Pausing of reverse transcriptase on retroviral RNA templates is influenced by secondary structures both 5' and 3' of the catalytic site.

abstract：:Upon infection of Escherichia coli by bacteriophage Qβ, the virus-encoded β-subunit recruits host translation elongation factors EF-Tu and EF-Ts and ribosomal protein S1 to form the Qβ replicase holoenzyme complex, which is responsible for amplifying the Qβ (+)-RNA genome. Here, we use X-ray crystallography, NMR spect...

journal_title：Nucleic acids research

authors： Gytz H,Mohr D,Seweryn P,Yoshimura Y,Kutlubaeva Z,Dolman F,Chelchessa B,Chetverin AB,Mulder FA,Brodersen DE,Knudsen CR

更新日期：2015-12-15 00:00:00

abstract：:Direct visualization of DNA and proteins allows researchers to investigate DNA-protein interactions with great detail. Much progress has been made in this area as a result of increasingly sensitive single-molecule fluorescence techniques. At the same time, methods that control the conformation of DNA molecules have be...

journal_title：Nucleic acids research

authors： van Mameren J,Peterman EJ,Wuite GJ

更新日期：2008-08-01 00:00:00

abstract：:DNA polymerase III (DNA pol III) efficiently replicates the Escherichia coli genome, but it cannot bypass DNA damage. Instead, translesion synthesis (TLS) DNA polymerases are employed to replicate past damaged DNA; however, the exchange of replicative for TLS polymerases is not understood. The umuD gene products, whic...

journal_title：Nucleic acids research

authors： Silva MC,Nevin P,Ronayne EA,Beuning PJ

更新日期：2012-07-01 00:00:00

abstract：:Stability of aromatic phosphoramidates was studied using 2',3'-O-dibenzoyluridine 5'-phosphoramidates and N,2',3'-O-tribenzoylcytidine 5'-phosphate. The effect of dicyclohexylcarbodiimide in this mixture was investigated. Decomposition of the anilidate was slower in the presence of DCC. Substituted anilidates of uridi...

journal_title：Nucleic acids research

authors： Otsuka E,Honda A,Shigyo H,Morioka S,Sugiyama T

更新日期：1974-02-01 00:00:00

abstract：:Interaction detection methods have led to the discovery of thousands of interactions between proteins, and discerning relevance within large-scale data sets is important to present-day biology. Here, a spectral method derived from graph theory was introduced to uncover hidden topological structures (i.e. quasi-cliques...

journal_title：Nucleic acids research

authors： Bu D,Zhao Y,Cai L,Xue H,Zhu X,Lu H,Zhang J,Sun S,Ling L,Zhang N,Li G,Chen R

更新日期：2003-05-01 00:00:00

abstract：:Melting of DNA in a segment bounded at both ends by regions of greater stability during electrophoresis in denaturing gradient gels show complex properties, not accommodated with standard melting theory. Compact bands of some DNA molecules become anomalously broadened at the retardation level in a denaturing gradient,...

journal_title：Nucleic acids research

authors： Abrams ES,Murdaugh SE,Lerman LS

更新日期：1995-07-25 00:00:00

abstract：:WorfDB (Worm ORFeome DataBase; http://worfdb.dfci.harvard.edu) was created to integrate and disseminate the data from the cloning of complete set of approximately 19 000 predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans (also referred to as the 'worm ORFeome'). WorfDB serves as a central ...

journal_title：Nucleic acids research

authors： Vaglio P,Lamesch P,Reboul J,Rual JF,Martinez M,Hill D,Vidal M

更新日期：2003-01-01 00:00:00

abstract：:The human mitochondrial translation apparatus, which synthesizes the core subunits of the oxidative phosphorylation system, is of central interest as mutations in several genes encoding for mitoribosomal proteins or translation factors cause severe human diseases. Little is known, how this complex machinery assembles ...

journal_title：Nucleic acids research

authors： Lavdovskaia E,Kolander E,Steube E,Mai MM,Urlaub H,Richter-Dennerlein R

更新日期：2018-09-19 00:00:00

abstract：:U6 RNA is a member of a class of small abundant stable nuclear RNAs that are essential for splicing. In all species examined so far, the U6 RNA is a RNA polymerase III transcript. The U6 gene of the fission yeast Schizosaccharomyces pombe is unusual in that it is interrupted by an intron whose structure is similar to ...

journal_title：Nucleic acids research

authors： Potashkin J,Frendewey D

更新日期：1989-10-11 00:00:00

abstract：:We have isolated and sequenced a cDNA clone coding for human Retinol Binding Protein. The sequence indicates that Retinol Binding Protein is synthesized as a single polypeptide chain precursor which is then matured to the secreted protein by removal of a leader peptide. Southern and Northern blot analysis suggest that...

