Abstract：
:Analysis of haplotypes is an important tool in population genetics, familial heredity and gene mapping. Determination of haplotypes of multiple single nucleotide polymorphisms (SNPs) or other simple mutations is time consuming and expensive when analyzing large populations, and often requires the help of computational and statistical procedures. Based on double PCR amplification of specific alleles, described previously, we have developed a simple, rapid and low-cost method for direct haplotyping of multiple SNPs and simple mutations found within relatively short specific regions or genes (micro-haplotypes). Using this method, it is possible to directly determine the physical linkage of multiple heterozygous alleles, by conducting a series of double allele-specific PCR amplification sets with simple analysis by gel electrophoresis. Application of the method requires prior information as to the sequence of the segment to be haplotyped, including the polymorphic sites. We applied the method to haplotyping of nine sites in the chicken HSP108 gene. One of the haplotypes in the population apparently arose by recombination between two existing haplotypes, and we were able to locate the point of recombination within a segment of 19 bp. We anticipate rapidly growing needs for SNP haplotyping in human (medical and pharmacogenetics), animal and plant genetics; in this context, the multiple double PCR amplifications of specific alleles (MD-PASA) method offers a useful haplotyping tool.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Eitan Y,Kashi Ydoi
10.1093/nar/gnf062keywords:
subject
Has Abstractpub_date
2002-06-15 00:00:00pages
e62issue
12eissn
0305-1048issn
1362-4962journal_volume
30pub_type
杂志文章abstract：:Major efforts are underway to elucidate the spatial distribution of ribosomal RNAs (rRNAs) in the ribosome. An especially informative approach is the identification of likely base-base tertiary interactions within the RNA by phylogenetic comparison. Herein evidence is presented for three heretofore unrecognized candid...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.6.2215
更新日期：1989-03-25 00:00:00
abstract：:Mutations in human mitochondrial DNA are often associated with incurable human neuromuscular diseases. Among these mutations, an important number have been identified in tRNA genes, including 29 in the gene MT-TL1 coding for the tRNA(Leu(UUR)). The m.3243A>G mutation was described as the major cause of the MELAS syndr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr546
更新日期：2011-10-01 00:00:00
abstract：:Dimerization of HIV-1 genomic RNA is an essential step of the viral cycle, initiated at a conserved stem-loop structure which forms a 'kissing complex' involving loop-loop interactions (dimerization initiation site, DIS). A 19mer RNA oligonucleotide (DIS-19) has been synthesized which forms a stable symmetrical dimer ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.15.3567
更新日期：1998-08-01 00:00:00
abstract：:We describe here the cloning, characterization and expression in E. coli of the gene coding for a DNA methylase from Spiroplasma sp. strain MQ1 (M.SssI). This enzyme methylates completely and exclusively CpG sequences. The Spiroplasma gene was transcribed in E. coli using its own promoter. Translation of the entire me...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.5.1145
更新日期：1990-03-11 00:00:00
abstract：:Twenty AdoMet-dependent methyltransferases (MTases) have been characterized structurally by X-ray crystallography and NMR. These include seven DNA MTases, five RNA MTases, four protein MTases and four small molecule MTases acting on the carbon, oxygen or nitrogen atoms of their substrates. The MTases share a common co...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/29.18.3784
更新日期：2001-09-15 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
pub_type： 杂志文章
doi：10.1093/nar/gky656
更新日期：2018-10-12 00:00:00
abstract：:Multiple sequence alignments play a central role in the annotation of novel genomes. Given the biological and computational complexity of this task, the automatic generation of high-quality alignments remains challenging. Since multiple alignments are usually employed at the very start of data analysis pipelines, it i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki1020
更新日期：2005-12-16 00:00:00
