Abstract：
:A new method is described for the direct construction of randomly mutagenized genes by applying the polymerase chain reaction (PCR) to an oligonucleotide synthesized using doped nucleotide reservoirs. We have demonstrated the utility of this method by generating a library of mutant HIV-1 tat genes. Several arbitrarily selected, inactive tat clones were sequenced to evaluate the extent of the mutagenesis. Moreover, fourteen recombinants encoding varying levels of transcriptional trans-activator activity were isolated by transient transfection of sub-library pools into a HeLa cell line bearing an HIV-LTR-chloramphenicol acetyltransferase (CAT) reporter gene. Sequence data revealed a spectrum of alterations including nucleotide substitutions, insertions, and deletions, suggesting that mutations arose from both the doped DNA synthesis and the subsequent PCR 'rescue' of full-length product. Sequence comparison between inactive and active Tat clones revealed a selection pressure against amino-acid substitutions within the N-terminal domains of Tat, indicating the importance of this region to trans-activation competence. In addition, single and double missense mutations within the basic-rich, TAR RNA-binding domain were seen to be tolerated within active Tat clones.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Siderovski DP,Matsuyama T,Frigerio E,Chui S,Min X,Erfle H,Sumner-Smith M,Barnett RW,Mak TWdoi
10.1093/nar/20.20.5311keywords:
subject
Has Abstractpub_date
1992-10-25 00:00:00pages
5311-20issue
20eissn
0305-1048issn
1362-4962journal_volume
20pub_type
杂志文章abstract：:The sigma(54) factor associates with core RNA polymerase (RNAP) to form a holoenzyme that is unable to initiate transcription unless acted on by an activator protein. sigma(54) is closely involved in many steps of activator-dependent transcription, such as core RNAP binding, promoter recognition, activator interaction...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp419
更新日期：2009-07-01 00:00:00
abstract：:The occurrence of DNA tracts of the three binary base combinations: R.Y, K.M and W;S has been mapped in the complete genomes of Haemophilus influenzae and Escherichia coli. A highly significant over-representation of W tracts is observed in both bacteria. The excess of W tracts is particularly striking in the 10% inte...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.22.4491
更新日期：1999-11-15 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：:The investigation of RNA structure, dynamics and biological function often requires the site-specific incorporation of non-natural moieties. Here we describe the functionalization of RNA transcripts by aldehyde-hydrazine chemistry using a simple initiator nucleotide that carries an acetal-protected aldehyde function. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl1110
更新日期：2007-01-01 00:00:00
abstract：:We have previously mapped a repression domain from the active transcriptional repressor E4BP4 to a 65 amino acid segment near the C-terminus of the polypeptide. Here we show that the E4BP4 repression domain interacts specifically with the TBP binding repressor protein Dr1. Mutants that affect the ability of E4BP4 to b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.18.3607
更新日期：1996-09-15 00:00:00
abstract：:We recently identified a region of preferential replication initiation, oriGNAI3, near the 3' end of the Chinese hamster GNAI3 gene. oriGNAI3 is co-amplified in mutants selected for AMPD2 amplification, a process generating chromosomal rearrangements. In this report we have taken advantage of cell lines with truncated...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.7.1600
更新日期：1999-04-01 00:00:00
abstract：:The 'regions' method for multisequence alignment used in the previously reported program MALIGN has been generalized to include recursive refinement so that unaligned portions between two regions at the current level of resolution can be handled with increased resolution. Additionally, there is incorporated a limiting...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.5.1683
更新日期：1988-03-11 00:00:00
abstract：:mRNA deadenylation is under the control of cis-acting regulatory elements, which include AU-rich elements (AREs) and microRNA (miRNA) targeting sites, within the 3' untranslated region (3' UTRs) of eukaryotic mRNAs. Deadenylases promote miRNA-induced mRNA decay through their interaction with miRNA-induced silencing co...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv959
更新日期：2015-12-15 00:00:00
abstract：:7,8-Dihydro-8-oxo-deoxyguanosine (8oxodG) is a highly premutagenic DNA lesion due to its ability to mispair with adenine. Schizosaccharomyces pombe lacks homologs for relevant enzymes that repair 8oxodG, which suggests that this lesion could be persistent and must be tolerated. Here we show that SpPol4, the unique Pol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku711
更新日期：2014-09-01 00:00:00
abstract：:Telomerase activity, not detectable in somatic cells but frequently activated during carcinogenesis, confers immortality to tumors. Mechanisms governing expression of the catalytic subunit hTERT, the limiting factor for telomerase activity, still remain unclear. We previously proposed a model in which the binding of t...
