Abstract:
:A mathematical model and a computer simulation were used to study PCR specificity. The model describes the occurrences of non-targeted PCR products formed through random primer-template interactions. The PCR simulation scans DNA sequence databases with primers pairs. According to the model prediction, PCR with complex templates should rarely yield non-targeted products under typical reaction conditions. This is surprising as such products are often amplified in real PCR under conditions optimized for stringency. The causes for this 'PCR paradox' were investigated by comparing the model predictions with simulation results. We found that deviations from randomness in sequences from real genomes could not explain the frequent occurrence of non-targeted products in real PCR. The most likely explanation to the 'PCR paradox' is a relatively high tolerance of PCR to mismatches. The model also predicts that mismatch tolerance has the strongest effect on the number of non-targeted products, followed by primer length, template size and product size limit. The model and the simulation can be utilized for PCR studies, primer design and probing DNA uniqueness and randomness.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Rubin E,Levy AAdoi
10.1093/nar/24.18.3538subject
Has Abstractpub_date
1996-09-15 00:00:00pages
3538-45issue
18eissn
0305-1048issn
1362-4962pii
6s0313journal_volume
24pub_type
杂志文章abstract::The histone methyl transferase Suv39H1 is involved in silencing by pericentric heterochromatin. It specifically methylates K9 of histone H3, thereby creating a high affinity binding site for HP1 proteins. We and others have shown recently that it is also involved in transcriptional repression by the retinoblastoma pro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.2.475
更新日期:2002-01-15 00:00:00
abstract::For the isolation of single stranded plasmid DNA, various E. coli and E. coli-Streptomyces shuttle plasmids were equipped with the phage f1 replication origin. The transformation of some representative Streptomyces species with plasmid vectors occurred irrespective of whether single or double stranded DNA was used. In...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.4.727
更新日期:1991-02-25 00:00:00
abstract::The effect of amino groups attached at positions 2 and 8 of the hypoxanthine moiety in the structure, reactivity and stability of DNA duplexes and triplexes is studied by means of quantum mechanical calculations, as well as extended molecular dynamics (MD) and thermodynamic integration (MD/TI) simulations. Theoretical...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.12.2522
更新日期:2001-06-15 00:00:00
abstract::KRAS is one of the most mutated genes in human cancer. It is controlled by a G4 motif located upstream of the transcription start site. In this paper, we demonstrate that 8-oxoguanine (8-oxoG), being more abundant in G4 than in non-G4 regions, is a new player in the regulation of this oncogene. We designed oligonucleo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1142
更新日期:2018-01-25 00:00:00
abstract::Many infectious diseases are caused by viral infections, and in particular by RNA viruses such as MERS, Ebola and Zika. To understand viral disease, detection and identification of these viruses are essential. Although PCR is widely used for rapid virus identification due to its low cost and high sensitivity and speci...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1095
更新日期:2017-01-04 00:00:00
abstract::Zar1 was one of the earliest mammalian maternal-effect genes to be identified. Embryos derived from Zar1-null female mice are blocked before zygotic genome activation; however, the underlying mechanism remains unclear. By knocking out Zar1 and its homolog Zar2 in mice, we revealed a novel function of these genes in oo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz863
更新日期:2019-12-02 00:00:00
abstract::Extracts of the human glioma cell line A1235 (lacking O(6)-methylguanine-DNA methyltransferase) are known to restore a G:T mismatch to a normal G:C pair in a G:T-containing model (45 bp) DNA substrate. Herein we demonstrate that substitution of G:T with O(6)-methylguanine:T (m6G:T) results in extract-induced intra-str...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.11.2409
更新日期:2001-06-01 00:00:00
abstract::The chicken erythroid proteins binding to the histone H5 5' promoter and 3' erythroid-specific enhancer regions were identified. In DNase I footprinting and gel mobility shift experiments with immature adult erythrocyte nuclear extracts, we have demonstrated the binding of proteins to the GC-box, a high affinity Sp1 b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.23.6385
更新日期:1992-12-11 00:00:00
abstract::The somatic V(D)J recombination for the assembly of the Ig and TCR genes is mediated by the recombination signal sequences (Rss) and the V(D)J recombinase. A cDNA clone was isolated from a lambda gt11 expression library made from mouse thymocyte poly(A)+ RNA, using the Rss as a ligand. The deduced amino acid sequence ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.22.5067
更新日期:1993-11-11 00:00:00
abstract::The Mouse Genome Database (MGD) (http://www.informatics.jax.org) one component of a community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understanding human biology. MGD strives to provide an extensively integrated information resource with experimental d...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg047
更新日期:2003-01-01 00:00:00
abstract::The nucleobase modification 5-methylcytosine (m(5)C) is widespread both in DNA and different cellular RNAs. The functions and enzymatic mechanisms of DNA m(5)C-methylation were extensively studied during the last decades. However, the location, the mechanism of formation and the cellular function(s) of the same modifi...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkp1117
更新日期:2010-03-01 00:00:00
abstract::Because of their high nucleotide sequence homology, the specific detection of mRNA transcripts of individual members of a gene family presents certain problems. Here we apply and defend the single nucleotide primer extension (SNuPE) as a simple, specific, and highly quantitative assay for this purpose. The method dist...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.23.4812
更新日期:1996-12-01 00:00:00
abstract::We examined the mechanism regulating the cellular levels of PNKP, the major kinase/phosphatase involved in the repair of oxidative DNA damage, and find that it is controlled by ATM phosphorylation and ubiquitylation-dependent proteasomal degradation. We discovered that ATM-dependent phosphorylation of PNKP at serines ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks909