abstract：:A dnaB-like protein from P. aeruginosa was purified to near homogeneity using as an assay the immunoprecipitation by E. coli dnaB antiserum in a solid-phase. In the chromatographic characteristics including the affinity to immobilized ATP the dnaB-like protein of P. aeruginosa is similar to the dnaB protein of E. coli...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.2.385
更新日期：1987-01-26 00:00:00
abstract：:RNA sequencing has become an important method to perform hypothesis-free characterization of global gene expression. One of the limitations of RNA sequencing is that most sequence reads represent highly expressed transcripts, whereas low level transcripts are challenging to detect. To combine the benefits of tradition...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks816
更新日期：2013-01-07 00:00:00
abstract：:The chemical synthesis of backbone deuterium labelled [r(CGCGAAU*U*CGCG)]2 (U* = [5'-2H]U) is described. An efficient purification procedure was developed using a polymeric reverse phase (PRP) HPLC column at 60 degrees C. This procedure provided pure RNA dodecamer in the multi-milligram quantities (39% overall yield) ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.19.5131
更新日期：1992-10-11 00:00:00
abstract：:The DNA sequence of the spacer (plus flanking) regions separating the 16S rRNA and 23S rRNA genes of two presumptive rDNA operons of the archaebacterium Methanococcus vannielii was determined. The spacers are 156 and 242 base pairs in size and they share a sequence homology of 49 base pairs following the 3' terminus o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.21.7537
更新日期：1983-11-11 00:00:00
abstract：:We have investigated the distribution of mitochondrial DNA polymorphisms in a rare maternally transmitted genetic trait that causes hypersensitivity to aminoglycoside antibiotics, in the hope that a characterization of its molecular basis might provide a molecular and cellular understanding of aminoglycoside-induced d...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.18.4174
更新日期：1993-09-11 00:00:00
abstract：:The numerous genomic sequences and ESTs released by the Arabidopsis thaliana Genome Initiative (AGI) have allowed a systematic and functional study of the DEAD box RNA helicase family. Sequencing and in silico analysis led to the characterization of 28 novel A. thaliana DEAD box RNA helicases forming a family of 32 me...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.2.628
更新日期：1999-01-15 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
pub_type： 杂志文章
doi：10.1093/nar/gku463
更新日期：2014-07-01 00:00:00
abstract：:The EcoRV DNA-(adenine-N(6))-methyltransferase (M.EcoRV) specifically modifies the first adenine residue within GATATC sequences. During catalysis, the enzyme flips its target base out of the DNA helix and binds it into a target base binding pocket which is formed in part by Lys16 and Tyr196. A cytosine residue is acc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.15.3137
更新日期：2001-08-01 00:00:00
abstract：:In flowering plants, RNA editing is a posttranscriptional process that converts specific C to U in organelle mRNAs. Nicotiana tabacum is an allotetraploid species derived from the progenitors of Nicotiana sylvestris and Nicotiana tomentosiformis. These Nicotiana species have been used as a model for understanding the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn629
更新日期：2008-11-01 00:00:00
abstract：:The identification and characterization of binding sites of DNA-binding molecules, including transcription factors (TFs), is a critical problem at the interface of chemistry, biology and molecular medicine. The Cognate Site Identification (CSI) array is a high-throughput microarray platform for measuring comprehensive...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn057
更新日期：2008-06-01 00:00:00
abstract：:Clustered damages are formed in DNA by ionising radiation and radiomimetic anticancer agents and are thought to be biologically severe. 7,8-dihydro-8-oxoguanine (8-oxoG), a major DNA damage resulting from oxidative attack, is highly mutagenic leading to a high level of G.C-->T.A transversions if not previously excised...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.5.1107
更新日期：2001-03-01 00:00:00
abstract：:Adaptation of eucaryotic cDNA to heterologous expression was studied by mutating the translation initiation (TI) region upstream (mTI) and downstream (MTI) of the start codon. In the mTI subregion the 8 bases flanking the invariant Shine-Dalgarno motif GG-AG were mutagenized exhaustively, while the MTI subregion was s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.12.3127
更新日期：1992-06-25 00:00:00
