Abstract:
:Synthesis of (p)ppRNA-DNA chains by purified HeLa cell DNA primase-DNA polymerase alpha (pol alpha-primase) was compared with those synthesized by a multiprotein form of DNA polymerase alpha (pol alpha 2) using unique single-stranded DNA templates containing the origin of replication for simian virus 40 (SV40) DNA. The nucleotide locations of 33 initiation sites were identified by mapping G*pppN-RNA-DNA chains and identifying their 5'-terminal ribonucleotide. Pol alpha 2 strongly preferred initiation sites that began with ATP rather than GTP, thus frequently preferring different initiation sites than pol alpha-primase, depending on the template examined. The initiation sites selected in vitro, however, did not correspond to the sites used during SV40 DNA replication in vivo. Pol alpha 2 had the greatest effect on RNA primer size, typically synthesizing primers 1-5 nucleotides long, while pol alpha-primase synthesized primers 6-8 nucleotides long. These differences were observed even at individual initiation sites. Thus, the multiprotein form of DNA primase-DNA polymerase alpha affects selection of initiation sites, the frequency at which the sites are chosen, and length of RNA primers.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Vishwanatha JK,Yamaguchi M,DePamphilis ML,Baril EFdoi
10.1093/nar/14.18.7305subject
Has Abstractpub_date
1986-09-25 00:00:00pages
7305-23issue
18eissn
0305-1048issn
1362-4962journal_volume
14pub_type
杂志文章abstract::The FSSP database presents a continuously updated classification of 3-D protein folds based on an all-against-all comparison of structures currently in the Protein Data Bank (PDB) [Bernstein et al. (1977) J. Mol. Biol., 112, 535- 542]. The database currently contains an extended structural family for each of 600 repre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.1.206
更新日期:1996-01-01 00:00:00
abstract::T7 RNA polymerase promoters consist of a highly conserved 23 base-pair sequence that spans the site of the initiation of transcription (+1) and extends from -17 to +6. To determine the bases within the T7 consensus promoter that are essential for promoter function a library of mutant T7 promoters was constructed, and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.10.2517
更新日期:1992-05-25 00:00:00
abstract::With the aid of a novel poly-dA tailing-partial restriction technique and S1-protection mapping, the 5' terminal coding sequence for the 40S precursor ribosomal RNA of Xenopus laevis has been exactly identified. Since the promoter sequence for the 40S RNA should lie close to its 5' terminal coding sequence, we are abl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.12.3733
更新日期:1979-08-24 00:00:00
abstract::The efficiency of Nucleotide Excision Repair (NER)process is crucial for maintaining genomic integrity because in many organisms, including humans, it represents the only system able to repair a wide range of DNA damage. The aim of the work was to investigate whether the efficiency of the repair of photoproducts induc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv081
更新日期:2015-02-27 00:00:00
abstract::At the DNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs. Until now, few attempts had been made in writing general purpose search programs that take into account both sequence and structure criteria. Indeed, the most successful structure scanning programs are usua...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.8.1395
更新日期:1996-04-15 00:00:00
abstract::I have used a novel single-sided specific polymerase chain reaction (PCR) strategy inspired by ligation-mediated PCR to clone fragments of divergent homeobox genes from a flatworm, the planarian Polycelis nigra. Eight homeobox-containing fragments were amplified, belonging to the Hox, msh, NK-1 and NK-2 classes. Toget...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.8.1547
更新日期:1996-04-15 00:00:00
abstract::Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid-liquid phase separation (LLPS), a process that relies on multivalent weak interactions of the constituent proteins and other macromole...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz848
更新日期:2020-01-08 00:00:00
abstract::DNA double-strand breaks (DSBs) are repaired by either the non-homologous end joining (NHEJ) or homologous recombination (HR) pathway. Pathway choice is determined by the generation of 3΄ single-strand DNA overhangs at the break that are initiated by the action of the Mre11-Rad50-Xrs2 (MRX) complex to direct repair to...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx221
更新日期:2017-06-02 00:00:00
abstract::The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. By combining the different types of expression data, GXD aims to provide increasingly complete information about the expression profiles of genes in different mouse strains and mutants, thus enabling val...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.1.98
更新日期:2001-01-01 00:00:00
abstract::We attempted to use the polymerase chain reaction (PCR) to monitor in vitro recombination in a plasmid containing directly repeated sequences. Some of the plasmid preparations which had not been exposed to recombination conditions were however found to behave in the PCR test as if they had undergone homologous recombi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.9.2423
更新日期:1991-05-11 00:00:00
abstract::Studies of bacterial chromosomes and plasmids indicate that their replication initiator proteins bind to origins of replication at many double-stranded sites and also at AT-rich regions where single-stranded DNA is exposed during origin opening. Single-strand binding apparently promotes origin opening by stabilizing a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa826
更新日期:2020-11-04 00:00:00
abstract::MicroRNA (miRNA) 5'-isoforms, or 5'-isomiRs, are small-RNA species that originate from the same genomic loci as the major miRNAs with their 5' ends shifted from the 5' ends of the miRNAs by a few nucleotides. Although 5'-isomiRs have been reported, their origins, properties and potential functions remain to be examine...
