A short 5' region of the long terminal repeat is required for regulation by hormone and heat shock of Drosophila retrotransposon 1731.

abstract：:The binding of nine aminoalkyl adenylates to isoleucyl-tRNA synthetase from Escherichia coli MRE 600 was measured and compared with the binding of the cognate amino acids. It was found that they bind rather tightly to the enzyme, the Kd's ranging from 3.1.10(-4) M with glycinol-AMP ester to 3.7.10(-9) M with L-isoleuc...

journal_title：Nucleic acids research

authors： Flossdorf J,Marutzky R,Messer K,Kula MR

更新日期：1977-03-01 00:00:00

abstract：:Two similar, but not identical, models have been proposed for the amino acid-base pair contacts in the CAP-DNA complex ('Model I,' Weber, I. and Steitz, T., Proc. Natl. Acad. Sci. USA, 81, 3973-3977, 1984; 'Model II,' Ebright, et al., Proc. Natl. Acad. Sci. USA, 81, 7274-7278, 1984). One difference between the two mod...

journal_title：Nucleic acids research

authors： Gunasekera A,Ebright YW,Ebright RH

更新日期：1990-12-11 00:00:00

abstract：:The availability of a draft human genome sequence and ability to monitor the transcription of thousands of genes with DNA microarrays has necessitated the need for new computational tools that can analyze cis-regulatory elements controlling genes that display similar expression patterns. We have developed a tool desig...

journal_title：Nucleic acids research

authors： Zhang H,Ramanathan Y,Soteropoulos P,Recce ML,Tolias PP

更新日期：2002-11-01 00:00:00

abstract：:Software has been developed to assist RNA fingerprinting analysis. One program generates, from a DNA sequence data file, the oligonucleotides resulting from digestion of an RNA transcript labeled with any specified nucleotide(s). Oligonucleotides are sorted according to their position on the fingerprint. Expected mola...

journal_title：Nucleic acids research

authors： Gegenheimer P

更新日期：1988-03-11 00:00:00

abstract：:Conflicts between replication and transcription challenge chromosome duplication. Escherichia coli replisome movement along transcribed DNA is promoted by Rep and UvrD accessory helicases with Δrep ΔuvrD cells being inviable under rapid growth conditions. We have discovered that mutations in a tRNA gene, aspT, in an a...

journal_title：Nucleic acids research

authors： Myka KK,Hawkins M,Syeda AH,Gupta MK,Meharg C,Dillingham MS,Savery NJ,Lloyd RG,McGlynn P

更新日期：2017-03-17 00:00:00

abstract：:Phage_Finder, a heuristic computer program, was created to identify prophage regions in completed bacterial genomes. Using a test dataset of 42 bacterial genomes whose prophages have been manually identified, Phage_Finder found 91% of the regions, resulting in 7% false positive and 9% false negative prophages. A searc...

journal_title：Nucleic acids research

authors： Fouts DE

更新日期：2006-01-01 00:00:00

abstract：:The chicken c-myb gene and the v-myb oncogene transduced by avian myeloblastosis virus (AMV) encode DNA binding transcription activators. The DNA binding domain of AMV v-Myb displays a number of amino acid changes relative to c-Myb; v-Myb proteins in which one or more of three crucial residues in the DNA binding domai...

journal_title：Nucleic acids research

authors： Weston K

更新日期：1992-06-25 00:00:00

abstract：:It is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. ConSurf (http://consurf.tau.ac.il) and ConSeq (http://conseq.tau.ac.il) are two well-established web servers for calculating the evolutionar...

journal_title：Nucleic acids research

authors： Ashkenazy H,Erez E,Martz E,Pupko T,Ben-Tal N

更新日期：2010-07-01 00:00:00

abstract：:Variable regions within ribosomal RNAs frequently vary in length as a result of incorporating products of slippage. This makes constructing secondary structure models problematic because base homology is difficult or impossible to establish between species. Here, we model such a region by comparing the results of the ...

journal_title：Nucleic acids research

authors： Hancock JM,Vogler AP

更新日期：1998-04-01 00:00:00

abstract：:We have sequenced the genome of Shigella flexneri serotype 2a, the most prevalent species and serotype that causes bacillary dysentery or shigellosis in man. The whole genome is composed of a 4 607 203 bp chromosome and a 221 618 bp virulence plasmid, designated pCP301. While the plasmid shows minor divergence from th...

journal_title：Nucleic acids research

authors： Jin Q,Yuan Z,Xu J,Wang Y,Shen Y,Lu W,Wang J,Liu H,Yang J,Yang F,Zhang X,Zhang J,Yang G,Wu H,Qu D,Dong J,Sun L,Xue Y,Zhao A,Gao Y,Zhu J,Kan B,Ding K,Chen S,Cheng H,Yao Z,He B,Chen R,Ma D,Qiang B,