abstract：:Ditercalinium, an antitumor bifunctional intercalator which forms a high affinity reversible complex with DNA, was found to be specifically cytotoxic for polA and lig7 E. coli strains. In the polA strain, the cytotoxic effect of ditercalinium was suppressed by the uvrA mutation. DNA single strand breaks accumulated in...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.3.1063
更新日期：1988-02-11 00:00:00
abstract：:G-DNA, a polymorphic family of four-stranded DNA structures, has been proposed to play roles in a variety of biological processes including telomere function, meiotic recombination and gene regulation. Here we report the purification and cloning of TGP1, a G-DNA specific binding protein from Tetrahymena thermophila. T...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.7.1613
更新日期：1998-04-01 00:00:00
abstract：:A very mild and efficient procedure has been developed for the preparation of C-5 substituted deoxyuridines. The substituent carries a masked primary aliphatic amino group. These compounds are readily converted into their phosphoramidites and can be used to prepare oligonucleotides carrying one or more aliphatic amino...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.12.4857
更新日期：1987-06-25 00:00:00
abstract：:Cell cycle checkpoints induced by DNA damage play an integral role in preservation of genomic stability by allowing cells to limit the propagation of deleterious mutations. The retinoblastoma tumor suppressor (RB) is crucial for the maintenance of the DNA damage checkpoint function because it elicits cell cycle arrest...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg919
更新日期：2004-01-02 00:00:00
abstract：:The structural gene and the regulatory DNA sequence of the yeast Hansenula polymorpha methanol oxidase have been isolated. According to the nucleotide sequence data obtained, the structural gene encodes a 664 amino acids long protein, contains no intervening sequences, and the 5'- and 3'-non-coding region contains sev...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.9.3063
更新日期：1985-05-10 00:00:00
abstract：:A modification of previously described methods of electron microscopic gene mapping and of gene enrichment based on the avidin-biotin interaction is presented. The modification consists of coupling cytochrome-c instead of pentane diamine to the oxidized 2', 3' terminus of an RNA by Schiff base formation and BH-4 reduc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.2.385
更新日期：1978-02-01 00:00:00
abstract：:Publicly available database of co-expressed gene sets would be a valuable tool for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory investigation. Here, we report the construction of an Arabidopsis thaliana trans-factor and cis-element prediction data...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl783
更新日期：2007-01-01 00:00:00
abstract：:A new thermodynamic database for normal and modified nucleic acids has been developed. This Thermodynamic Database for Nucleic Acids (NTDB) includes sequence, structure and thermodynamic information as well as experimental methods and conditions. In this release, there are 1851 sequences containing both normal and mod...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.1.230
更新日期：2001-01-01 00:00:00
abstract：:The dhp1+ gene of Schizosaccharomyces pombe is a homolog of Saccharomyces cerevisiae HKE1/RAT1/TAP1 gene that is involved in RNA metabolism such as RNA trafficking and RNA synthesis. dhp1+ is also related to S. cerevisiae DST2 (SEP1) that encodes a DNA strand exchange protein required for sporulation and homologous re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.3.357
更新日期：1995-02-11 00:00:00
abstract：:The specific recognition of homopurine-homo pyrimidine regions in duplex DNA by triplex-forming oligonucleotides (TFOs) provides an attractive strategy for genetic manipulation. Alkylation of nucleobases with functionalized TFOs would have the potential for site-directed mutagenesis. Recently, we demonstrated that a T...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gng031
更新日期：2003-03-15 00:00:00
abstract：:The nucleotide sequence of the control region of the divergent argECBH operon has been established in the wild type and in mutants affecting expression of these genes. The argE and argCBH promoters face each other and overlap with an operator region containing two domains which may act as distinct repressor binding si...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.24.8031
更新日期：1982-12-20 00:00:00
