Abstract:
:A simple method, primer specific and mispair extension analysis (PSMEA) with pfu DNA polymerase was developed for genotyping. PSMEA is based on the unique properties of 3'-->5' exonuclease proofreading activity. In the presence of an incomplete set of dNTPs, pfu was found to be extremely discriminative in nucleotide incorporation and proofreading at the initiation step of DNA synthesis, completely preventing primer extension when mispair(s) are found adjacent to the 3'-end of the primer. This has allowed us to accurately detect nucleotide variations, deletions and insertions for fast genotyping.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Hu YW,Balaskas E,Kessler G,Issid C,Scully LJ,Murphy DG,Rinfret A,Giulivi A,Scalia V,Gill Pdoi
10.1093/nar/26.21.5013subject
Has Abstractpub_date
1998-11-01 00:00:00pages
5013-5issue
21eissn
0305-1048issn
1362-4962pii
gkb760journal_volume
26pub_type
杂志文章abstract::Highly regulated induction systems enabling dose-dependent and reversible fine-tuning of protein expression output are beneficial for engineering complex biosynthetic pathways. To address this, we developed PhiReX, a novel red/far-red light-regulated protein expression system for use in Saccharomyces cerevisiae. PhiRe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx610
更新日期:2017-09-06 00:00:00
abstract::A circular trans-acting ribozyme designed to adopt the motif of the hepatitis delta virus (HDV) trans-acting ribozyme was produced. The circular form was generated in vitro by splicing a modified group I intron precursor RNA in which the relative order of the 5' and 3' splice sites, flanking the single HDV-like ribozy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.18.4253
更新日期:1993-09-11 00:00:00
abstract::Multiple pathways counteract DNA replication stress to prevent genomic instability and tumorigenesis. The recently identified human SDE2 is a genome surveillance protein regulated by PCNA, a DNA clamp and processivity factor at replication forks. Here, we show that SDE2 cleavage after its ubiquitin-like domain generat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz054
更新日期:2019-05-07 00:00:00
abstract::The surface accessibility of macromolecules plays a key role in modulating molecular recognition events. RNA is a complex and dynamic molecule involved in many aspects of gene expression. However, there are few experimental methods available to measure the accessible surface of RNA. Here, we investigate the accessible...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1062
更新日期:2008-03-01 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
pub_type: 杂志文章
doi:10.1093/nar/gkh159
更新日期:2004-01-09 00:00:00
abstract::The mRNAs for different variant surface antigens of Trypanosoma brucei start with the same 35 nucleotides. This sequence is encoded by a separate mini-exon, located in a 1.35-kb repetitive element. We have reported that trypanosomes contain many transcripts that hybridize to mini-exon probes, even if they do not make ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.9.3777
更新日期:1984-05-11 00:00:00
abstract::Glutaminyl-tRNA synthetase from Deinococcus radiodurans possesses a C-terminal extension of 215 residues appending the anticodon-binding domain. This domain constitutes a paralog of the Yqey protein present in various organisms and part of it is present in the C-terminal end of the GatB subunit of GatCAB, a partner of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1164
更新日期:2007-01-01 00:00:00
abstract::The A site of the small ribosomal subunit participates in the fidelity of decoding by switching between two states, a resting 'off' state and an active decoding 'on' state. Eight crystal structures of RNA duplexes containing two minimal decoding A sites of the Homo sapiens mitochondrial wild-type, the A1555G mutant or...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn112
更新日期:2008-05-01 00:00:00
abstract::Assessment of the fidelity of gene expression is crucial to understand cell homeostasis. Here we present a highly sensitive method for the systematic Quantification of Rare Amino acid Substitutions (QRAS) using absolute quantification by targeted mass spectrometry after chromatographic enrichment of peptides with miss...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1319
更新日期:2019-04-08 00:00:00
abstract::The purine rich oligodeoxyribonucleotides 1C, d(ATGACGGAATA) and 2C, d(ATGAGCGAATA) alone exhibit highly cooperative melting transitions. Analysis of the concentration dependence of melting, and electrophoretic studies indicate that these oligomers can form an unusual purine rich offset double helix. The unusual duple...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.11.5137
更新日期:1988-06-10 00:00:00
abstract::Basic region-leucine zipper (B-ZIP) proteins are a class of dimeric sequence-specific DNA-binding proteins unique to eukaryotes. We have identified 67 B-ZIP proteins in the Arabidopsis thaliana genome. No A.thaliana B-ZIP domains are homologous with any Homo sapiens B-ZIP domains. Here, we predict the dimerization spe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh653
更新日期:2004-06-29 00:00:00
abstract::We have recently shown that phosphorothioate (PS) oligodeoxynucleotide (ODN) analogs, unlike their normal congeners, exhibit significant anti-HIV activity (Matsukura et al., (1987) Proc. Natl. Acad. Sci. USA 84, 7706-7710). We now report the syntheses, melting temperatures (Tm), and nuclease susceptibilities of a seri...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.8.3209
更新日期:1988-04-25 00:00:00
abstract::DNA methylation and chromatin DNaseI sensitivity were analyzed in and adjacent to D4Z4 repeat arrays, which consist of 1 to approximately 100 tandem 3.3-kb units at subtelomeric 4q and 10q. D4Z4 displayed hypomethylation in some cancers and hypermethylation in others relative to normal tissues. Surprisingly, in cancer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn055
更新日期:2008-04-01 00:00:00
abstract::Protein-DNA binding is a fundamental component of gene regulatory processes, but it is still not completely understood how proteins recognize their target sites in the genome. Besides hydrogen bonding in the major groove (base readout), proteins recognize minor-groove geometry using positively charged amino acids (sha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx915
更新日期:2017-12-01 00:00:00