更新日期:2012-12-01 00:00:00
abstract::The human 5S rRNA genes are found in clusters of tandem repeated units. We have cloned and partially characterized six restriction fragments from two clusters of 2.3 kb and 1.6 kb repeats, respectively. Four fragments from the cluster of 2.3 kb repeats contain a 5S rRNA gene and one fragment contains a gene variant wi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.15.4147
更新日期:1991-08-11 00:00:00
abstract::The oligomerization state and mode of binding to DNA of the GIY-YIG endonuclease II (EndoII) from bacteriophage T4 was studied using gel filtration and electrophoretic mobility shift assays with a set of mutants previously found to have altered enzyme activity. At low enzyme/DNA ratios all mutants except one bound to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp652
更新日期:2009-10-01 00:00:00
abstract::Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and appli...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky356
更新日期:2018-07-02 00:00:00
abstract::Virulence factor database (VFDB) was set up in 2004 dedicated for providing current knowledge of virulence factors (VFs) from various medical significant bacterial pathogens to facilitate pathogenomic research. Nowadays, complete genome sequences of almost all the major pathogenic microbes have been determined, which ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm951
更新日期:2008-01-01 00:00:00
abstract::Cyclic AMP response element binding protein (CREB) activates transcription of cAMP response element (CRE)-containing promoters following an elevation of intracellular cAMP. Here we show that CREB and the highly related protein ATF-1 are also potent transcription inhibitors. Strikingly, CREB inhibits transcription of m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.12.2907
更新日期:1993-06-25 00:00:00
abstract::Infection of cultured cells with herpes simplex virus (HSV) results in the transcriptional induction of a small number of cellular genes. Although the majority of such genes are dependent upon viral protein synthesis for their induction, a small minority are not. These genes are induced by events occurring prior to th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.23.9261
更新日期:1986-12-09 00:00:00
abstract::The complete DNA sequence of pO157, the large virulence plasmid of EHEC strain O157:H7 EDL 933, is presented. The 92 kb F-like plasmid is composed of segments of putative virulence genes in a framework of replication and maintenance regions, with seven insertion sequence elements, located mostly at the boundaries of t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.18.4196
更新日期:1998-09-15 00:00:00
abstract::Proteins interacting with pre-mRNAs during early stages of spliceosome formation in a HeLa nuclear extract were investigated by photochemical RNA-protein crosslinking. The level of protein crosslinking to a beta-globin pre-mRNA was positively correlated with the presence of an intron. Proteins of 110,000, 59,000 and 3...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.11.3307
更新日期:1990-06-11 00:00:00
abstract::The three dimensional crystal structure of T5 5'-3' exonuclease was compared with that of two other members of the 5'-3' exonuclease family: T4 ribonuclease H and the N-terminal domain of Thermus aquaticus DNA polymerase I. Though these structures were largely similar, some regions of these enzymes show evidence of si...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.21.4224
更新日期:1997-11-01 00:00:00
abstract::In many eukaryotic mRNAs one or more short 'upstream' open reading frames, uORFs, precede the initiator of the main coding sequence. Upstream ORFs are functionally diverse as illustrated by their variety of features in polyamine pathway biosynthetic mRNAs. Their propensity to act as sensors for regulatory circuits and...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkp1037
更新日期:2010-01-01 00:00:00
abstract::In order to investigate the possible role of RNA secondary structure in determining the efficiency and specificity of mRNA splicing, the structures of sequences at three acceptor splice sites in adenovirus were studied. Transcripts spanning intron-exon junctions were synthesized using SP6 RNA polymerase and analyzed u...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.22.8437
更新日期:1984-11-26 00:00:00
abstract::We identify a new subgroup of Type I Restriction-Modification enzymes that modify cytosine in one DNA strand and adenine in the opposite strand for host protection. Recognition specificity has been determined for ten systems using SMRT sequencing and each recognizes a novel DNA sequence motif. Previously characterized...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw743
更新日期:2016-11-02 00:00:00
abstract::Increasing evidence indicates that active DNA demethylation is involved in several processes in mammals, resulting in developmental stage-specificity and cell lineage-specificity. The recently discovered Ten-Eleven Translocation (TET) dioxygenases are accepted to be involved in DNA demethylation by initiating 5-mC oxi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1019
更新日期:2014-02-01 00:00:00
abstract::EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and-a new addition-its transport proteins. MetaCyc is a new metabolic-pathway database that describes pathways and enzymes of many different organisms, with a microbial...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.1.56
更新日期:2000-01-01 00:00:00
abstract::LOCtarget is a web server and database that predicts and annotates sub-cellular localization for structural genomics targets; LOCnet is one of the methods used in LOCtarget that can predict sub-cellular localization for all eukaryotic and prokaryotic proteins. Targets are taken from the central registration database f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh441
更新日期:2004-07-01 00:00:00
abstract::The reaction of fluorescamine with primary amino groups of tRNAs was investigated. The reagent was attached under mild conditions to the 3'-end of tRNAPhe-C-C-A(3'NH) from yeast and to the minor nucleoside x in E. coli tRNAArg, tRNALys, tRNAMet, tRNAIle and tRNAPhe. The primary aliphatic amino groups of these tRNAs re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.12.4837
更新日期:1978-12-01 00:00:00
abstract::Recombinase proteins assembled into helical filaments on DNA are believed to be the catalytic core of homologous recombination. The assembly, disassembly and dynamic rearrangements of this structure must drive the DNA strand exchange reactions of homologous recombination. The sensitivity of eukaryotic recombinase acti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki640
更新日期:2005-06-08 00:00:00