更新日期：2002-10-15 00:00:00

abstract：:A study of the synthesis of oligothymidylates via phosphotriester intermediates on a polystyrene support is described. The sequence involves condensation of a phenyl nucleoside-3' -phosphorochloridate with the 5'-hydroxyl group of the carrier bound oligonucleotide derivative in the presence of 1-methylimidazole. Condi...

journal_title：Nucleic acids research

authors： Pless RC,Letsinger RL

更新日期：1975-06-01 00:00:00

abstract：:In kinetoplastid protozoa, mitochondrial (mt) mRNAs are post-transcriptionally edited by insertion and deletion of uridylate residues, the information being provided by guide (g)RNAs. Currently popular mechanisms for the editing process envisage a series of consecutive 'cut-and-paste' reactions, carried out by a compl...

journal_title：Nucleic acids research

authors： Blom D,Burg Jv,Breek CK,Speijer D,Muijsers AO,Benne R

更新日期：2001-07-15 00:00:00

abstract：:PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB). Started at the Real World Computing Partnership (RWCP) in August 1997, it developed to the present system of PDB-REPRDB. In April 2001, the system was moved to the Computational Biology Research Center (CBRC), National Institut...

journal_title：Nucleic acids research

authors： Noguchi T,Akiyama Y

更新日期：2003-01-01 00:00:00

abstract：:Lambda-red system-based recombinogenic engineering is a powerful new method to engineer DNA without the need for restriction enzymes or ligases. Here, we report the use of a single selectable marker to enhance the usefulness of this approach. The strategy is to utilize the thymidylate synthase A (thyA) gene, which enc...

journal_title：Nucleic acids research

authors： Wong QN,Ng VC,Lin MC,Kung HF,Chan D,Huang JD

更新日期：2005-03-30 00:00:00

abstract：:The RNA-Seq technology has revolutionized transcriptome characterization not only by accurately quantifying gene expression, but also by the identification of novel transcripts like chimeric fusion transcripts. The 'fusion' or 'chimeric' transcripts have improved the diagnosis and prognosis of several tumors, and have...

journal_title：Nucleic acids research

authors： Li Y,Heavican TB,Vellichirammal NN,Iqbal J,Guda C

更新日期：2017-07-27 00:00:00

abstract：:Previously, we have shown that all class-1 polypeptide release factors (RFs) share a common glycine-glycine-glutamine (GGQ) motif, which is critical for RF activity. Here, we subjected to site-directed mutagenesis two invariant amino acids, Gln185 and Arg189, situated in the GGQ minidomain of human eRF1, followed by d...

journal_title：Nucleic acids research

authors： Seit-Nebi A,Frolova L,Justesen J,Kisselev L

更新日期：2001-10-01 00:00:00

abstract：:BsoFI , ItaI and Fsp4HI are isoshizomers of Fnu4HI (5'-GC NGC-3'). Both Fnu4HI and BsoFI have previously been shown to be inhibited by cytosine-specific methylation within the recognition sequence. Fnu4HI is inhibited if either the internal cytosine at position 2 or the external cytosine at position 5 of the restricti...

journal_title：Nucleic acids research

authors： Ramsahoye BH,Burnett AK,Taylor C

更新日期：1997-08-15 00:00:00

abstract：:Calf thymus nucleosomes exhibit two different and independent hydrodynamic responses to diminishing salt concentration. One change is gradual over the range 40 to 0.2 mM Na+ and is accompanied by decreases in contact-site cross-linking efficiency. The other change is abrupt, being centered between 1 and 2 mM Na+. We f...

journal_title：Nucleic acids research

authors： Burch JB,Martinson HG

更新日期：1980-11-11 00:00:00

abstract：:Base excision repair (BER), which is initiated by DNA N-glycosylase proteins, is the frontline for repairing potentially mutagenic DNA base damage. The NTHL1 glycosylase, which excises DNA base damage caused by reactive oxygen species, is thought to be a tumor suppressor. However, in addition to NTHL1 loss-of-function...

journal_title：Nucleic acids research

authors： Limpose KL,Trego KS,Li Z,Leung SW,Sarker AH,Shah JA,Ramalingam SS,Werner EM,Dynan WS,Cooper PK,Corbett AH,Doetsch PW

更新日期：2018-05-18 00:00:00

abstract：:DnaD and DnaB are essential DNA-replication-initiation proteins in low-G+C content Gram-positive bacteria. Here we use sensitive Hidden Markov Model-based techniques to show that the DnaB and DnaD proteins share a common structure that is evident across all their structural domains, termed DDBH1 and DDBH2 (DnaD DnaB H...

journal_title：Nucleic acids research

authors： Marston FY,Grainger WH,Smits WK,Hopcroft NH,Green M,Hounslow AM,Grossman AD,Craven CJ,Soultanas P

更新日期：2010-11-01 00:00:00

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...