journal_title：Nucleic acids research

authors： Colantuoni V,Romano V,Bensi G,Santoro C,Costanzo F,Raugei G,Cortese R

更新日期：1983-11-25 00:00:00

abstract：:Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library prepa...

journal_title：Nucleic acids research

authors： Harkins KM,Schaefer NK,Troll CJ,Rao V,Kapp J,Naughton C,Shapiro B,Green RE

更新日期：2020-05-07 00:00:00

abstract：:Planarian flatworms are in the midst of a renaissance as a model system for regeneration and stem cells. Besides two well-studied model species, hundreds of species exist worldwide that present a fascinating diversity of regenerative abilities, tissue turnover rates, reproductive strategies and other life history trai...

journal_title：Nucleic acids research

authors： Brandl H,Moon H,Vila-Farré M,Liu SY,Henry I,Rink JC

更新日期：2016-01-04 00:00:00

abstract：:The sequence requirements for transcriptional stimulation of the adenovirus major late promoter (MLP) by the products of the early transcription unit Ela and by the replication of viral DNA were analyzed by in vitro transcription. Sequences upstream of +33 are involved in the moderate Ela-responsiveness of the MLP, wh...

journal_title：Nucleic acids research

authors： Jansen-Durr P,Boeuf H,Kédinger C

更新日期：1988-05-11 00:00:00

abstract：:The dicistrovirus intergenic internal ribosome entry site (IGR IRES) directly recruits the ribosome and initiates translation using a non-AUG codon. A subset of IGR IRESs initiates translation in either of two overlapping open reading frames (ORFs), resulting in expression of the 0 frame viral structural polyprotein a...

journal_title：Nucleic acids research

authors： Ren Q,Au HH,Wang QS,Lee S,Jan E

更新日期：2014-08-01 00:00:00

abstract：:The leaf senescence database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. Through manual curation and extensive annotation, we updated the LSD to a new version LSD 3.0, which contains 5853 genes and 617 mutants from 68 species. To provide sustainable and reli...

journal_title：Nucleic acids research

authors： Li Z,Zhang Y,Zou D,Zhao Y,Wang HL,Zhang Y,Xia X,Luo J,Guo H,Zhang Z

更新日期：2020-01-08 00:00:00

abstract：:We attempted to use the polymerase chain reaction (PCR) to monitor in vitro recombination in a plasmid containing directly repeated sequences. Some of the plasmid preparations which had not been exposed to recombination conditions were however found to behave in the PCR test as if they had undergone homologous recombi...

journal_title：Nucleic acids research

authors： Marton A,Delbecchi L,Bourgaux P

更新日期：1991-05-11 00:00:00

abstract：:The high mobility group protein (HMG)-box is a DNA-binding domain found in many proteins that bind preferentially to DNA of irregular structures in a sequence-independent manner and can bend the DNA. We show here that GST-fusion proteins of HMG domains from HMG1 and HMG2 promote a triple-stranded complex formation bet...

journal_title：Nucleic acids research

authors： Suda T,Mishima Y,Takayanagi K,Asakura H,Odani S,Kominami R

更新日期：1996-12-01 00:00:00

abstract：UNLABELLED:The PubMed® database of biomedical citations allows the retrieval of scientific articles studying the function of chemicals in biology and medicine. Mining millions of available citations to search reported associations between chemicals and topics of interest would require substantial human time. We have im...

journal_title：Nucleic acids research

authors： Gijón-Correas JA,Andrade-Navarro MA,Fontaine JF

更新日期：2014-07-01 00:00:00

abstract：:Using the quenched flow technique the mechanism of seryl tRNA synthetase action has been investigated with respect to the presteady state kinetics of individual steps. Under conditions where the strong binding sites of the enzyme are nearly saturated and the steady state turnover number is about 1 s-1, rate constants ...

journal_title：Nucleic acids research

authors： Dibbelt L,Pachmann U,Zachau HG

更新日期：1980-09-11 00:00:00

abstract：:Genetic recombination in meiosis plays an important role in generating diversity of genetic information. In yeast an Escherichia coli RecA-like gene, DMC1, is expressed in meiotic prophase and its product co-localizes with Rad51 protein on zygotene chromosomes. We have cloned the mouse and human homologs of the yeast ...

