Abstract:
:A simple and efficient method is described to introduce structurally pre-determined mutations into recombinant genomes of filamentous phage M13. The method rests on gapped duplex DNA (gdDNA) molecules of the phage M13 genome as the key intermediate. In this gdDNA, the (+) and the (shorter) (-) strand carry different genetic markers in such a way, that a rigorous selection can be applied for phage carrying the markers of the (-) strand. For introduction of the mutation, a synthetic oligonucleotide with partial homology to a target site within the single stranded DNA region is annealed to the gdDNA. The oligonucleotide subsequently becomes part of the (-) strand by enzymatic DNA gap filling and sealing. This physical linkage is preserved at the genetic level after transfection of a recipient E.coli strain deficient in DNA mismatch correction, so that the synthetic marker can be selected from the phage progeny independent from its potential phenotype. It is demonstrated that by this method mutants can be constructed with marker yields in excess of 70%.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kramer W,Drutsa V,Jansen HW,Kramer B,Pflugfelder M,Fritz HJdoi
10.1093/nar/12.24.9441subject
Has Abstractpub_date
1984-12-21 00:00:00pages
9441-56issue
24eissn
0305-1048issn
1362-4962journal_volume
12pub_type
杂志文章abstract::The cyanobacteirum Synechocystis sp. strain PCC 6803 possesses nine species of the sigma (sigma)-factor gene for RNA polymerase (RNAP). Here, we identify and characterize the novel-type promoter recognized by a group 3 sigma-factor, SigF. SigF autoregulates its own transcription and recognizes the promoter of pilA1 th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn453
更新日期:2008-09-01 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
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn886
更新日期:2009-01-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.12.2873
更新日期:1998-06-15 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq917
更新日期:2011-01-01 00:00:00
abstract::Random amplified polymorphic DNA (RAPD) markers are used widely to develop high resolution genetic maps and for genome fingerprinting. Typically, single oligomers of approximately 10 nucleotides are used to PCR amplify characteristic RAPD marker fragments. We describe an efficient method for the direct end-sequencing ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.19.e28
更新日期:1999-10-01 00:00:00
abstract::Homeodomains appear to be one of the most frequently employed DNA-binding domains in a superfamily of transacting factors. It is likely that during evolution several sub-types of homeodomain have evolved from a common ancestral domain, resulting in distinct but closely related DNA-binding preferences. Here we describe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.7.1202
更新日期:1994-04-11 00:00:00
abstract::Previous studies have shown that the yeast Candida albicans encodes a unique seryl-tRNA(CAG) that should decode the leucine codon CUG as serine. However, in vitro translation of several different CUG-containing mRNAs in the presence of this unusual seryl-tRNA(CAG) result in an apparent increase in the molecular weight...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.9.1481
更新日期:1995-05-11 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv486
更新日期:2015-07-01 00:00:00
abstract::The mitochondrial DNA of Neurospora crassa has a heterogeneous intramolecular base distribution. A contiguous piece, representing at least 30% of the total genome, has a G+C content that is 6% lower than the overall G+C content of the DNA. The genes for both ribosomal RNAs are contained in the remaining, relatively G+...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.1.129
更新日期:1977-01-01 00:00:00
abstract::Addition of thiol compounds containing an anionic group to the 3'-terminal unsaturated sugar of the 5' fragment obtained from an oligonucleotide containing an AP site cleaved by beta-elimination, can be followed by gel electrophoresis. The technique enables to distinguish between two mechanisms of cleavage of the C3'-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.20.9489
更新日期:1988-10-25 00:00:00
abstract::DNA tandem repeats (TRs) are ubiquitous genomic features which consist of two or more adjacent copies of an underlying pattern sequence. The copies may be identical or approximate. Variable number of tandem repeats or VNTRs are polymorphic TR loci in which the number of pattern copies is variable. In this paper we des...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku642
更新日期:2014-08-01 00:00:00
abstract::Short interfering RNAs (siRNAs) are valuable reagents for sequence-specific inhibition of gene expression via the RNA interference (RNAi) pathway. Although it has been proposed that the relative thermodynamic stability at the 5'-ends of siRNAs plays a crucial role in siRNA strand selection, we demonstrate here that a ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn584
更新日期:2008-10-01 00:00:00
abstract::The bacterial transcription terminator, Rho, terminates transcription at half of the operons. According to the classical model derived from in vitro assays on a few terminators, Rho is recruited to the transcription elongation complex (EC) by recognizing specific sites (rut) on the nascent RNA. Here, we explored the m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku690
更新日期:2014-09-01 00:00:00
