Abstract：
:Specific binding of HIV-1 viral protein NCp7 to a unique 35-base RNA stem-loop SL1 is critical for formation and packaging of the genomic RNA dimer found within HIV-1 virions. NCp7 binding stimulates refolding of SL1 from a metastable kissing dimer (KD) into thermodynamically stable linear dimer (LD). Using UV melting, gel electrophoresis and heteronuclear NMR, we investigated effects of various site-specific mutations within the full-length SL1 on temperature- or NCp7-induced refolding in vitro. Refolding involved intramolecular melting of SL1 stems but not dissociation of the intermolecular KD interface. Refolding required only two NCp7 molecules per KD but was limited by the amount of NCp7 present, implying that the protein does not catalytically promote refolding. Efficient refolding depended strictly on the presence and, to a lesser degree, on sequence of a highly conserved G-rich internal loop that normally limits thermal stability of the SL1 stem. Adding two base pairs to the lower stem created a hyperstable SL1 mutant that failed to refold, even when bound by NCp7 at high stoichiometries. NMR analysis of these kinetically trapped mutant RNA-protein complexes indicated that NCp7 initiates refolding by dissociating base pairs in the upper stem of SL1. This study illuminates structural transitions critical for HIV-1 assembly and replication.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Mujeeb A,Ulyanov NB,Georgantis S,Smirnov I,Chung J,Parslow TG,James TLdoi
10.1093/nar/gkm097subject
Has Abstractpub_date
2007-01-01 00:00:00pages
2026-34issue
6eissn
0305-1048issn
1362-4962pii
gkm097journal_volume
35pub_type
杂志文章abstract：:Various in vivo mutagenesis methods have been developed to facilitate fast and efficient continuous evolution of proteins in cells. However, they either modify the DNA region that does not match the target gene, or suffer from low mutation rates. Here, we report a mutator, eMutaT7 (enhanced MutaT7), with very fast in ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1231
更新日期：2021-01-06 00:00:00
abstract：:The aminoacylation kinetics of T7 transcripts representing defined regions of Escherichia coli serine tRNAs were determined using purified E.coli seryl-tRNA synthetase (SerRS) and the kinetic values were used to estimate the relative contribution of various tRNA(Ser) domains to recognition by SerRS. The analysis revea...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.19.4467
更新日期：1993-09-25 00:00:00
abstract：:We recently developed a new type of pyrrole (Py)-imidazole (Im) polyamide-tetrahydrocyclopropabenzindolone (CBI) conjugate with an indole linker as a stable sequence-specific alkylating agent. In this study, we investigated the gene silencing activities of polyamides A, B and C, which selectively alkylate specific seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl005
更新日期：2006-02-25 00:00:00
abstract：:Treatment of cells with DNA damaging agents leads to induction of a variety of genes involved in different cellular processes. We have applied a lacZ-based gene trap strategy to search for new mammalian genes induced by genotoxic stress. A population of 32 x 10(3) neo r clones stably transfected with a gene trap vecto...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.23.4803
更新日期：1997-12-01 00:00:00
abstract：:Exposure of pyrimidines of DNA to ionizing radiation under aerobic conditions or oxidizing agents results in attack on the 5,6 double bond of the pyrimidine ring or on the exocyclic 5-methyl group. The primary product of oxidation of the 5,6 double bond of thymine is thymine glycol, while oxidation of the 5-methyl gro...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.16.3239
更新日期：1995-08-25 00:00:00
abstract：:A novel expression system was established that allows expression and propagation of the human hepatitis B virus (HBV) genome in cultured animal cells. An overlength HBV genome encoding the viral pregenomic RNA was put under transcriptional control of the human metallothionein IIA promoter thereby replacing the endogen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.24.10117
更新日期：1987-12-23 00:00:00
abstract：:The stability of chromosome ends, the telomeres, is dependent on the ribonucleoprotein telomerase. In vitro, telomerase requires at least one RNA molecule and a reverse transcriptase-like protein. However, for telomere homeostasis in vivo, additional proteins are required. Telomerase RNAs of different species vary in ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt514
更新日期：2013-09-01 00:00:00
abstract：:Muscle creatine kinase (MCK) is a major enzyme of cellular energy metabolism that is expressed upon differentiation of myoblasts into myotubes. Previously we cloned and sequenced the entire rabbit enzyme cDNA which was used as a probe in these studies to obtain a genomic clone from a rabbit library. The transcription ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.11.3027
更新日期：1991-06-11 00:00:00
abstract：:Here we employ a set of RNA Polymerase II (Pol II) activity mutants to determine the consequences of increased or decreased Pol II catalysis on gene expression in Saccharomyces cerevisiae. We find that alteration of Pol II catalytic rate, either fast or slow, leads to decreased Pol II occupancy and apparent reduction ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx037
更新日期：2017-05-05 00:00:00
abstract：:Most microbes have not been cultured, and many of those that are cultivatable are difficult, dangerous or expensive to propagate or are genetically intractable. Routine cloning of large genome fractions or whole genomes from these organisms would significantly enhance their discovery and genetic and functional charact...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq119
更新日期：2010-05-01 00:00:00
abstract：:A fiber optic biosensor was used for the fluorimetric detection of T/AT triple-helical DNA formation. The surfaces of two sets of fused silica optical fibers were functionalized with hexaethylene oxide linkers from which decaadenylic acid oligonucleotides were grown in the 3'to 5'and 5'to 3'direction, respectively, us...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.20.4139
更新日期：1997-10-15 00:00:00
abstract：:Single nucleotide polymorphisms (SNPs) are, together with copy number variation, the primary source of variation in the human genome. SNPs are associated with altered response to drug treatment, susceptibility to disease and other phenotypic variation. Furthermore, during genetic screens for disease-associated mutatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm979
