Abstract：
:The multifunctional HCV core protein consists of a hydrophilic RNA interacting D1 domain and a hydrophobic D2 domain interacting with membranes and lipid droplets. The core D1 domain was found to possess nucleic acid annealing and strand transfer properties. To further understand these chaperone properties, we investigated how the D1 domain and two peptides encompassing the D1 basic clusters chaperoned the annealing of complementary canonical nucleic acids that correspond to the DNA sequences of the HIV-1 transactivation response element TAR and its complementary cTAR. The core peptides were found to augment cTAR-dTAR annealing kinetics by at least three orders of magnitude. The annealing rate was not affected by modifications of the dTAR loop but was strongly reduced by stabilization of the cTAR stem ends, suggesting that the core-directed annealing reaction is initiated through the terminal bases of cTAR and dTAR. Two kinetic pathways were identified with a fast pre-equilibrium intermediate that then slowly converts into the final extended duplex. The fast and slow pathways differed by the number of base pairs, which should be melted to nucleate the intermediates. The three peptides operate similarly, confirming that the core chaperone properties are mostly supported by its basic clusters.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sharma Kk,Didier P,Darlix JL,de Rocquigny H,Bensikaddour H,Lavergne JP,Pénin F,Lessinger JM,Mély Ydoi
10.1093/nar/gkq094subject
Has Abstractpub_date
2010-06-01 00:00:00pages
3632-42issue
11eissn
0305-1048issn
1362-4962pii
gkq094journal_volume
38pub_type
杂志文章abstract：:The unwinding of supercoiled phi X174 RFI DNA induced by the tumorigenic (+) and non-tumorigenic (-) enantiomers of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) has been investigated by agarose slab-gel and ethidium titration tube gel electrophoresis. The differences in adduct conformat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.23.6167
更新日期：1992-12-11 00:00:00
abstract：:Ribosomal recruitment of cellular mRNAs depends on binding of eIF4F to the mRNA's 5'-terminal 'cap'. The minimal 'cap0' consists of N7-methylguanosine linked to the first nucleotide via a 5'-5' triphosphate (ppp) bridge. Cap0 is further modified by 2'-O-methylation of the next two riboses, yielding 'cap1' (m7GpppNmN) ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1321
更新日期：2014-03-01 00:00:00
abstract：:The carbon catabolite repressor protein 4 (Ccr4)-Negative on TATA (Not) complex controls gene expression at two levels. In the nucleus, it regulates the basal transcription machinery, nuclear receptor-mediated transcription and histone modifications. In the cytoplasm, the complex is required for messenger RNA (mRNA) t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr011
更新日期：2011-05-01 00:00:00
abstract：:In the past year, DDBJ (http://www.ddbj.nig.ac.jp) collected and released 1,956,826 entries or 1,741,313,111 bases. The released data include approximately 90,000 ESTs and cDNAs of Macaca fascicularis, and 280 million bases of mouse GSS. In addition to the data collection, we have indexed the submitted data to the Int...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj111
更新日期：2006-01-01 00:00:00
abstract：:The cartilage matrix is composed of characteristic components including type II collagen, aggrecan and link protein. In this paper, we report two DNA elements that regulate the link protein gene. Using transient transfection assays with link protein gene constructs in chondrocytes, chloramphenicol acetyl transferase (...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.12.2305
更新日期：1995-06-25 00:00:00
abstract：:PROtein Domain Organization and Comparison (PRODOC) comprises several programs that enable convenient comparison of proteins as a sequence of domains. The in-built dataset currently consists of approximately 698 000 proteins from 192 organisms with complete genomic data, and all the SWISSPROT proteins obtained from th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki474
更新日期：2005-07-01 00:00:00
abstract：:The nucleotide sequence of the faeD gene of Escherichia coli and the amino acid sequence of its product is presented. The faeD product is an outer membrane protein required for transport of K88ab fimbrial subunits across the outer membrane. The protein is synthesized as a precursor containing a signal peptide, and the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.6.2443
更新日期：1986-03-25 00:00:00
abstract：:We have used fluorescein-11-dUTP in a nick-translation format to produce fluoresceinated human nucleic acid probes. After in situ hybridization of fluoresceinated DNAs to human metaphase chromosomes, the detection sensitivity was found to be 50-100 kb. The feasibility and the increase in detection sensitivity of micro...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.12.3237
更新日期：1991-06-25 00:00:00
abstract：:A UCSD Pascal program was developed which can analyze nucleic acid dot matrices of up to 9500 X 9500 in size on the Apple II computer. Although matrices of such size consume large amounts of computer memory, this program minimizes these problems by analyzing only small strips of the matrix at a time, and then transfer...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part2.767
更新日期：1984-01-11 00:00:00
abstract：:The CDC16 gene is involved in the process of chromosome segregation in mitosis and a cdc16ts mutant accumulates the predominant microtubule-associated protein at the nonpermissive temperature. We find that the CDC16 gene open reading frame (ORF) is capable of encoding a protein whose calculated molecular weight and pI...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.20.8439
更新日期：1987-10-26 00:00:00
abstract：:Many cellular proteins are methylated on lysine residues and this has been most intensively studied for histone proteins. Lysine methylations on non-histone proteins are also frequent, but in most cases the functional significance of the methylation event, as well as the identity of the responsible lysine (K) specific...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx432