journal_title:Nucleic acids research
pub_type: 杂志文章,meta分析
doi:10.1093/nar/gkt967
更新日期:2014-02-01 00:00:00
abstract::Effective drug discovery and optimization can be accelerated by techniques capable of deconvoluting the complexities often present in targeted biological systems. We report a single-molecule approach to study the binding of an alternative splicing regulator, muscleblind-like 1 protein (MBNL1), to (CUG)n = 4,6 and the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt330
更新日期:2013-07-01 00:00:00
abstract::For characterizing in vivo functions of a mammalian protein, it is informative to obtain conditional mutations and apply them to the mouse genetic system. However, the isolation of conditional mutations has been quite difficult in cultured cells. We report here that functional expression of a heterologous mammalian ge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.20.4229
更新日期:1994-10-11 00:00:00
abstract::The sequence requirements for specific and efficient transcription from the 16S/23S rRNA promoter of Sulfolobus shibatae were analysed by point mutations and by cassette mutations using an in vitro transcription system. The examination of the box A-containing distal promoter element (DPE) showed the great importance o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.20.5423
更新日期:1992-10-25 00:00:00
abstract::We have isolated a unique fragment of the HLA-DR alpha gene and probed human genomic DNA at low stringency to search for homologous sequences. A minimum of six non-polymorphic cross-hybridizing high molecular weight fragments were found in all DNAs examined. In order to obtain molecular clones of these cross-hybridizi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.20.7515
更新日期:1985-10-25 00:00:00
abstract::Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt915
更新日期:2014-01-01 00:00:00
abstract::Transcriptional regulation of the delta-aminolevulinic acid synthetase gene of Rhizobium meliloti was investigated under conditions of normal vegetative growth and during symbiosis with the legume host alfalfa. S1 nuclease mapping and DNA sequence analysis indicated that transcription originates from two sites separat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.16.5965
更新日期:1985-08-26 00:00:00
abstract::RNase P RNA (RPR), the catalytic subunit of the essential RNase P ribonucleoprotein, removes the 5' leader from precursor tRNAs. The ancestral eukaryotic RPR is a Pol III transcript generated with mature termini. In the branch of the arthropod lineage that led to the insects and crustaceans, however, a new allele aros...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz572
更新日期:2019-09-19 00:00:00
abstract::A hybrid plasmid was constructed containing beta-lactamase gene of plasmid pBR322 and cloned coding sequences of bovine growth hormone (BGH). The constructed plasmid contains all DNA sequences required to encode BGH, and when used as a hybridization probe it detects one growth hormone gene in the bovine genome. The cl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.1.19
更新日期:1981-01-10 00:00:00
abstract::GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 9.9 trillion base pairs from over 2.1 billion nucleotide sequences for 478 000 formally described species. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverag...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1023
更新日期:2021-01-08 00:00:00
abstract::A short histone-like fusion RNA, generated when the RNA 3' processing signal from a mouse histone H4 gene is inserted into a heterologous transcription unit, becomes correctly down-regulated in G1-arrested cells of a temperature-sensitive mouse mastocytoma cell cycle mutant (21-Tb; Stauber et al., EMBO J. 5, 3297-3303...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.20.9399
更新日期:1988-10-25 00:00:00
abstract::Here we report that the poor binding of methylphosphonate oligodeoxynucleosides (MP-ODNs) to their nucleic acid targets can be improved by additional inversion of the anomeric configuration (from beta to alpha) in the sugar moieties to give a new class of analogs, MP alpha-oligonucleosides. MP alpha-dT12and MP 5' alph...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.20.4551
更新日期:1998-10-15 00:00:00
abstract::Differential expression analysis of RNA sequencing (RNA-seq) data typically relies on reconstructing transcripts or counting reads that overlap known gene structures. We previously introduced an intermediate statistical approach called differentially expressed region (DER) finder that seeks to identify contiguous regi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw852
更新日期:2017-01-25 00:00:00
abstract::The evolution of regulatory networks in Bacteria has largely been explained at macroevolutionary scales through lateral gene transfer and gene duplication. Transcription factors (TF) have been found to be less conserved across species than their target genes (TG). This would be expected if TFs accumulate mutations fas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa162
更新日期:2020-05-07 00:00:00
abstract::A new method for identifying secretory signal sequences and for predicting the site of cleavage between a signal sequence and the mature exported protein is described. The predictive accuracy is estimated to be around 75-80% for both prokaryotic and eukaryotic proteins. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.11.4683
更新日期:1986-06-11 00:00:00
abstract::Cytosines in genomic DNA are sometimes methylated. This affects many biological processes and diseases. The standard way of measuring methylation is to use bisulfite, which converts unmethylated cytosines to thymines, then sequence the DNA and compare it to a reference genome sequence. We describe a method for the cri...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks275
更新日期:2012-07-01 00:00:00
abstract::The products of the RAG-1 and RAG-2 genes are essential for the recombination of the DNA encoding the antigen receptors of the developing immune system. Little is known of the specific role these genes play. We have explored the sequences encoding mouse RAG-1 by deleting large parts of the gene and by introducing loca...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.24.5644
更新日期:1993-12-11 00:00:00
abstract::Genomes mutate and evolve in ways simple (substitution or deletion of bases) and complex (e.g. chromosome shattering). We do not fully understand what types of complex mutation occur, and we cannot routinely characterize arbitrarily-complex mutations in a high-throughput, genome-wide manner. Long-read DNA sequencing m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1266
更新日期:2018-02-28 00:00:00
abstract::The three-dimensional Poisson-Boltzmann equation for the distribution of counterion charge density around double helical DNA has been solved by an iterative procedure. These computations have been performed for 0.01M monovalent salt solutions. A systematic study of the ten possible sequences found among adjacent nucle...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.3.1479
更新日期:1986-02-11 00:00:00