abstract::The 279-bp major breakpoint region (mbr) within the 3'-untranslated region (3'-UTR) of the BCL2 gene is a binding site of special AT-rich sequence binding protein 1 (SATB1) that is well known to participate in the long-range regulation of gene transcription. Our previous studies have revealed that the mbr could regula...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr023
更新日期:2011-06-01 00:00:00
abstract::Archival formalin-fixed, paraffin-embedded and ethanol-fixed tissues represent a potentially invaluable resource for gene expression analysis, as they are the most widely available material for studies of human disease. Little data are available evaluating whether RNA obtained from fixed (archival) tissues could produ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.2.e4
更新日期:2002-01-15 00:00:00
abstract::Compounds that are covalent analogues of nucleic acid base pairs of normal, long, and short C1' to C1' dimensions [B. Devadas and N.J. Leonard (1990) J. Am. Chem. Soc., 112, 3125-3135.] have been added to the oligodeoxyribonucleotide d(A)6 with bacteriophage T4 RNA ligase as a prelude to placing them at defined loci w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.3.585
更新日期:1991-02-11 00:00:00
abstract::Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. We introduce PatternQuery, a web-based application designed for detection and fast extraction of such patterns. The application uses a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv561
更新日期:2015-07-01 00:00:00
abstract::The antitumour antibiotics bleomycin and actinomycin are commonly used therapeutically in combination. One causes metal ion- and oxygen-dependent oxidative damage to DNA, while the other acts at the level of DNA via intercalation of its phenoxazone chromophore and probable inhibition of topoisomerases. Both drugs bind...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.8.1516
更新日期:1997-04-15 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz419
更新日期:2019-07-09 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1025
更新日期:2016-02-29 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.14.2950
更新日期:2001-07-15 00:00:00
abstract::Oligonucleotide models of ribosomal RNA domains are powerful tools to study the binding and molecular recognition of antibiotics that interfere with bacterial translation. Techniques such as selective chemical modification, fluorescence labeling and mutations are cumbersome for the whole ribosome but readily applicabl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq159
更新日期:2010-07-01 00:00:00
abstract::We present the LGA (Local-Global Alignment) method, designed to facilitate the comparison of protein structures or fragments of protein structures in sequence dependent and sequence independent modes. The LGA structure alignment program is available as an online service at http://PredictionCenter.llnl.gov/local/lga. D...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg571
更新日期:2003-07-01 00:00:00
abstract::Dictyostelium intermediate repeat sequence 1 (DIRS-1) is the founding member of a poorly characterized class of retrotransposable elements that contain inverse long terminal repeats and tyrosine recombinase instead of DDE-type integrase enzymes. In Dictyostelium discoideum, DIRS-1 forms clusters that adopt the functio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1337
更新日期:2014-03-01 00:00:00
abstract::In an extensive analysis, using a range of restriction endonucleases, HinfI and TaqI were found to differentiate satellites I, II and III & IV. Satellite I is resistant to digestion by TaqI, but is cleaved by HinfI to yield three major fragments of approximate size 770, 850 and 950bp, associated in a single length of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.2.547
更新日期:1982-01-22 00:00:00
abstract::Mixed-lineage leukemia (MLL) maintains the expression of cellular memory genes during development, while leukemic MLL fusion proteins aberrantly maintain expression of hematopoietic stem cell program genes such as HOXA9 to cause leukemia. However, the molecular mechanism of gene activation is unclear. Here we show tha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1394
更新日期:2014-04-01 00:00:00
abstract::RegulonDB, first published 20 years ago, is a comprehensive electronic resource about regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from classic molecular biology experiments, and recently also from high-throughput genomic methodologies. We curated the literature to keep Reg...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1077
更新日期:2019-01-08 00:00:00
abstract::Analysis of phylogenetically conserved secondary structure has been important in the development of models for the secondary structure of structural RNAs. In this paper, we apply this type of analysis to several families of informational RNAs to evaluate its usefulness in developing secondary structure models for mRNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.23.8645
更新日期:1985-12-09 00:00:00
abstract::Genes in the germline (micronuclear) genome of hypotrichous ciliates are interrupted by multiple, short, non-coding, AT-rich sequences called internal eliminated segments, or IESs. During conversion of a micronucleus to a somatic nucleus (macronucleus) after cell mating, all IESs are excised from the germline genes an...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/27.5.1243
更新日期:1999-03-01 00:00:00