Abstract:
:Melting of DNA in a segment bounded at both ends by regions of greater stability during electrophoresis in denaturing gradient gels show complex properties, not accommodated with standard melting theory. Compact bands of some DNA molecules become anomalously broadened at the retardation level in a denaturing gradient, or double bands may appear in a uniform denaturant concentration. These properties are associated only with molecules for which the distribution of stability calculated by the Poland-Fixman-Freire algorithms indicates that the region of lowest stability does not extend to an end of the molecule. Retention of helicity at the ends is shown by the difference in the effect of base substitution in the end domains and in the least stable domain. Both the appearance of double bands and band broadening can be explained by invoking a hypothetical metastable intermediate in melting, which is converted into the equilibrium melted form at a relatively slow rate, depending on both denaturant concentration and field strength. A kinetic model permits plausible rate constants to be inferred from the patterns. Despite the increased band width, sequence variants with base changes in the least stable domain result in readily detectable band shifts in the gradient.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Abrams ES,Murdaugh SE,Lerman LSdoi
10.1093/nar/23.14.2775subject
Has Abstractpub_date
1995-07-25 00:00:00pages
2775-83issue
14eissn
0305-1048issn
1362-4962pii
5j0127journal_volume
23pub_type
杂志文章abstract::The Mouse Genome Database (MGD) (http://www.informatics.jax.org) is the community model organism database resource for the laboratory mouse, a premier animal model for the study of genetic and genomic systems relevant to human biology and disease. MGD maintains a comprehensive catalog of genes, functional RNAs and oth...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1225
更新日期:2014-01-01 00:00:00
abstract::The mRNA export complex TREX (TREX) is known to contain Aly, UAP56, Tex1 and the THO complex, among which UAP56 is required for TREX assembly. Here, we systematically investigated the role of each human TREX component in TREX assembly and its association with the mRNA. We found that Tex1 is essentially a subunit of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1188
更新日期:2013-01-01 00:00:00
abstract::In plant organelles, RNA editing alters specific cytidine residues to uridine in transcripts. All of the site-specificity factors of RNA editing identified so far are pentatricopeptide repeat (PPR) proteins. A defect in a specific PPR protein often impairs RNA editing at multiple sites, at which the cis-acting element...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks164
更新日期:2012-06-01 00:00:00
abstract::Peptide nucleic acids (PNAs) can bind to homopurine/homopyrimidine sequences of double-stranded DNA targets in a sequence-specific manner and form [PNA]2/DNA triplexes with single-stranded DNA D-loop structures at the PNA binding sites. These D-loop structures have been found to have a capacity to initiate transcripti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.13.2806
更新日期:1999-07-01 00:00:00
abstract::Aberrant DNA methylation at CpG dinucleotides can result in epigenetic silencing of tumour suppressor genes and represents one of the earliest events in tumourigenesis. To date, however, high-throughput tools that are capable of surveying the methylation status of multiple gene promoters have been restricted to a limi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni072
更新日期:2005-04-28 00:00:00
abstract::Comparative genome hybridization (CGH) to DNA microarrays (array CGH) is a technique capable of detecting deletions and duplications in genomes at high resolution. However, array CGH studies of the human genome noting false negative and false positive results using large insert clones as probes have raised important c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki643
更新日期:2005-06-16 00:00:00
abstract::The deoxyoctanucleotide 5'd (AAGGAGGT) which is complementary to the 3' terminus of 16S RNA has been used as a probe to measure the potential of this rRNA region to engage in intermolecular basepairing. The site specific binding of the octanucleotide is shown by labeling 16S RNA in situ at its 3' end with [32P]pCp and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.6.1425
更新日期:1981-03-25 00:00:00
abstract::For the rapid and sensitive detection of p53 'hot spot' mutations, we combined polymerase chain reaction based single-strand conformational polymorphism (PCR-SSCP) analysis with sequence specific-clamping by peptide nucleic acids (PNAs) in a one-step reaction tube protocol. For this purpose, we designed two PNA molecu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.5.1356
更新日期:1998-03-01 00:00:00
abstract::Recent rapid advances in next generation RNA sequencing (RNA-Seq)-based provide researchers with unprecedentedly large data sets and open new perspectives in transcriptomics. Furthermore, RNA-Seq-based transcript profiling can be applied to non-model and newly discovered organisms because it does not require a predefi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks540
更新日期:2012-07-01 00:00:00
abstract::Elongation factor P (EF-P) is a conserved ribosome-binding protein that structurally mimics tRNA to enable the synthesis of peptides containing motifs that otherwise would induce translational stalling, including polyproline. In many bacteria, EF-P function requires post-translational modification with (R)-β-lysine by...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1296
更新日期:2014-03-01 00:00:00
abstract::A method is presented for the purification of mRNAs and the identification of structural gene sequences in recombinant DNA molecules. RNA is hybridized to double-stranded linear DNA such that R-loops are formed between most DNAs and their complementary RNA sequences. These R-loops are purified from unhybridized RNAs b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.7.2483
更新日期:1979-06-11 00:00:00
abstract::DNA polymerase gamma from purified nuclei of EMT-6 cells (mice) seems to be identical to the mitochondrial DNA polymerase from the same source following several criteria. These two enzyme activities are strongly inhibited by ethidium bromide and acriflavin, while proflavin, acridine orange, daunomycin and chloroquine ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.6.2197
更新日期:1978-06-01 00:00:00
abstract::DIAL (dihedral alignment) is a web server that provides public access to a new dynamic programming algorithm for pairwise 3D structural alignment of RNA. DIAL achieves quadratic time by performing an alignment that accounts for (i) pseudo-dihedral and/or dihedral angle similarity, (ii) nucleotide sequence similarity a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm334
