Abstract：
:RNase D was recently reported as a new enzymatic activity associated with HIV-1 reverse transcriptase (RT), cleaving RNA at two positions within the double-stranded region of the tRNA primer-viral RNA template complex (Ben-Artzi et al., Proc. Natl. Acad. Sci. USA 89 (1992) 927-931). This would make RNase D a fourth distinct activity of HIV-1 RT, in addition to RNA- and DNA-dependent DNA polymerase and RNase H. Using a specific substrate containing tRNA(Lys,3) hybridized to the primer binding site, we were able to detect the reported RNase D activity in our preparations of recombinant HIV-1 RT. This activity was also present in several active-site mutants of RT, suggesting that it is independent of the RNase H and polymerase functionalities of RT. Furthermore, we found that the cleavage specificity of RNase D is the same as that of RNase III isolated from E.coli. A likely explantation of these results--that the observed RNase D activity is attributable to traces of RNase III contamination--was further strengthened by the finding that the recombinant preparations of HIV-1 RT can specifically cleave a phage T7-derived double-stranded RNA processing signal, which has been used as a model substrate for detection of E.coli RNase III. Moreover, RT purified from an RNase III- strain of E.coli displayed no cleavage of the tRNA primer-RNA template complex.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Hostomsky Z,Hudson GO,Rahmati S,Hostomska Zdoi
10.1093/nar/20.21.5819keywords:
subject
Has Abstractpub_date
1992-11-11 00:00:00pages
5819-24issue
21eissn
0305-1048issn
1362-4962journal_volume
20pub_type
杂志文章abstract：:Homeodomains appear to be one of the most frequently employed DNA-binding domains in a superfamily of transacting factors. It is likely that during evolution several sub-types of homeodomain have evolved from a common ancestral domain, resulting in distinct but closely related DNA-binding preferences. Here we describe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.7.1202
更新日期：1994-04-11 00:00:00
abstract：:A search of sequence information in the GenBank files shows that tracts of 15-30 contiguous purines are greatly overrepresented in all eukaryotic species examined, ranging from yeast to human. Such an overabundance does not occur in prokaryotic sequences. The large increase in the number of oligopurine tracts cannot b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.4.689
更新日期：1995-02-25 00:00:00
abstract：:The molecular basis for the DNA binding specificity of the thyroid transcription factor 1 homeodomain (TTF-1HD) has been investigated. Methylation and ethylation interference experiments show that the TTF-1HD alone recapitulates the DNA binding properties of the entire protein. Studies carried out with mutant derivati...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.15.3075
更新日期：1994-08-11 00:00:00
abstract：:Interactions between proteins, drugs, water and B-DNA minor groove have been analyzed in crystal structures of 60 protein-DNA and 14 drug-DNA complexes. It was found that only purine N3, pyrimidine O2, guanine N2 and deoxyribose O4' are involved in the interactions, and that contacts to N3 and O2 are most frequent and...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.5.1182
更新日期：2002-03-01 00:00:00
abstract：:To study the effect of intron size on splicing efficiency we have varied the size of the avian leukosis virus (ALV) env mRNA intron in a cloned ALV genome. This was accomplished by deletion of ALV sequences or insertion of phage lambda DNA. The effect of these modifications on splicing was analyzed by microinjection o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.19.6177
更新日期：1982-10-11 00:00:00
abstract：:The locus DXS269 (P20) defines a deletion hotspot in the distal part of the Duchenne Muscular Dystrophy gene. We have cloned over 90 kilobase-pairs of genomic DNA from this region in overlapping cosmids. The use of whole cosmids as probes in a competitive DNA hybridization analysis proves a fast and convenient method ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.14.5611
更新日期：1989-07-25 00:00:00
abstract：:A new system, ZCURVE 1.0, for finding protein- coding genes in bacterial and archaeal genomes has been proposed. The current algorithm, which is based on the Z curve representation of the DNA sequences, lays stress on the global statistical features of protein-coding genes by taking the frequencies of bases at three c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg254
更新日期：2003-03-15 00:00:00
abstract：:Details of polynucleotide flexibility may be probed through a combination of semiempirical potential energy calculations and statistical mechanical analyses. The pseudorotational motions of the furanose and the long-range correlated rotations of the chain backbone are described briefly here. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.3.777
更新日期：1982-02-11 00:00:00
abstract：:Exposure to many endogenous and exogenous agents can give rise to DNA alkylation, which constitutes a major type of DNA damage. Among the DNA alkylation products, alkyl phosphotriesters have relatively high frequencies of occurrence and are resistant to repair in mammalian tissues. However, little is known about how t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky140
更新日期：2018-05-04 00:00:00
abstract：:We have created a database of comparatively derived group I intron secondary structure diagrams. This collection currently contains a broad sampling of phylogenetically and structurally similar and diverse structures from over 200 publicly available intron sequences. As more group I introns are sequenced and added to ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.17.3508
更新日期：1994-09-01 00:00:00
abstract：:The identification of genes with specific patterns of change (e.g. down-regulated and methylated) as phenotype drivers or samples with similar profiles for a given gene set as drivers of clinical outcome, requires the integration of several genomic data types for which an 'integrate by intersection' (IBI) approach is ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1503
更新日期：2016-04-20 00:00:00
abstract：:Two factors are mainly responsible for the stability of the DNA double helix: base pairing between complementary strands and stacking between adjacent bases. By studying DNA molecules with solitary nicks and gaps we measure temperature and salt dependence of the stacking free energy of the DNA double helix. For the fi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj454
