Abstract:
:We have studied a novel class of DNA sequences that cause DNA polymerases to pause. These sequences have the central consensus Py-G-C and are not necessarily adjacent to hairpins in the DNA template. Since most consensus sequences do not cause pauses under standard conditions, additional template features must exist that make it difficult to incorporate nucleotides at these positions. We believe that these pauses result from constraints that make the conformation change involved in nucleotide selection more difficult. These pauses can obscure parts of DNA sequencing ladders and prevent DNA amplification by the polymerase chain reaction. The addition of betaine, and some related compounds, relieves these pauses.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Mytelka DS,Chamberlin MJdoi
10.1093/nar/24.14.2774subject
Has Abstractpub_date
1996-07-15 00:00:00pages
2774-81issue
14eissn
0305-1048issn
1362-4962pii
6g0106journal_volume
24pub_type
杂志文章abstract::Long non-coding RNAs (lncRNAs) play critical roles in diverse cellular processes; however, their involvement in many critical aspects of the immune response including the interferon (IFN) response remains poorly understood. To address this gap, we compared the global gene expression pattern of primary human hepatocyte...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku713
更新日期:2014-01-01 00:00:00
abstract::We have generated a codon usage table for Pseudomonas aeruginosa. Codon usage in P. aeruginosa is extremely biased. In contrast to E. coli and yeast, P. aeruginosa preferentially uses those codons within a synonymous codon group with the strongest predicted codon-anticodon interaction. We were unable to correlate a pa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.19.9323
更新日期:1988-10-11 00:00:00
abstract::Ribosomes transit between two conformational states, non-rotated and rotated, through the elongation cycle. Here, we present evidence that an internal loop in the essential yeast ribosomal protein rpL10 is a central controller of this process. Mutations in this loop promote opposing effects on the natural equilibrium ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1107
更新日期:2014-02-01 00:00:00
abstract::The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1072
更新日期:2017-01-04 00:00:00
abstract::The 80S ribosome from Saccharomyces cerevisiae has been reconstructed from cryo electron micrographs to a resolution of 35 A. It is strikingly similar to the 70S ribosome from Escherichia coli, while displaying the characteristic eukaryotic features familiar from reconstructions of ribosomes from higher eukaryotes. As...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.2.655
更新日期:1998-01-15 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::Fully modified 4'-thioDNA, an oligonucleotide only comprising 2'-deoxy-4'-thionucleosides, exhibited resistance to an endonuclease, in addition to preferable hybridization with RNA. Therefore, 4'-thioDNA is promising for application as a functional oligonucleotide. Fully modified 4'-thioDNA was found to behave like an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn011
更新日期:2008-04-01 00:00:00
abstract::The gene, rpb1, encoding the largest subunit of RNA polymerase II has been cloned from Schizosaccharomyces pombe using the corresponding gene, RPB1, of Saccharomyces cerevisiae as a cross-hybridization probe. We have determined the complete sequence of this gene, and parts of PCR-amplified rpb1 cDNA. The predicted cod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.3.461
更新日期:1991-02-11 00:00:00
abstract::The mutation patterns at Cas9 targeted sites contain unique information regarding the nuclease activity and repair mechanisms in mammalian cells. However, analytical framework for extracting such information are lacking. Here, we present a novel computational platform called Rational InDel Meta-Analysis (RIMA) that en...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky653
更新日期:2018-09-19 00:00:00
abstract::The far upstream region of herpes simplex virus (HSV) immediate early (IE) gene 3 has previously been shown to increase gene expression in an enhancer-like manner, and to contain sequences which respond to stimulation of transcription by a virion polypeptide, Vmw65. To analyse the specific DNA sequences which mediate ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.2.929
更新日期:1986-01-24 00:00:00
abstract::Molecular beacons (MBs) have the potential to provide a powerful tool for rapid RNA detection in living cells, as well as monitoring the dynamics of RNA expression in response to external stimuli. To exploit this potential, it is necessary to distinguish true signal from background signal due to non-specific interacti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq050
更新日期:2010-05-01 00:00:00
abstract::The E3 ubiquitin ligase HUWE1/Mule/ARF-BP1 plays an important role in integrating/coordinating diverse cellular processes such as DNA damage repair and apoptosis. A previous study has shown that HUWE1 is required for the early step of DNA damage-induced apoptosis, by targeting MCL-1 for proteasomal degradation. Howeve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv325
更新日期:2015-05-19 00:00:00
abstract::RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions (UTRs). Yet, the underlying mechanisms and coding requirements for efficient co-transcriptional folding remain unclear. Traditional a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1036
更新日期:2007-01-01 00:00:00
abstract::We have recently described three group I introns inserted into a single gene, orf142, of the staphylococcal bacteriophage Twort and suggested the presence of at least two additional self-splicing introns in this phage genome. Here we report that two previously uncharacterized introns, 429 and 1087 nt in length, interr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.9.1935