abstract::In the haploid genome of Xenopus laevis there are two genes coding for the r-protein L14. It is not known if they are located on the same chromosome. cDNA clones deriving from the transcripts of the two genes have been isolated from an oocyte messenger cDNA bank showing that they are both expressed. We have studied th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.19.7633
更新日期:1986-10-10 00:00:00
abstract::Type I CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR-associated) systems exist in bacterial and archaeal organisms and provide immunity against foreign DNA. The Cas protein content of the DNA interference complexes (termed Cascade) varies between different CRISPR-Cas subtypes. A minima...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv882
更新日期:2015-10-15 00:00:00
abstract::We created a single cell sorting system to screen for enzyme activity in Escherichia coli producing 3,4 dihydroxy benzoate (34DHB). To do so, we engineered a transcription factor regulon controlling the expression of green fluorescent protein (GFP) for induction by 34DHB. An autoregulated transcription factor, pcaU, w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku444
更新日期:2014-07-01 00:00:00
abstract::With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; representing cellular processes or pathways is no exception. VISIBIOweb is a free, open-source, we...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq352
更新日期:2010-07-01 00:00:00
abstract::Modified bases, such as O6-methylguanines, are produced in cells exposed to alkylating agents and cause apoptosis. In human cells treated with N-methyl-N-nitrosourea, we detected a protein complex composed of MutSalpha, MutLalpha and PCNA on damaged DNA by immunoprecipitation method using chromatin extracts, in which ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki878
更新日期:2005-10-04 00:00:00
abstract::We have developed a new method for analysis of complex genetic systems by a combination of the Amplification Refractory Mutation System (ARMS) and Single-Strand Conformation Polymorphism (SSCP) analysis: ARMS-SSCP. Thus, a complex allelic series is subdivided into a number of groups by ARMS followed by the identificat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.5.1005
更新日期:1992-03-11 00:00:00
abstract::Cells continuously monitor protein synthesis to prevent accumulation of aberrant polypeptides. Insufficient capacity of cellular degradative systems, chaperone shortage or high levels of mistranslation by ribosomes can result in proteotoxic stress and endanger proteostasis. One of the least explored reasons for mistra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa068
更新日期:2020-04-17 00:00:00
abstract::NusG is an essential transcription factor that plays multiple key regulatory roles in transcription elongation, termination and coupling translation and transcription. The core role of NusG is to enhance transcription elongation and RNA polymerase processivity. Here, we present the structure of Escherichia coli RNA po...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1159
更新日期:2017-01-25 00:00:00
abstract::We have used DNase I footprinting to examine the association kinetics of GA-, GT- and CT-containing oligonucleotides with the target sequence (GGA)5GG. (CCT)5CC. These reactions are slow yielding bimolecular association rate constants between 50 and 2000 M-1s-1. We find that GT-containing oligonucleotides bind much fa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.16.3269
更新日期:1997-08-15 00:00:00
abstract::The human lymphoid cell lines Walker and Daudi constitute a particularly suitable system for studies on the chromatin structure of K light chain genes (see preceding paper). The rearranged and non-rearranged alleles of Walker cells were found to be about equally sensitive towards digestion with DNAase I. A DNAase I hy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.18.7007
更新日期:1984-09-25 00:00:00
abstract::Transposable elements (TEs) comprise a large proportion of long non-coding RNAs (lncRNAs). Here, we employed CRISPR to delete a short interspersed nuclear element (SINE) in Malat1, a cancer-associated lncRNA, to investigate its significance in cellular physiology. We show that Malat1 with a SINE deletion forms diffuse...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1176
更新日期:2020-03-18 00:00:00
abstract::We have modeled local DNA sequence parameters to search for DNA architectural motifs involved in transcription regulation and promotion within the Xenopus laevis ribosomal gene promoter and the intergenic spacer (IGS) sequences. The IGS was found to be shaped into distinct topological domains. First, intrinsic bends s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.18.3433
更新日期:2000-09-15 00:00:00
abstract::TORQUE is a tool for cross-species querying of protein-protein interaction networks. It aims to answer the following question: given a set of proteins constituting a known complex or a pathway in one species, can a similar complex or pathway be found in the protein network of another species? To this end, Torque seeks...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp474
更新日期:2009-07-01 00:00:00
abstract::As large-scale re-sequencing of genomes reveals many protein mutations, especially in human cancer tissues, prediction of their likely functional impact becomes important practical goal. Here, we introduce a new functional impact score (FIS) for amino acid residue changes using evolutionary conservation patterns. The ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr407
更新日期:2011-09-01 00:00:00
abstract::Hybridization solutions containing chaotropes may be used to modulate the thermal stability (Tm or Td) of oligodeoxynucleotide (ODN) duplexes or hybrids over a 90 degrees C range. Modulation of Td allows formulation of hybridization solutions that permit ambient temperature hybridization using most combinations of pro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.19.5143
更新日期:1991-10-11 00:00:00
abstract::Advances in genomic sequencing have enormous potential to revolutionize personalized medicine, however distinguishing disease-causing from benign variants remains a challenge. The increasing number of human genome and exome sequences available has revealed areas where unfavourable variation is removed through purifyin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz457
更新日期:2019-07-02 00:00:00