Hairpin telomeres present an uninterrupted DNA chain to the replication machinery overcoming ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt832
更新日期:2013-12-01 00:00:00
abstract::The discovery of hydroxymethyl-, formyl- and carboxylcytosine, generated through oxidation of methylcytosine by TET dioxygenases, raised the question how these modifications contribute to epigenetic regulation. As they are subjected to complex regulation in vivo, we dissected links to gene expression with in vitro mod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku552
更新日期:2014-07-01 00:00:00
abstract::Genome-wide association studies (GWAS) have become a preferred method to identify new genetic susceptibility loci. This technique aims to understanding the molecular etiology of common diseases, but in many cases, it has led to the identification of loci with no obvious biological relevance. Herein, we show that previ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks169
更新日期:2012-06-01 00:00:00
abstract::Dnmt3a and Dnmt3b are paralogous enzymes responsible for de novo DNA methylation but with distinguished biological functions. In mice, disruption of Dnmt3b but not Dnmt3a causes global DNA hypomethylation, especially in repetitive sequences, which comprise the large majority of methylated DNA in the genome. By measuri...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq456
更新日期:2010-10-01 00:00:00
abstract::The alpha/beta-hydrolase fold is characterized by a beta-sheet core of five to eight strands connected by alpha-helices to form a alpha/beta/alpha sandwich. In most of the family members the beta-strands are parallels, but some show an inversion in the order of the first strands, resulting in antiparallel orientation....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh141
更新日期:2004-01-01 00:00:00
abstract::The U1 snRNP-specific 70K protein is one of the few snRNP proteins from higher eukaryotic cells that is phosphorylated in vivo (1,2). Immunoaffinity purified spliceosomal snRNPs (U1, U2, U5, and U4/U6) were tested for their ability to phosphorylate in vitro the U1-specific 70K protein. An snRNP-associated kinase activ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.12.2815
更新日期:1993-06-25 00:00:00
abstract::Three-dimensional structures have been solved for several naturally occurring RNA triple helices, although all are limited to six or fewer consecutive base triples, hindering accurate estimation of global and local structural parameters. We present an X-ray crystal structure of a right-handed, U•A-U-rich RNA triple he...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1222
更新日期:2020-04-06 00:00:00
abstract::Several authors have suggested or inferred that modest changes in microRNA expression can potentiate or impinge on their capacity to mediate gene repression, and that doing so could play a significant role in diseases. Such interpretations are based on several assumptions, namely: (i) changes in microRNA expression co...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv720
更新日期:2015-09-03 00:00:00
abstract::Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-transla...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1229
更新日期:2013-01-01 00:00:00
abstract::The log kobs vs. pH profiles were determined in the intermediate acidity region for the glycosyl hydrolysis of guanosine and its 8-amino, 8-monomethylamino, 8-dimethylamino and 8-bromo derivatives. The decreased rate of the 8-amino and enhanced rate of the 8-bromo compound compared to guanosine support an A type mecha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.3.697
更新日期:1977-03-01 00:00:00
abstract::Two different genomic genes for the COUP-transcription factor, COUP-TF I and COUP-TF II, have been isolated from a human cosmid genomic library using a [32P]-labeled cDNA probe. Data obtained from Southern blot analysis of these cosmid clones indicated that two closely related genes exist in the human genome and have ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.23.6857
更新日期:1990-12-11 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
pub_type: 杂志文章
doi:10.1093/nar/gks619
更新日期:2012-09-01 00:00:00
abstract::A role for BRCA1 in the direct and indirect regulation of transcription is well established. However, a comprehensive view of the degree to which BRCA1 impacts transcriptional regulation on a genome-wide level has not been defined. We performed genome-wide expression profiling and ChIP-chip analysis, comparison of whi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr679
更新日期:2011-12-01 00:00:00
abstract::A tetradecanucleotide U-A-G-C(U-C-G)2G-G-C-Up corresponding to bases 21-34 of a nascent sequence of formylmethionyl tRNA of E. coli has been synthesized by the joining of two combinations of chemically synthesized oligonucleotides: 1) U-A-G-C + U-C-G-U-C-G + G-G-C-Up and 2) U-A-G-C + U-C-G-U + C-G-G-G-C-Up. In reactio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.17.3909
更新日期:1980-09-11 00:00:00