更新日期：2006-01-31 00:00:00
abstract：:MeCP2 is a methyl-CpG binding protein that can repress transcription of nearby genes. In humans, mutations in the MECP2 gene are the major cause of Rett syndrome. By searching expressed sequence tag (EST) databases we have found a novel MeCP2 splice isoform (MeCP2alpha) which encodes a distinct N-terminus. We demonstr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh349
更新日期：2004-03-19 00:00:00
abstract：:Unwanted side effects of drugs are a burden on patients and a severe impediment in the development of new drugs. At the same time, adverse drug reactions (ADRs) recorded during clinical trials are an important source of human phenotypic data. It is therefore essential to combine data on drugs, targets and side effects...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1075
更新日期：2016-01-04 00:00:00
abstract：:Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1195
更新日期：2021-01-11 00:00:00
abstract：:Previous studies have established a critical role of both TFIIB and RNA polymerase II (RNAPII) in start site selection in the yeast Saccharomyces cerevisiae. However, it remains unclear how the TFIIB-RNAPII interaction impacts on this process since such an interaction can potentially influence both preinitiation compl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf422
更新日期：2002-07-15 00:00:00
abstract：:Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteri...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku269
更新日期：2014-06-01 00:00:00
abstract：:Protein synthesis elongation factor 2 (EF-2) from all archaebacteria so far analysed, is susceptible to inactivation by diphtheria toxin, a property which it shares with EF-2 from the eukaryotic 8OS translation system. To resolve the structural basis of diphtheria toxin susceptibility, the structural gene for the EF-2...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.16.7817
更新日期：1988-08-25 00:00:00
abstract：:The thermal stability of the Tn10 encoded tetracycline resistance (TET) gene control region is investigated by melting studies using purified DNA restriction fragments containing various amounts of flanking sequences. In order to study the thermodynamic properties of this control region under conditions, where enough ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.8.2685
更新日期：1982-04-24 00:00:00
abstract：:The webPDBinder (http://pdbinder.bio.uniroma2.it/PDBinder) is a web server for the identification of small ligand-binding sites in a protein structure. webPDBinder searches a protein structure against a library of known binding sites and a collection of control non-binding pockets. The number of similarities identifie...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt457
更新日期：2013-07-01 00:00:00
abstract：:The interaction of the high mobility group proteins, HMG14 and HMG17, with nucleosome core particles has been studied. The results show that two molecules of HMG14/17 can be bound tightly but reversibly to each core particle and that their affinity for core particles is greater than their affinity for histone-free DNA...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.17.3757
更新日期：1980-09-11 00:00:00
abstract：:An investigation of the mobility of short duplexes of DNA -octamers and decamers-on polyacrylamide gels is presented, showing that molecules containing less than one helical turn exhibit sequence dependent mobilities. Analysis of chains with different sequences indicates that any arrangement of two or more adjacent A....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.14.6803
更新日期：1988-07-25 00:00:00
abstract：:The pDd56 mRNA sequence is highly enriched in prestalk over prespore cells and is inducible by DIF, the putative Dictyostelium stalk-specific morphogen. We show that the pDd56 gene is composed of forty one copies of a twenty four amino acid, cysteine rich repeat. This is highly homologus to a repeat which we have prev...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.18.7463
更新日期：1987-09-25 00:00:00
abstract：:A human telomere ends in a single-stranded 3' tail, composed of repeats of T2AG3. G-quadruplexes (GQs) formed from four consecutive repeats have been shown to possess high-structural and mechanical diversity. In principle, a GQ can form from any four repeats that are not necessarily consecutive. To understand the dyna...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz906
更新日期：2019-12-02 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku556
更新日期：2014-09-01 00:00:00
abstract：:The ribosomal frameshifting signal of the mouse embryonal carcinoma differentiation regulated (Edr) gene represents the sole documented example of programmed -1 frameshifting in mammalian cellular genes [Shigemoto,K., Brennan,J., Walls,E,. Watson,C.J., Stott,D., Rigby,P.W. and Reith,A.D. (2001), Nucleic Acids Res., 29...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki299
更新日期：2005-03-14 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn1010
更新日期：2009-02-01 00:00:00
abstract：:It is a central issue to elucidate the new type of molecular recognition accompanied by a global structural change of a molecule upon binding to its targets. Here we investigate the driving force for the binding of R12 (a ribonucleic acid aptamer) and P16 (a partial peptide of a prion protein) during which P16 exhibit...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku382
更新日期：2014-06-01 00:00:00
abstract：:The ORFDB (http://orf.invitrogen.com/) represents an ongoing effort at Invitrogen Corporation to integrate relevant scientific data with an evolving collection of human and mouse Open Reading Frame (ORF) clones (Ultimate ORF Clones). The ORFDB serves as a central data warehouse enabling researchers to search the ORF c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh118
更新日期：2004-01-01 00:00:00
abstract：:The 5'- and 3'-untranslated regions (5'- and 3'-UTRs) of eukaryotic mRNAs are known to play a crucial role in post-transcriptional regulation of gene expression modulating nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and stability. UTRdb is a specialized database of 5' and 3' unt...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.1.335
更新日期：2002-01-01 00:00:00