更新日期：2017-08-21 00:00:00
abstract：:We describe a method for anchoring bacteriophage lambda DNA by one end to gold by Au-biotin-streptavidin-biotin-DNA bonds. DNA anchored to a microfabricated Au line could be aligned and stretched in flow and electric fields. The anchor was shown to resist a force of at least 11 pN, a linkage strong enough to allow DNA...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.3.492
更新日期：1994-02-11 00:00:00
abstract：:The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1010
更新日期：2010-01-01 00:00:00
abstract：:The budding yeast Saccharomyces cerevisiae is proving to be an useful and accurate model for eukaryotic DNA replication. It contains both DNA polymerase alpha (I) and delta (III). Recently, proliferating cell nuclear antigen (PCNA), which in mammalian cells is an auxiliary subunit of DNA polymerase delta and is essent...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.2.261
更新日期：1990-01-25 00:00:00
abstract：:Treatment of responsive cells by interferons (IFNs) induces within a few hours a rise in the concentration of several proteins and mRNAs. In order to characterize these IFN-induced mRNA species, we have cloned in E. coli the cDNA made from a 17-18S poly(A)+ RNA of human fibroblastoid cells (SV80) treated with IFN-beta...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.5.1213
更新日期：1983-03-11 00:00:00
abstract：:Two residues are invariant in all bZip basic regions: asparagine -18 and arginine -10 (we define the first leucine of the leucine zipper of GCN4 as +1). X-ray structures of two specific GCN4-DNA complexes (Ellenberger et al., Cell, 71, 1223-1237, 1992; König & Richmond, J. Mol. Biol., 233, 139-154, 1993) demonstrate t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.21.4395
更新日期：1994-10-25 00:00:00
abstract：:A simple and effective modified ethanol precipitation-based protocol is described for the preparation of DNA from ancient human bones. This method is fast and requires neither hazardous chemicals nor special devices. After the powdering and incubating of the bone samples Dextran Blue was added as a carrier for removin...
journal_title：Nucleic acids research
pub_type： 历史文章,杂志文章
doi：10.1093/nar/28.12.e67
更新日期：2000-06-15 00:00:00
abstract：:A physical mapping strategy has been developed to verify and accelerate the assembly and gap closure phase of a microbial genome shotgun-sequencing project. The protocol was worked out during the ongoing Pseudomonas putida KT2440 genome project. A macro-restriction map was constructed by linking probe hybridisation of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.22.e110
更新日期：2001-11-15 00:00:00
abstract：:Many multimeric transcription factors recognize DNA sequence patterns by cooperatively binding to bipartite elements composed of half sites separated by a flexible spacer. We developed a novel bipartite algorithm, bipartite pattern discovery (Bipad), which produces a mathematical model based on information maximizatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh825
更新日期：2004-09-23 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq827
更新日期：2011-02-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.10.1887
更新日期：1996-05-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.8.1735
更新日期：1993-04-25 00:00:00
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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：:LOCtarget is a web server and database that predicts and annotates sub-cellular localization for structural genomics targets; LOCnet is one of the methods used in LOCtarget that can predict sub-cellular localization for all eukaryotic and prokaryotic proteins. Targets are taken from the central registration database f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh441
更新日期：2004-07-01 00:00:00
abstract：:OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the al...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1238
更新日期：2011-01-01 00:00:00
abstract：:A class of heterogeneous nuclear RNA (hnRNA) molecules contain an internal transcribed poly A sequence of close to 25 uninterrupted AMP residues. HnRNA molecules containing this sequence are separable from those containing the large 3' terminal poly A sequence on the basis of their differential affinity for oligo dT c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.3.1097
更新日期：1979-03-01 00:00:00
abstract：:A mathematical model and a computer simulation were used to study PCR specificity. The model describes the occurrences of non-targeted PCR products formed through random primer-template interactions. The PCR simulation scans DNA sequence databases with primers pairs. According to the model prediction, PCR with complex...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.18.3538
更新日期：1996-09-15 00:00:00
abstract：:Computational modelling of mammalian cell cycle regulation is a challenging task, which requires comprehensive knowledge on many interrelated processes in the cell. We have developed a web-based integrated database on cell cycle regulation in mammals in normal and pathological states (Cyclonet database). It integrates...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl912
更新日期：2007-01-01 00:00:00
abstract：:This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene e...
journal_title：Nucleic acids research
pub_type：
doi：10.1093/nar/gkw1188
更新日期：2017-01-04 00:00:00
abstract：:With the abundant mammalian lncRNAs identified recently, a comprehensive annotation resource for these novel lncRNAs is an urgent need. Since its first release in November 2016, AnnoLnc has been the only online server for comprehensively annotating novel human lncRNAs on-the-fly. Here, with significant updates to mult...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa368
更新日期：2020-07-02 00:00:00