journal_title：Nucleic acids research

authors： Habu T,Taki T,West A,Nishimune Y,Morita T

更新日期：1996-02-01 00:00:00

abstract：:The GeneNet system is designed for collection and analysis of the data on gene and metabolic networks, signal transduction pathways and kinetic characteristics of elementary processes. In the past 2 years, the GeneNet structure was considerably improved: (i) the current version of the database is now implemented using...

journal_title：Nucleic acids research

authors： Ananko EA,Podkolodny NL,Stepanenko IL,Podkolodnaya OA,Rasskazov DA,Miginsky DS,Likhoshvai VA,Ratushny AV,Podkolodnaya NN,Kolchanov NA

更新日期：2005-01-01 00:00:00

abstract：:We characterized and purified a protein from rat liver which specifically binds to a DNA motif present in a liver-specific enhancer of the rat tyrosine aminotransferase (TAT) gene, when offered as single-stranded DNA. Binding is highly sequence-specific and coincides with a region known to be essential for function of...

journal_title：Nucleic acids research

authors： Jansen-Dürr P,Boshart M,Lupp B,Bosserhoff A,Frank RW,Schütz G

更新日期：1992-03-25 00:00:00

abstract：:Bursts of free radicals produced by ionization of water in close vicinity to DNA can produce clusters of opposed DNA lesions and these are termed multiply damaged sites (MDS). How MDS are processed by the Escherichia coli DNA glycosylases, endonuclease (endo) III and endo VIII, which recognize oxidized pyrimidines, is...

journal_title：Nucleic acids research

authors： Harrison L,Hatahet Z,Purmal AA,Wallace SS

更新日期：1998-02-15 00:00:00

abstract：:Inosine was prepared (15% yield) by treatment of 5-amino-1-beta-D-ribofuranosyl-4-imidazolecarboxamide (AICA-riboside) with chloroform in the presence of sodium methoxide. This ring closure can be reasonably explained by assuming the formation of dichlorocarbene from chloroform and alkali. Carbon tetrachloride or hexa...

journal_title：Nucleic acids research

authors： Okutsu M,Yamazaki A

更新日期：1976-01-01 00:00:00

abstract：:We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5'-alternative splicing, 3'-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein s...

journal_title：Nucleic acids research

authors： Huang HD,Horng JT,Lin FM,Chang YC,Huang CC

更新日期：2005-01-01 00:00:00

abstract：:The extent of base pairing in Escherichia coli and Bacillus stearothermophilus 5S RNAs was determined by infrared spectroscopy. From the infrared spectra taken at 20 degrees and 52 degrees C it is concluded that E. coli and B. stearothermophlius 5S RNAs possess a large number of base pairs (Table I). Comparison of our...

journal_title：Nucleic acids research

authors： Appel B,Erdmann VA,Stulz J,Ackerman T

更新日期：1979-10-25 00:00:00

abstract：:The molecular organization of the dunce gene of Drosophila melanogaster has proved to be particularly complex, with two divergently transcribed genes, Sgs-4 and Pig-1, nested within its 79 kb intron (1). Here we report the identification and the molecular characterization of a third gene nested within the transcriptio...

journal_title：Nucleic acids research

authors： Furia M,Digilio FA,Artiaco D,Giordano E,Polito LC

更新日期：1990-10-11 00:00:00

abstract：:Amino acid sequences of 2 giant non-structural polyproteins (F1 and F2) of infectious bronchitis virus (IBV), a member of Coronaviridae, were compared, by computer-assisted methods, to sequences of a number of other positive strand RNA viral and cellular proteins. By this approach, juxtaposed putative RNA-dependent RN...

journal_title：Nucleic acids research

authors： Gorbalenya AE,Koonin EV,Donchenko AP,Blinov VM

更新日期：1989-06-26 00:00:00

abstract：:The genetic etiology of premature ovarian insufficiency (POI) has been well established to date, however, the role of long noncoding RNAs (lncRNAs) in POI is largely unknown. In this study, we identified a down-expressed lncRNA HCP5 in granulosa cells (GCs) from biochemical POI (bPOI) patients, which impaired DNA dama...

journal_title：Nucleic acids research

authors： Wang X,Zhang X,Dang Y,Li D,Lu G,Chan WY,Leung PCK,Zhao S,Qin Y,Chen ZJ

更新日期：2020-05-07 00:00:00

abstract：:The chromatin structure of yeast ribosomal DNA was analyzed in vivo by crosslinking intact cells with psoralen. We found that in exponentially growing cultures the regions coding for the 35S rRNA precursor fall into two distinct classes. One class was highly accessible to psoralen and associated with nascent RNAs, cha...

journal_title：Nucleic acids research

authors： Dammann R,Lucchini R,Koller T,Sogo JM

更新日期：1993-05-25 00:00:00