更新日期：2008-01-01 00:00:00
abstract：:Eukaryotic gene expression is regulated by enhancer-promoter interactions but the molecular mechanisms that govern specificity have remained elusive. Genome-wide studies utilizing STARR-seq identified two enhancer classes in Drosophila that interact with different core promoters: housekeeping enhancers (hkCP) and deve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1114
更新日期：2017-02-28 00:00:00
abstract：:The covalent attachment of thiol-modified DNA oligomers; to self-assembled monolayer silane films on fused silica and oxidized silicon substrates is described. A heterobifunctional crosslinking molecule bearing both thiol- and amino-reactive moieties was used to tether a DNA oligomer (modified at its terminus with a t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.15.3031
更新日期：1996-08-01 00:00:00
abstract：:Yeast two-hybrid (Y2H) screenings result in identification of many out-of-frame (OOF) clones that code for short (2-100 amino acids) peptides with no sequence homology to known proteins. We hypothesize that these peptides can reveal common short linear motifs (SLiMs) responsible for their selection. We present a new p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr600
更新日期：2011-10-01 00:00:00
abstract：:Recent studies show that the region of DNA brought into close proximity to the fetal gamma-globin genes in deletional forms of hereditary persistence of fetal hemoglobin (HPFH) is selectively hypomethylated (and presumably active) in normal erythroid tissue. This region is normally located approximately 100 kilobases ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.13.5169
更新日期：1987-07-10 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：:GenBank(®) (http://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 300 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing proj...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1216
更新日期：2015-01-01 00:00:00
abstract：:Chromatin fragments released from intact Friend erythroleukemia cell nuclei during limited incubation with micrococcal nuclease, DNase II or DNase I were analyzed to determine the distribution of DNA methyltransferase in chromatin. The enzyme was released in a free form when internucleosomal DNA was digested with micr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.20.5359
更新日期：1981-10-24 00:00:00
abstract：:The thermal stabilities of RNA:DNA hybrids are substantially greater than those of DNA:DNA duplexes in aqueous electrolyte solutions containing high concentrations of formamide. Association rates to form DNA:DNA duplexes and DNA:RNA hybrids have been measured in these solvents. There is a temperature range in which DN...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.5.1539
更新日期：1977-01-01 00:00:00
abstract：:During telomere replication in yeast, chromosome ends acquire a long single-stranded extension of the strand making the 3' end. Previous work showed that these 3' tails are generated late in S-phase, when conventional replication is virtually complete. In addition, the extensions were also observed in cells that lacke...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.23.5365
更新日期：1998-12-01 00:00:00
abstract：:The reported binding preference of human hnRNP protein A1 for the 3'-splice site of some introns (Swanson and Dreyfuss (1988) EMBO J. 7, 3519-3529; Mayrand and Pederson (1990) Nucleic Acids Res. 18, 3307-3318) was tested by assaying in vitro the binding of purified recombinant A1 protein (expressed in bacteria) to syn...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.22.6595
更新日期：1990-11-25 00:00:00
abstract：:Adaptation of the P1 phage-derived Cre /loxP site- specific recombination system to the gene targeting technique allows for the conditional deletion of genes in mice. To selectively modify genes in B lymphocytes, we have generated mice (designated CD19-Cre) which express cre under the transcriptional control of the B ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.6.1317
更新日期：1997-03-15 00:00:00
abstract：:The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1133
更新日期：2017-01-04 00:00:00
abstract：:Increasingly large-scale expression compendia for different species are becoming available. By exploiting the modularity of the coexpression network, these compendia can be used to identify biological processes for which the expression behavior is conserved over different species. However, comparing module networks ac...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1275
更新日期：2011-04-01 00:00:00
abstract：:Cloned ribosomal DNA (rDNA) of Locusta migratoria was analyzed by restriction site mapping and SI nuclease experiments. The repeat unit is 18 kb long. The nontranscribed spacer region (NTS) is very large (11 kb) and homogeneous in length, but many of the restriction sites are heterogeneous among the repeat units. Two ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.4.1251
更新日期：1985-02-25 00:00:00
abstract：:To unravel the network of transcription factors established during development it is important to understand how genes specifically expressed during embryogenesis are regulated. Oct-4 is a transcription factor whose expression is associated with an undifferentiated cell phenotype in the early mouse embryo and is downr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.6.901
更新日期：1994-03-25 00:00:00
abstract：:While proteins are highly biochemically competent, DNA offers the ability to program, both reactions and the assembly of nanostructures, with a control that is unprecedented by any other molecule. Their joining: DNA-protein conjugates - offer the ability to combine the programmability of DNA with the competence of pro...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx707
更新日期：2017-10-13 00:00:00
abstract：:Cell differentiation is a central process in development and in cancer growth and dissemination. OCT4 (POU5F1) and NANOG are essential for cell stemness and pluripotency; yet, the mechanisms that regulate their expression remain largely unknown. Repetitive elements account for almost half of the Human Genome; still, t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw095
更新日期：2016-06-02 00:00:00
abstract：:A 9.2 kb segment of the maxi-circle of Trypanosoma brucei mitochondrial DNA contains the genes for cytochrome c oxidase subunits I and II (coxI and coxII) and seven Unassigned Reading Frames ("URFs"). The genes for coxI and coxII display considerable homology at the aminoacid level (38 and 25%, respectively) to the co...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.19.7327
更新日期：1984-10-11 00:00:00