更新日期:2007-07-01 00:00:00
abstract::Motor proteins that translocate on nucleic acids are key players in gene expression and maintenance. While the function of these proteins is diverse, they are driven by highly conserved core motor domains. In transcription-coupled DNA repair, motor activity serves to remove RNA polymerase stalled on damaged DNA, makin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp680
更新日期:2009-10-01 00:00:00
abstract::Ribosomal DNA (rDNA) from Xenopus laevis contains several heterogeneities in all three transcribed spacers, as revealed by analysis of cloned and uncloned amplified rDNA from oocytes and cloned chromosomal rDNA from erythrocytes. Heterogeneities include single base changes and length variants of one to several nucleot...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.3.629
更新日期:1983-02-11 00:00:00
abstract::A growing number of whole genome sequencing projects, in combination with development of phylogenetic methods for reconstructing gene evolution, have provided us with a window into genomes that existed millions, and even billions, of years ago. Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1009
更新日期:2019-01-08 00:00:00
abstract::In order to characterize structure-function relationships, the kinetic behavior of chimeric RNA/DNA ribozyme was compared with that of all RNA ribozyme. Determined kcat values were proven to represent the chemical-cleavage step and not the product-dissociation step. In agreement with the finding by Dahm and Uhlenbeck ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.24.5656
更新日期:1993-12-11 00:00:00
abstract::Single-nucleotide variation and gene expression of disease samples represent important resources for biomarker discovery. Many databases have been built to host and make available such data to the community, but these databases are frequently limited in scope and/or content. BioMuta, a database of cancer-associated si...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx907
更新日期:2018-01-04 00:00:00
abstract::Unmethylated CpG rich islands are a feature of vertebrate DNA: they are associated with housekeeping and many tissue specific genes. CpG islands on the active X chromosome of mammals are also unmethylated. However, islands on the inactive X chromosome are heavily methylated. We have identified a CpG island in the 5' r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.20.9527
更新日期:1988-10-25 00:00:00
abstract::The principal early promoter of human papillomaviruses (HPVs), designated P97 in the case of HPV-16, contains four characteristically aligned cis-responsive elements, namely one binding site for Sp1, two for the viral E2 proteins, and the TATA box. The Sp1 binding site is needed to mediate activation of P97 by the rem...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.2.251
更新日期:1992-01-25 00:00:00
abstract::Hepatitis B virus (HBV) replication is initiated by HBV RT binding to the highly conserved encapsidation signal, epsilon, at the 5' end of the RNA pregenome. Epsilon contains an apical stem-loop, whose residues are either totally conserved or show rare non-disruptive mutations. Here we present the structure of the api...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl582
更新日期:2006-01-01 00:00:00
abstract::The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a premier public resource for literature-based, manually curated associations between chemicals, gene products, phenotypes, diseases, and environmental exposures. In this biennial update, we present our new chemical-phenotype module that codes chemi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky868
更新日期:2019-01-08 00:00:00
abstract::Ten transgenic mouse lines harboring the -346/-103 fragment of the rat insulin I enhancer linked to a heterologous promoter and a reporter gene (Eins-Ptk-CAT construct) were produced. Expression of the hybrid transgene was essentially observed in pancreas and to a lesser extent in brain. These results indicate that th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.18.4925
更新日期:1991-09-25 00:00:00
abstract::Nucleic acid triplexes may regulate many important biological processes. Persistent accumulation of the oncogenic 7-kb long noncoding RNA MALAT1 is dependent on an unusually long intramolecular triple helix. This triplex structure is positioned within a conserved ENE (element for nuclear expression) motif at the lncRN...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1171
更新日期:2019-02-20 00:00:00
abstract::The newest genomic advances have uncovered an unprecedented degree of structural variation throughout genomes, with great amounts of data accumulating rapidly. Here we introduce InvFEST (http://invfestdb.uab.cat), a database combining multiple sources of information to generate a complete catalogue of non-redundant hu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1122
更新日期:2014-01-01 00:00:00
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
pub_type: 杂志文章
doi:10.1093/nar/gkw447
更新日期:2016-08-19 00:00:00
abstract::The direction of replication of DNA within replicons of Physarum polycephalum was studied by pulse-labelling with 5-bromouracil-deoxyriboside (BrdUrd) and 3H-adenosine deoxyriboside (dAdo), followed by ultraviolet- (UV) -photolysis and analysis of molecular weights of single strand DNA fragments on alkaline sucrose gr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.3.713
更新日期:1978-03-01 00:00:00
abstract::DNA target recognizing domains of different multispecific DNA-cytosine-methyltransferases can be rearranged through engineering of the corresponding genes to generate enzymes with novel combinations of target recognition. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.14.6649
更新日期:1988-07-25 00:00:00
abstract::DNA primer sets, labeled with two fluorescent dyes to exploit fluorescence energy transfer (ET), can be efficiently excited with a single laser line and emit strong fluorescence at distinctive wavelengths. Such ET primers are superior to single fluorophore-labeled primers for DNA sequencing and other multiple color-ba...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.6.1144
更新日期:1996-03-15 00:00:00
abstract::A complete nucleotide sequence of human aldolase B mRNA was determined with a recombinant cDNA (pHABL120-3). The cDNA insert was composed of 1,652 bases excluding poly(A) tail and the sequence was consistent with the previous results reported by others. However, S1 nuclease mapping and subsequent genomic analysis allo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.14.5055
更新日期:1985-07-25 00:00:00