Intron mobility in phage T4 is dependent upon a distinctive class of endonucleases and independent of DNA sequences encoding the intron core: mechanistic and evolutionary implications.

abstract：:T7 RNA polymerase promoters consist of a highly conserved 23 base-pair sequence that spans the site of the initiation of transcription (+1) and extends from -17 to +6. To determine the bases within the T7 consensus promoter that are essential for promoter function a library of mutant T7 promoters was constructed, and ...

journal_title：Nucleic acids research

authors： Ikeda RA,Ligman CM,Warshamana S

更新日期：1992-05-25 00:00:00

abstract：:A 15-residue sequence motif has been found in many polymerases from various species and involving DNA and RNA dependence and product. The motif is characterized by a Tyr-Gly-Asp-(Thr)-Asp core flanked by hydrophobic spans five residues in length. An mRNA maturase segment is also suggested to display the motif pattern....

journal_title：Nucleic acids research

authors： Argos P

更新日期：1988-11-11 00:00:00

abstract：:The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to s...

journal_title：Nucleic acids research

authors： Zhang X,Zhang Y,Zhang W

更新日期：2020-07-09 00:00:00

abstract：:YASS is a DNA local alignment tool based on an efficient and sensitive filtering algorithm. It applies transition-constrained seeds to specify the most probable conserved motifs between homologous sequences, combined with a flexible hit criterion used to identify groups of seeds that are likely to exhibit significant ...

journal_title：Nucleic acids research

authors： Noé L,Kucherov G

更新日期：2005-07-01 00:00:00

abstract：:The solubility of adult beta-globin chromatin (beta A chromatin) from immature chicken red blood cells can be controlled by the presence or absence of n-butyrate in a cell incubation medium. In the absence of n-butyrate, only a small percentage (approximately 4%) of the total beta A chromatin is in a soluble chromatin...

journal_title：Nucleic acids research

authors： Ferenz CR,Nelson DA

更新日期：1985-03-25 00:00:00

abstract：:Synthesis and radioiodination of a stannyl oligodeoxyribonucleotide were undertaken to evaluate a gamma ray emitting ODN ligand for thrombus imaging in vivo . Synthesis of the ODN was based on modified automatedbeta-cyanoethyl phosphoramidite chemistry with an organotin nucleoside (dU*) coupled to a thrombin binding a...

journal_title：Nucleic acids research

authors： Dougan H,Hobbs JB,Weitz JI,Lyster DM

更新日期：1997-07-15 00:00:00

abstract：:The Kruppel-like factor 5 (KLF5/IKLF) belongs to the Kruppel family of genes which bind GC-rich DNA elements and activate or repress their target genes in a promoter context and/or cellular environment-dependent manner. In the present study, we used the Gal4 fusion assay system to characterize the mechanism of transac...

journal_title：Nucleic acids research

authors： Zhang Z,Teng CT

更新日期：2003-04-15 00:00:00

abstract：:Hfq, a bacterial RNA-binding protein, was recently shown to contain the Sm1 motif, a characteristic of Sm and LSm proteins that function in RNA processing events in archaea and eukaryotes. In this report, comparative structural modeling was used to predict a three-dimensional structure of the Hfq core sequence. The pr...

journal_title：Nucleic acids research

authors： Sun X,Zhulin I,Wartell RM

更新日期：2002-09-01 00:00:00

abstract：:Restriction endonucleases HindII and TaqI, but not SalI, were found to efficiently cleave synthetic hexadecanucleotide duplexes which contained either an A/C or a G/T mismatch within their respective restriction sites. Double-stranded M13 DNAs with identical mismatches were also cleaved under the assay conditions. The...

journal_title：Nucleic acids research

authors： Jiricny J,Martin D

更新日期：1986-03-11 00:00:00

abstract：:The RDM1 gene encodes a RNA recognition motif (RRM)-containing protein involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. We previously reported a cDNA encoding the full-length human RDM1 protein. Here, we describe the identification of 11 human cDNAs encoding RDM1 protein isoforms. Th...

