Abstract：
:The rolling circle DNA replication structures generated by the in vitro phage T4 replication system were analyzed using two-dimensional agarose gels. Replication structures were generated in the presence or absence of T4 primase (gp61), permitting the analysis of replication forks with either duplex or single-stranded tails. A characteristic arc shape was visualized when forks with single-stranded tails were cleaved by a restriction enzyme with the help of an oligonucleotide that anneals to restriction sites in the single-stranded tail. After calibrating the gel system with this well-studied rolling circle replication reaction, we then analyzed the in vivo replication directed by a T4 replication origin cloned within a plasmid. DNA samples were generated from infections with either wild-type or primase-deletion mutant phage. The only replicative arc that could be detected in the wild-type sample corresponded to duplex Y forms, consistent with very efficient lagging strand synthesis. Surprisingly, we obtained evidence for both duplex and single-stranded DNA tails in the samples from the primase-deficient infection. We conclude that a relatively inefficient mechanism primes lagging strand DNA synthesis in vivo when gp61 is absent.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Belanger KG,Mirzayan C,Kreuzer HE,Alberts BM,Kreuzer KNdoi
10.1093/nar/24.11.2166subject
Has Abstractpub_date
1996-06-01 00:00:00pages
2166-75issue
11eissn
0305-1048issn
1362-4962pii
5j0772journal_volume
24pub_type
杂志文章abstract：:The study of bacterial isolates or communities requires the analysis of the therein included plasmids in order to provide an extensive characterization of the organisms. Plasmids harboring resistance and virulence factors are of especial interest as they contribute to the dissemination of antibiotic resistance. As the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1050
更新日期：2019-01-08 00:00:00
abstract：:Point mutations in mitochondrial tRNA genes are responsible for individual subgroups of mitochondrial encephalomyopathies. We have recently reported that point mutations in the tRNA(Leu)(UUR) and tRNA(Lys) genes cause a defect in the normal modification at the first nucleotide of the anticodon. As part of a systematic...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.19.3779
更新日期：2000-10-01 00:00:00
abstract：:Escherichia coli mRNA translation is facilitated by sequences upstream and downstream of the initiation codon, called Shine-Dalgarno (SD) and downstream box (DB) sequences, respectively. In E.coli enhancing the complementarity between the DB sequences and the 16S rRNA penultimate stem resulted in increased protein acc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.4.970
更新日期：2001-02-15 00:00:00
abstract：:The paper describes an improved method for the synthesis of oligodeoxyribonucleotides using phosphoramidite chemistry. Our procedure relies on novel phosphoramidite intermediates, the deoxyribonucleoside-3'-morpholine-methoxyphosphins. These compounds are extremely stable and can be purified readily. Condensation reac...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.9.2575
更新日期：1983-05-11 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：:The speed of the new DNA sequencing techniques has created a need for computer programs to handle the data produced. This paper describes simple programs designed specifically for use by people with little or no computer experience. The programs are for use on small computers and provide facilities for storage, editin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.11.4037
更新日期：1977-11-01 00:00:00
abstract：:The D. melanogaster Adh gene is transcribed from two different promoters; a proximal (larval) promoter is active during late embryonic and larval stages, and a distal (adult) promoter is active primarily in third instar larvae and in adult flies (1). Genetic analyses suggest that several species of the mulleri subgrou...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.19.6899
更新日期：1985-10-11 00:00:00
abstract：:Quantitative real-time PCR has revolutionized many aspects of genetic research, biomedical diagnostics and pathogen detection. Nevertheless, the full potential of this technology has yet to be realized, primarily due to the limitations of the threshold-based methodologies that are currently used for quantitative analy...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnh177
更新日期：2004-12-15 00:00:00
abstract：:In Trypanosoma brucei, the mutually exclusive expression of the major surface antigens, the variant surface glycoprotein (VSG) of the bloodstream form and procyclin of the procyclic form, is due to a stage-specific accumulation of the respective mRNAs. Through the targeting of a reporter construct in the procyclin pro...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.11.1862
更新日期：1995-06-11 00:00:00
abstract：:The binding of transposase (Tnp) to the specific Tn5 end sequences is the first dedicated reaction during transposition. In this study, comparative DNA-binding analyses were performed using purified full-length Tnp and a C-terminal deletion variant (delta369) that lacks the putative dimerization domain. The shape of t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.19.3790
更新日期：1996-10-01 00:00:00
abstract：:To bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources, we have created the Online Bioinformatics Resources Collection (OBRC) at the Health Sciences Library System (HSLS) at the University of Pittsburgh. The OBRC, c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl781
更新日期：2007-01-01 00:00:00
abstract：:PrimPol is a primase-polymerase involved in nuclear and mitochondrial DNA replication in eukaryotic cells. Although PrimPol is predicted to possess an archaeo-eukaryotic primase and a UL52-like zinc finger domain, the role of these domains has not been established. Here, we report that the proposed zinc finger domain ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku214
更新日期：2014-05-01 00:00:00
abstract：:Explicit solvent molecular dynamics (MD) simulations were carried out for sarcin-ricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop, G-bulged cross-strand A-stack, flexible region and duplex part. Detailed analysis of the overall dynamics, base pairing, ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj470
更新日期：2006-02-02 00:00:00