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
abstract：:The effect of amino groups attached at positions 2 and 8 of the hypoxanthine moiety in the structure, reactivity and stability of DNA duplexes and triplexes is studied by means of quantum mechanical calculations, as well as extended molecular dynamics (MD) and thermodynamic integration (MD/TI) simulations. Theoretical...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.12.2522
更新日期：2001-06-15 00:00:00
abstract：:In continuation with work regarding the evaluation of the energy of association of various RNA bases with various base pairs, the results of the computations of the electrostatic interaction energy of A-U base pair with four RNA bases viz. Adenine, Uracil, Guanine and Cytosine have been reported. Non bonded induced po...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.17.3983
更新日期：1980-09-11 00:00:00
abstract：:The conditions under which Drosophila melanogaster are grown markedly influence the amount of the hypermodified nucleoside Q found in certain tRNAs. This effect on Q biosynthesis was found in both the wild-type and the suppressor of sable [su(s)2] mutant. Suppressed vermilion flies [su(s)2v; bw] with 78% of the tyrosi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.11.3919
更新日期：1977-11-01 00:00:00
abstract：:Precursor tRNAAsp molecules, containing a 26-base 5' leader, were treated with diethylpyrocarbonate, 50% hydrazine or anhydrous hydrazine/3M NaCl and then subjected to processing by RNase P RNAs from Escherichia coli or Bacillus subtilis. Fully processed tRNAs and material not successfully cleaved by the catalytic RNA...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.4.885
更新日期：1991-02-25 00:00:00
abstract：:The catalytic function of the hairpin ribozyme has been investigated by modification-interference analysis of both ribozyme and substrate, using ribonucleoside phosphorothioates. Thiophosphate substitutions in two ribozyme domains were examined by using a novel and highly efficient two-piece ribozyme assembled from tw...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.11.2835
更新日期：1992-06-11 00:00:00
abstract：:Transcription termination defines accurate transcript 3'-ends and ensures programmed transcriptomes, making it critical to life. However, transcription termination mechanisms remain largely unknown in Archaea. Here, we reported the physiological significance of the newly identified general transcription termination fa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa702
更新日期：2020-09-25 00:00:00
abstract：:The bacteriophage ø29 DNA packaging motor that assembles on the precursor capsid (prohead) contains an essential 174-nt structural RNA (pRNA) that forms multimers. To determine the structural features of the CE- and D-loops believed to be involved in multimerization of pRNA, 35- and 19-nt RNA molecules containing the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm874
更新日期：2008-02-01 00:00:00
abstract：:To explain the activation of transcription by a remote enhancer, two models are most often considered, namely looping and scanning. A scanning model, also referred to as 'polymerase entry site' model predicts that for two adjacent promoters the one proximal to an enhancer would be preferentially activated. Preferentia...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.22.8931
更新日期：1989-11-25 00:00:00
abstract：:Many interacting proteins regulate and/or assist the activities of RAD51, a recombinase which plays a critical role in both DNA repair and meiotic recombination. Yeast two-hybrid screening of a human testis cDNA library revealed a new protein, RAD51AP2 (RAD51 Associated Protein 2), that interacts strongly with RAD51. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl665
更新日期：2006-01-01 00:00:00
abstract：:Bacterial Rho-independent terminators (RITs) are important genomic landmarks involved in gene regulation and terminating gene expression. In this investigation we present RNIE, a probabilistic approach for predicting RITs. The method is based upon covariance models which have been known for many years to be the most a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr168