journal_title：Nucleic acids research

authors： Messaoudi L,Yang YG,Kinomura A,Stavreva DA,Yan G,Bortolin-Cavaillé ML,Arakawa H,Buerstedde JM,Hainaut P,Cavaillé J,Takata M,Van Dyck E

更新日期：2007-01-01 00:00:00

abstract：:Post-translational modifications (such as ubiquitination) of clock proteins are critical in maintaining the precision and robustness of the evolutionarily conserved circadian clock. Ubiquitination of the core clock transcription factor BMAL1 (brain and muscle Arnt-like 1) has recently been reported. However, it remain...

journal_title：Nucleic acids research

authors： Gossan NC,Zhang F,Guo B,Jin D,Yoshitane H,Yao A,Glossop N,Zhang YQ,Fukada Y,Meng QJ

更新日期：2014-05-01 00:00:00

abstract：:3'-O-(5'-phosphoryldeoxycytidyl) phosphorothioate and fluorescent 3'-O-(5'-phosphoryldeoxycytidyl) S-bimane phosphorothioate can be ligated to tRNA by T4 RNA ligase. They are also efficient donors for the enzymatic ligation to oligodeoxynucleotides bearing a 3'-cytidine terminus. Cytidine 3',5'-bisphosphate is also a ...

journal_title：Nucleic acids research

authors： Cosstick R,McLaughlin LW,Eckstein F

更新日期：1984-02-24 00:00:00

abstract：:Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and appli...

journal_title：Nucleic acids research

authors： Kuriata A,Gierut AM,Oleniecki T,Ciemny MP,Kolinski A,Kurcinski M,Kmiecik S

更新日期：2018-07-02 00:00:00

abstract：:Here we examined the role of cellular vitamin C in genotoxicity of carcinogenic chromium(VI) that requires reduction to induce DNA damage. In the presence of ascorbate (Asc), low 0.2-2 microM doses of Cr(VI) caused 10-15 times more chromosomal breakage in primary human bronchial epithelial cells or lung fibroblasts. D...

journal_title：Nucleic acids research

authors： Reynolds M,Stoddard L,Bespalov I,Zhitkovich A

更新日期：2007-01-01 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

authors： Sylvester I,Schöler HR

更新日期：1994-03-25 00:00:00

abstract：:We present a theory of pluralistic and stochastic gene regulation. To bridge the gap between empirical studies and mathematical models, we integrate pre-existing observations with our meta-analyses of the ENCODE ChIP-Seq experiments. Earlier evidence includes fluctuations in levels, location, activity, and binding of ...

journal_title：Nucleic acids research

authors： Salas EN,Shu J,Cserhati MF,Weeks DP,Ladunga I

更新日期：2016-06-02 00:00:00

abstract：:Gene expression is a multi-step process involving many layers of regulation. The main regulators of the pathway are DNA and RNA binding proteins. While over the years, a large number of DNA and RNA binding proteins have been identified and extensively studied, it is still expected that many other proteins, some with y...

journal_title：Nucleic acids research

authors： Paz I,Kligun E,Bengad B,Mandel-Gutfreund Y

更新日期：2016-07-08 00:00:00

abstract：:We have demonstrated that the DNA sequence between two triplex-forming polypurine.polypyrimidine (Pu.Py) tracts was protected from DNA modifying enzymes upon formation of triplex DNA structures with an oligodeoxyribonucleotide in which two triplex-forming Pu or Py tracts were placed at the termini (triplex-bridge form...

journal_title：Nucleic acids research

authors： Kiyama R,Oishi M

更新日期：1995-02-11 00:00:00

abstract：:Instability of complex mammalian genomic DNA inserts is commonplace in cosmid libraries constructed in conventional multicopy vectors. To develop a means to construct stable libraries, we have developed a low copy number cosmid vector based on the E. coli F factor replicon (Fosmid). We have tested relative stability o...

journal_title：Nucleic acids research

authors： Kim UJ,Shizuya H,de Jong PJ,Birren B,Simon MI

更新日期：1992-03-11 00:00:00

abstract：:Using a combination of bioinformatic and molecular biology approaches a Drosophila melanogaster protein, DmTTF, has been identified, which exhibits sequence and structural similarity with two mitochondrial transcription termination factors, mTERF (human) and mtDBP (sea urchin). Import/processing assays indicate that D...