abstract：:Reliable prediction of orthology is central to comparative genomics. Approaches based on phylogenetic analyses closely resemble the original definition of orthology and paralogy and are known to be highly accurate. However, the large computational cost associated to these analyses is a limiting factor that often preve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq953
更新日期：2011-03-01 00:00:00
abstract：:Serine integrases are emerging as core tools in synthetic biology and have applications in biotechnology and genome engineering. We have designed a split-intein serine integrase-based system with potential for regulation of site-specific recombination events at the protein level in vivo. The ϕC31 integrase was split i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz936
更新日期：2019-12-02 00:00:00
abstract：:RNA structural complexity and flexibility present a challenge for computational modeling efforts. Experimental information and bioinformatics data can be used as restraints to improve the accuracy of RNA tertiary structure prediction. Regarding utilization of restraints, the fundamental questions are: (i) What is the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz427
更新日期：2019-06-20 00:00:00
abstract：:The PR264/SC35 splicing factor belongs to the family of SR proteins which function as essential and alternative splicing factors. Here, we report that the human PR264/SC35 locus is bidirectionally transcribed. Double in situ hybridization experiments have allowed simultaneous detection of sense and antisense RNA in hu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.22.4513
更新日期：1997-11-15 00:00:00
abstract：:From the general views of the eukaryotic transcription systems, L1 (or L1-like) retrotransposons that encode some proteins are unusual. L1, unlike other protein-coding elements, is transcribed through an internal promoter. And the L1 internal promoter, unlike other internal promoters, is thought to be RNA polymerase I...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.18.3704
更新日期：1995-09-25 00:00:00
abstract：:Nucleotide excision repair is initiated by two different damage recognition subpathways, global genome repair (GGR) and transcription-coupled repair (TCR). In GGR, XPC detects DNA lesions and recruits TFIIH via interaction with the pleckstrin homology (PH) domain of TFIIH subunit p62. In TCR, an elongating form of RNA...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx970
更新日期：2017-12-15 00:00:00
abstract：:We describe a database of macromolecular motions meant to be of general use to the structural community. The database, which is accessible on the World Wide Web with an entry point at http://bioinfo.mbb.yale.edu/MolMovDB , attempts to systematize all instances of protein and nucleic acid movement for which there is at...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.18.4280
更新日期：1998-09-15 00:00:00
abstract：:G-quadruplexes are dynamic structures folded in G-rich single-stranded DNA regions. These structures have been recognized as a potential nucleic acid based mechanism for regulating multiple cellular processes such as replication, transcription and genomic maintenance. So far, their transcriptional role in vivo during ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw011
更新日期：2016-05-19 00:00:00
abstract：:We report the synthesis of new phosphoramidite building blocks and their use for the modification of oligonucleotides with hydrazides. The reaction of these hydrazide oligonucleotides with active esters and aldehydes is demonstrated for solution conjugation and immobilization. Compared with the established amino modif...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf594
更新日期：2002-11-01 00:00:00
abstract：:The hexamer (m5 dC-dG)3 has been synthesized and its three-dimensional structure determined by a single crystal X-ray diffraction analysis. The structure has been refined to a final R value of 15.6% at 1.3 A resolution. The molecule forms a left-handed Z-DNA helix which is similar to the unmethylated Z-DNA structure. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.23.7879
更新日期：1982-12-11 00:00:00
abstract：:Embryonic stem cells (ESCs) and meiosis are featured by relatively higher frequent homologous recombination associated with DNA double strand breaks (DSB) repair. Here, we show that Pold3 plays important roles in DSB repair, telomere maintenance and genomic stability of both ESCs and spermatocytes in mice. By attempti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky098
更新日期：2018-04-20 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：:All exchangeable protons in a short DNA helix, d(CG)3 sodium salt, have been studied by proton nuclear magnetic resonance. The cytidine and guanosine amino protons have been assigned for the first time. As a function of temperature the cytidine amino protons and the imino protons behave very similarly, their relaxatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.21.8269
更新日期：1984-11-12 00:00:00
abstract：:Differential display relies on a series of anchored primers to divide the total mRNA population into subsets of roughly equal size. However, this will only occur if the dinucleotide targeted by the anchor region of the anchored primers has a random frequency distribution [i.e. each of the 12 possible dinucleotides pre...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.5.1386
更新日期：1999-03-01 00:00:00
abstract：:This paper describes a simple program that uses a digitizing device to enter DNA sequences directly from autoradiographs into a computer. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part2.499
更新日期：1984-01-11 00:00:00
abstract：:DNA lengths in the structural repeat units of Chinese hamster ovary (CHO) and chicken erythrocyte chromatin were compared by analyzing the sizes of DNA fragments produced after treatment of nuclei with staphylococcal nuclease. The repeat length of CHO chromatin (173 +- 4 BP) is about 20 base pairs (BP) smaller than th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.4.771
更新日期：1977-04-01 00:00:00
abstract：:Methylation of the 2'-hydroxyl-group of ribonucleotides is found in all major classes of RNA in eukaryotes and is one of the most abundant posttranscriptional modifications of stable RNAs. In spite of intense studies, the multiple functions of RNA 2'-O-methylation are still not understood. One major obstacle in the fi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw200
更新日期：2016-05-05 00:00:00