更新日期：2011-08-01 00:00:00
abstract：:Transcriptionally non-co-linear (NCL) transcripts can originate from trans-splicing (trans-spliced RNA; 'tsRNA') or cis-backsplicing (circular RNA; 'circRNA'). While numerous circRNAs have been detected in various species, tsRNAs remain largely uninvestigated. Here, we utilize integrative transcriptome sequencing of p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky032
更新日期：2018-04-20 00:00:00
abstract：:By screening a rabbit reticulocyte library, an alternative 15-LOX transcript of 3.6 kb (15-LOX mRNA2) was detected containing a 1019 nt longer 3'-untranslated region (UTR2) than the main 2.6 kb mRNA (15-LOX mRNA1). In anaemic animals, northern blotting showed that 15-LOX mRNA2 was predominantly expressed in non-erythr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.8.1828
更新日期：1999-04-15 00:00:00
abstract：:A new method is reported for the synthesis of oligodeoxyribonucleotides containing 2-aminopurine residues at selected sites. This method involves protection of the 2-aminopurine ribonucleoside, reduction to the deoxyribonucleoside and standard preparation of the 5'-0- (4,4'-dimethoxytrityl)-3'-O-(2-cyanoethyl)-N,N- di...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.4.754
更新日期：1996-02-15 00:00:00
abstract：:Melanotransferrin (MTf) is a tumor associated antigen found in abundance on the surface of melanoma cells. It is a transferrin-like protein found in low amount in most adult tissues and whose gene is reminiscent of house-keeping genes. With the goal of understanding the regulatory mechanisms which might explain the en...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.11.2853
更新日期：1992-06-11 00:00:00
abstract：:The iProClass database provides comprehensive, value-added descriptions of proteins and serves as a framework for data integration in a distributed networking environment. The protein information in iProClass includes family relationships as well as structural and functional classifications and features. The current v...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg044
更新日期：2003-01-01 00:00:00
abstract：:Three different types of repetitive Eco RI fragments, which comigrate within a visible band of approximately 500 bp at gel electrophoresis of Xenopus laevis DNA Eco RI digests have been cloned and sequenced. These sequences are designated as Repetitive Eco RI Monomers: REM 1, REM 2 and REM 3. The sequences contain dir...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.12.4921
更新日期：1984-06-25 00:00:00
abstract：:An efficient chemical procedure for the immobilization of carboxylate containing conjugate groups onto controlled pore glass (CPG) is described. The derivatized supports were used in the automated synthesis of an oligodeoxynucleotide (20-mer ODN) containing a 3' phosphodiester linked hexanol, aminohexyl, acridine, or ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.1.145
更新日期：1993-01-11 00:00:00
abstract：:When B cells differentiate into plasma cells, there is a large increase in the cellular content of mRNA coding for immunoglobulin. This increase cannot be fully accounted for by the increase in rate of transcription of the genes. We have investigated the possibility that the half-life of mu heavy chain mRNA increases ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.24.10439
更新日期：1989-12-25 00:00:00
abstract：:Two models have been proposed for triggering release of the lagging strand polymerase at the replication fork, enabling cycling to the primer for the next Okazaki fragment--either collision with the 5'-end of the preceding fragment (collision model) or synthesis of a new primer by primase (signaling model). Specific p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1098
更新日期：2014-02-01 00:00:00
abstract：:We have isolated an eight kilobase fragment of Bacillus subtilis DNA by specific integration and excision of a plasmid containing a sequence adjacent to ribosomal operon rrn O. The genetic locus of the cloned fragment was verified by linkage of the integrated vector to nearby genetic markers using both transduction an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.15.6307
更新日期：1984-08-10 00:00:00