journal_title：Nucleic acids research

authors： Roberti M,Polosa PL,Bruni F,Musicco C,Gadaleta MN,Cantatore P

更新日期：2003-03-15 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

authors： Rubin E,Levy AA

更新日期：1996-09-15 00:00:00

abstract：:The rolling circle DNA replication structures generated by the in vitro phage T4 replication system were analyzed using two-dimensional agarose gels. Replication structures were generated in the presence or absence of T4 primase (gp61), permitting the analysis of replication forks with either duplex or single-stranded...

journal_title：Nucleic acids research

authors： Belanger KG,Mirzayan C,Kreuzer HE,Alberts BM,Kreuzer KN

更新日期：1996-06-01 00:00:00

abstract：:No analogous nucleoside triphosphate was found which acts as well as ATP in binding to and supporting catalysis of leucyl-tRNA synthetase from Escherichia coli MRE 600. However, there are numerous nucleotides which are able to replace ATP, but with lower efficiency. The 6-amino group of the adenine ring and the 2'-hyd...

journal_title：Nucleic acids research

authors： Marutzky R,Flossdorf J,Kula MR

更新日期：1976-08-01 00:00:00

abstract：:X chromosome inactivation results in the cis-limited inactivation of most, but not all, genes on one of the two X chromosomes in mammalian females. The molecular basis for inactivation is unknown. In order to examine the transcriptional activity of human X-linked genes, a series of mouse-human somatic cell hybrids und...

journal_title：Nucleic acids research

authors： Brown CJ,Flenniken AM,Williams BR,Willard HF

更新日期：1990-07-25 00:00:00

abstract：:We have developed general methods for joining together, via cleavable disulfide bonds, either two unprotected polynucleotides or a polynucleotide and a peptide or protein. To join two oligonucleotides, each is first converted to an adduct in which cystamine is joined to the 5'-terminal phosphate of the oligonucleotide...

journal_title：Nucleic acids research

authors： Chu BC,Orgel LE

更新日期：1988-05-11 00:00:00

abstract：:The universal L-shaped tertiary structure of tRNAs is maintained with the help of nucleotide modifications within the D- and T-loops, and these modifications are most extensive within hyperthermophilic species. The obligate-commensal Nanoarchaeum equitans and its phylogenetically-distinct host Ignicoccus hospitalis gr...

journal_title：Nucleic acids research

authors： Rose S,Auxilien S,Havelund JF,Kirpekar F,Huber H,Grosjean H,Douthwaite S

更新日期：2020-07-09 00:00:00

abstract：:The field bean, Vicia faba L. var. minor, possesses two sub-families of 11 S legumin genes named A and B. We isolated from a genomic library a B-type gene (LeB4) and determined its primary DNA sequence. Gene LeB4 codes for a 484 amino acid residue prepropolypeptide, encompassing a signal peptide of 22 amino acid resid...

journal_title：Nucleic acids research

authors： Bäumlein H,Wobus U,Pustell J,Kafatos FC

更新日期：1986-03-25 00:00:00

abstract：:In a bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP)/transcription factor binding screen, we identified Mycobacterium smegmatis Ms6479 as the first c-di-GMP-responsive transcriptional factor in mycobacteria. Ms6479 could specifically bind with c-di-GMP and recognize the promoters of 37 lipid transport an...

journal_title：Nucleic acids research

authors： Li W,He ZG

更新日期：2012-12-01 00:00:00

abstract：:During erythropoiesis in the chick, the nucleosome repeat length increases from 190 base pairs to 212 base pairs. This increase is correlated with a dramatic increase in the concentration of the red cell specific histone H5 (from 0.2 molecules per nucleosome to 1 molecule per nucleosome) and with no change in the conc...

journal_title：Nucleic acids research

authors： Weintraub H

更新日期：1978-04-01 00:00:00

abstract：:The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of known protein structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and distant evolutionary relationships; the third, fold...

journal_title：Nucleic acids research

authors： Lo Conte L,Ailey B,Hubbard TJ,Brenner SE,Murzin AG,Chothia C

更新日期：2000-01-01 00:00:00