abstract::Defined DNA substrates containing discrete abasic sites or paired abasic sites set 1, 3, 5 and 7 bases apart on opposite strands were constructed to examine the reactivity of S1, mung bean and P1 nucleases towards abasic sites. None of the enzymes acted on the substrate containing discrete abasic sites. Under conditio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.19.3805
更新日期:1995-10-11 00:00:00
abstract::BioModels Database (http://www.ebi.ac.uk/biomodels/), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to the reference publication and gives the proper...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj092
更新日期:2006-01-01 00:00:00
abstract::Tight cell-cycle regulation of the histone H4-K20 methyltransferase PR-Set7 is essential for the maintenance of genome integrity. In mammals, this mainly involves the interaction of PR-Set7 with the replication factor PCNA, which triggers the degradation of the enzyme by the CRL4CDT2 E3 ubiquitin ligase. PR-Set7 is al...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky034
更新日期:2018-04-06 00:00:00
abstract::Galahad (https://galahad.esat.kuleuven.be) is a web-based application for analysis of drug effects. It provides an intuitive interface to be used by anybody interested in leveraging microarray data to gain insights into the pharmacological effects of a drug, mainly identification of candidate targets, elucidation of m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv436
更新日期:2015-07-01 00:00:00
abstract::This work presents a neutral filter elution method for detecting DNA double strand breaks in mouse L1210 cells after X-ray. The assay will detect the number of double strand breaks induced by as little as 1000 rad of X-ray. The rate of DNA elution through the filters under neutral conditions increases with X-ray dose....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.3.793
更新日期:1979-10-10 00:00:00
abstract::A computer program, BRUCE, was developed for the identification of transfer-messenger RNA (tmRNA) genes. The program employs heuristic algorithms to search for a tRNA(Ala)-like secondary structure surrounding a short sequence encoding the tag peptide. In the 57 completely sequenced bacterial genomes where tmRNA genes ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf459
更新日期:2002-08-01 00:00:00
abstract::The X chromosome-linked inhibitor of apoptosis protein (XIAP) is the most potent intrinsic caspase inhibitor and plays an important role in the maintenance of intestinal epithelial integrity. The RNA binding protein, HuR, regulates the stability and translation of many target transcripts. Here, we report that HuR asso...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp755
更新日期:2009-12-01 00:00:00
abstract::M13 RF IV DNA may be prepared in vitro to contain phosphorothioate-modified internucleotidic linkages in the (-)strand only. Certain restriction enzymes react with this modified DNA to hydrolyze the (+)strand exclusively when a phosphorothioate linkage occurs at the normal cleavage point in the (-)strand. The reaction...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.24.8765
更新日期:1985-12-20 00:00:00
abstract::Chromatin core particles near physiological ionic strength undergo a reversible transition induced by changes in pH near neutrality. While sedimentation studies indicate no significant effect on size or shape, changes in tyrosine fluorescence anisotropy and in circular dichroism suggest a somewhat looser structure at ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.10.4351
更新日期:1984-05-25 00:00:00
abstract::The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC). d(GCTTCTCTTC) has been solved and refined at 2.5 A resolution. The refinement procedure converged at R = 0.181 for all reflections in the range 20.0-2.5 A. In the crystal, the RNA/DNA hybrid duplex has an A' conformation with all but one of the nucleotide suga...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.2.555
更新日期:1999-01-15 00:00:00
abstract::We have previously identified a T lymphocyte protein which binds to a site within the LTR of the human immunodeficiency virus type 1 (HIV-1) and exerts an inhibitory effect on virus gene expression. The palindromic site (site B) recognized by this protein is related to the palindromic binding sites of members of the s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.20.5429
更新日期:1992-10-25 00:00:00
abstract::Influenza A virus (IAV) genomes are composed of eight single-stranded RNA segments that are coated by viral nucleoprotein (NP) molecules. Classically, the interaction between NP and viral RNA (vRNA) is depicted as a uniform pattern of 'beads on a string'. Using high-throughput sequencing of RNA isolated by crosslinkin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx584
更新日期:2017-09-06 00:00:00
abstract::7SK snRNA, an abundant RNA discovered in human nucleus, regulates transcription by RNA polymerase II (RNAPII). It sequesters and inhibits the transcription elongation factor P-TEFb which, by phosphorylation of RNAPII, switches transcription from initiation to processive elongation and relieves pauses of transcription....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq660
更新日期:2010-11-01 00:00:00