更新日期:2002-05-01 00:00:00
abstract::We have located and sequenced the murine homologue of the hst/k-FGF oncogene in genomic DNA clones that extend 3' from int-2 on mouse chromosome 7. The two genes are in the same transcriptional orientation, less than 20 kilobase pairs (kb) apart, and presumably evolved by tandem duplication of a common ancestral gene....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.11.4037
更新日期:1989-06-12 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 mutation in a gene dicA of Escherichia coli leads to temperature-sensitive cell division, by allowing expression of a nearby division inhibition gene dicB (1). We have now established the sequence of the DicA region and identified DicA as a 15.5 KD protein. A second gene dicC transcribed divergently from dicA and co...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.17.6821
更新日期:1986-09-11 00:00:00
abstract::Bursts of free radicals produced by ionization of water in close vicinity to DNA can produce clusters of opposed DNA lesions and these are termed multiply damaged sites (MDS). How MDS are processed by the Escherichia coli DNA glycosylases, endonuclease (endo) III and endo VIII, which recognize oxidized pyrimidines, is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.4.932
更新日期:1998-02-15 00:00:00
abstract::Dictyostelium discoideum is of increasing interest as a model eukaryotic cell because its many attributes have recently been expanded to include improved genetic and biochemical manipulability. The ability to transform Dictyostelium using drug resistance as a selectable marker (1) and to gene target by high frequency ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.14.6617
更新日期:1988-07-25 00:00:00
abstract::Homologous recombination provides a means for the in vivo construction of recombinant DNA molecules that may be problematic to assemble in vitro. We have investigated the efficiency of recombination within the Caenorhabditis elegans germ line as a function of the length of homology between recombining molecules. Our f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm857
更新日期:2007-01-01 00:00:00
abstract::Crotonaldehyde is a representative alpha,beta-unsaturated aldehyde endowed of mutagenic and carcinogenic properties related to its propensity to react with DNA. Cyclic crotonaldehyde-derived deoxyguanosine (CrA-PdG) adducts can undergo ring opening in duplex DNA to yield a highly reactive aldehydic moiety. Here, we de...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn334
更新日期:2008-07-01 00:00:00
abstract::Oligonucleotide-directed mutagenesis was used to introduce an A to C transversion at position 523 in the 16S ribosomal RNA gene of Escherichia coli rrnB operon cloned in plasmid pKK3535. E. coli cells transformed with the mutated plasmid were resistant to streptomycin. The mutated ribosomes isolated from these cells w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.20.9631
更新日期:1988-10-25 00:00:00
abstract::The 3' splice site of the second intron (I2) of the human apolipoprotein-AII gene, (GT)16GGGCAG, is unique in that, although fully functional, a stretch of alternating guanine and thymine residues replaces the polypyrimidine tract usually associated with 3' splice junctions. The transient expression of successive 5' d...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.9.3787
更新日期:1987-05-11 00:00:00
abstract::Specific targeting of protein–nucleic acid interactions is an area of current interest, for example, in the regulation of gene-expression. Most transcription factor proteins bind in the DNA major groove; however, we are interested in an approach using small molecules to target the minor groove to control expression by...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1232
更新日期:2017-02-17 00:00:00
abstract::We show that using low denaturation temperatures (80-88 degrees C) during ligation mediated PCR (LM PCR) of bacterial DNA leads to the amplification of limited sets of the less stable DNA fragments. A set of electrophoretic patterns of such fragments obtained at different denaturation temperatures forms the PCR meltin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng116
更新日期:2003-09-15 00:00:00
abstract::IMGT, the international ImMunoGeneTics database (http://imgt.cines. fr:8104 ), is a high-quality integrated database specialising in Immunoglobulins (Ig), T cell Receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species, created in 1989 by Marie-Paule Lefranc, Université Montpellie...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.1.219
更新日期:2000-01-01 00:00:00
abstract::A novel method combining elements of suppression subtractive hybridization with high throughput differential screening permits the efficient and rapid cloning of rarely transcribed differentially expressed genes. The experimental strategy virtually excludes the possibility of isolating false positive clones. The poten...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.13.2598
更新日期:1997-07-01 00:00:00
abstract::Methylation of CpG motifs in DNA is involved in the control of gene expression and in several other epigenic effects. It suppresses also the immuno-stimulation properties of bacterial or viral DNAs that contain CPGS: However, effects of methylation on the DNA structure and dynamics are not clear. Here we carried out a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.11.2314
更新日期:2001-06-01 00:00:00
abstract::The hypoxanthine-guanine phosphoribosyltransferase (HGPRT) enzyme of Trypanosoma brucei and related parasites provides a rational target for the treatment of African sleeping sickness and several other parasitic diseases. To characterize the T. brucei HGPRT enzyme in detail, the T. brucei hgprt was isolated within a 4...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.23.5431
更新日期:1993-11-25 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