journal_title：Nucleic acids research

authors： Siderovski DP,Matsuyama T,Frigerio E,Chui S,Min X,Erfle H,Sumner-Smith M,Barnett RW,Mak TW

更新日期：1992-10-25 00:00:00

abstract：:The 3' splice site of the second intron (I2) of the human apolipoprotein-AII gene, (GT)16GGGCAG, is unique in that, although fully functional, a stretch of alternating guanine and thymine residues replaces the polypyrimidine tract usually associated with 3' splice junctions. The transient expression of successive 5' d...

journal_title：Nucleic acids research

authors： Shelley CS,Baralle FE

更新日期：1987-05-11 00:00:00

abstract：:Escherichia coli cells lacking the ribosomal RNA processing enzyme RNase III do no excise the normal RNA precursors p16a (17S) and p23a from nascent rRNA transcripts. These cells produce, instead, slightly larger p16b and p23b precursors. Digestion of p16b or p23b rRNA with RNases A plus T1 yields double-stranded frag...

journal_title：Nucleic acids research

authors： Gegenheimer P,Apirion D

更新日期：1980-04-25 00:00:00

abstract：:The nucleotide sequence of Drosophila melanogaster methionine tRNAi was determined to be: pA-G-C-A-G-A-G-U-m1G-m2G-C-G-C-A-G-U-G-G-A-A-G-C-G-U-m2G-C-U-G-G-G-C-C-C-A-U-t6A-A-C-C-C-A-G-A-G-m7G-D-m5C-C-C-G-A-G-G-A-U-C-G-m1A-A-A-C-C-U-U-G-C-U-C-U-G-C-U-A-C-C-A(OH). It differs from vertebrate initiator tRNAs in only 6 out ...

journal_title：Nucleic acids research

authors： Silverman S,Heckman J,Cowling GJ,Delaney AD,Dunn RJ,Gillam IC,Tener GM,Söll D,RajBhandary UL

更新日期：1979-02-01 00:00:00

abstract：:We have previously reported that transcription from a distal promoter (promoter B) of the estrogen receptor alpha (ERalpha) gene is responsible for the increased expression of ERalpha in human breast carcinomas. This paper first characterized the promoter B region in terms of transient transfection experiments with lu...

journal_title：Nucleic acids research

authors： Tanimoto K,Eguchi H,Yoshida T,Hajiro-Nakanishi K,Hayashi S

更新日期：1999-02-01 00:00:00

abstract：:Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-transla...

journal_title：Nucleic acids research

authors： Lu CT,Huang KY,Su MG,Lee TY,Bretaña NA,Chang WC,Chen YJ,Chen YJ,Huang HD

更新日期：2013-01-01 00:00:00

abstract：:Tunable induction of gene expression is an essential tool in biology and biotechnology. In spite of that, current induction systems often exhibit unpredictable behavior and performance shortcomings, including high sensitivity to transactivator dosage and plasmid take-up variation, and excessive consumption of cellular...

journal_title：Nucleic acids research

authors： Lillacci G,Benenson Y,Khammash M

更新日期：2018-10-12 00:00:00

abstract：:IL-2 gene expression in activated T-cells is initiated by chromatin remodeling at the IL-2 proximal promoter and conversion of a transcriptional repressor into a potent transcriptional activator. A purine-box regulator complex was purified from activated Jurkat T-cell nuclei based on sequence-specific DNA binding to t...

journal_title：Nucleic acids research

authors： Shi L,Qiu D,Zhao G,Corthesy B,Lees-Miller S,Reeves WH,Kao PN

更新日期：2007-01-01 00:00:00

abstract：:Dictyostelium intermediate repeat sequence 1 (DIRS-1) is the founding member of a poorly characterized class of retrotransposable elements that contain inverse long terminal repeats and tyrosine recombinase instead of DDE-type integrase enzymes. In Dictyostelium discoideum, DIRS-1 forms clusters that adopt the functio...

journal_title：Nucleic acids research

authors： Wiegand S,Meier D,Seehafer C,Malicki M,Hofmann P,Schmith A,Winckler T,Földesi B,Boesler B,Nellen W,Reimegård J,Käller M,Hällman J,Emanuelsson O,Avesson L,Söderbom F,Hammann C

更新日期：2014-03-01 00:00:00

abstract：:Trf4/5p-Air1/2p-Mtr4p polyadenylation complex (TRAMP) is an essential component of nuclear RNA surveillance in yeast. It recognizes a variety of nuclear transcripts produced by all three RNA polymerases, adds short poly(A) tails to aberrant or unstable RNAs and activates the exosome for their degradation. Despite the ...

journal_title：Nucleic acids research

authors： Holub P,Lalakova J,Cerna H,Pasulka J,Sarazova M,Hrazdilova K,Arce MS,Hobor F,Stefl R,Vanacova S

更新日期：2012-07-01 00:00:00