Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus.

abstract：:Microbial biosynthetic gene clusters are a valuable source of bioactive molecules. However, because they typically represent a small fraction of genomic material in most metagenomic samples, it remains challenging to deeply sequence them. We present an approach to isolate and sequence gene clusters in metagenomic samp...

journal_title：Nucleic acids research

authors： Xu P,Modavi C,Demaree B,Twigg F,Liang B,Sun C,Zhang W,Abate AR

更新日期：2020-05-07 00:00:00

abstract：:A cross index is presented for using the improved selectivity offered by the Hung and Wensink (Nucl. Acids Res. 12, 1863-1874, 1984) method of partially filling in 5'-extensions produced by type II restriction endonucleases. After this treatment, DNA fragments which normally cannot be ligated to one another, can be jo...

journal_title：Nucleic acids research

authors： Korch C

更新日期：1987-04-24 00:00:00

abstract：:The protein property prediction and testing database (PPT-DB) is a database housing nearly 30 carefully curated databases, each of which contains commonly predicted protein property information. These properties include both structural (i.e. secondary structure, contact order, disulfide pairing) and dynamic (i.e. orde...

journal_title：Nucleic acids research

authors： Wishart DS,Arndt D,Berjanskii M,Guo AC,Shi Y,Shrivastava S,Zhou J,Zhou Y,Lin G

更新日期：2008-01-01 00:00:00

abstract：:Advancement in the field of computational research has made it possible for the in silico methods to offer significant benefits to both regulatory needs and requirements for risk assessments, and pharmaceutical industry to assess the safety profile of a chemical. Here, we present ProTox-II that incorporates molecular ...

journal_title：Nucleic acids research

authors： Banerjee P,Eckert AO,Schrey AK,Preissner R

更新日期：2018-07-02 00:00:00

abstract：:The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provide...

journal_title：Nucleic acids research

authors： Markowitz VM,Chen IM,Palaniappan K,Chu K,Szeto E,Grechkin Y,Ratner A,Jacob B,Huang J,Williams P,Huntemann M,Anderson I,Mavromatis K,Ivanova NN,Kyrpides NC

更新日期：2012-01-01 00:00:00

abstract：:The C-terminal domain (CTD) of the large subunit of RNA polymerase II plays a role in transcription and RNA processing. Yeast ESS1, a peptidyl-prolyl cis/trans isomerase, is involved in RNA processing and can associate with the CTD. Using several types of assays we could not find any evidence of an effect of Pin1, the...

journal_title：Nucleic acids research

authors： Chao SH,Greenleaf AL,Price DH

更新日期：2001-02-01 00:00:00

abstract：:The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactio...

journal_title：Nucleic acids research

authors： Karp PD,Riley M,Paley SM,Pellegrini-Toole A,Krummenacker M

更新日期：1999-01-01 00:00:00

abstract：:Denaturing gradient gel electrophoresis (DGGE) is based upon the different melting behaviors of DNA molecules in a chemical denaturant gradient according to their sequences. This technique has recently become a widespread tool to detect mutations. The introduction of a GC-clamp enables the detection of most single bas...

journal_title：Nucleic acids research

authors： Weber CK,Shaffer DJ,Sidman CL

更新日期：1991-06-25 00:00:00

abstract：:A set of programs was developed for searching nucleic acid and protein sequence data bases for sequences similar to a given sequence. The programs, written in FORTRAN 77, were optimized for vector processing on a Hitachi S810-20 supercomputer. A search of a 500-residue protein sequence against the entire PIR data base...

journal_title：Nucleic acids research

authors： Gotoh O,Tagashira Y

更新日期：1986-01-10 00:00:00

abstract：:S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold. The data are mainly extracted from original publications, but a World Wide Web interface for direct...

journal_title：Nucleic acids research

authors： Liebich I,Bode J,Frisch M,Wingender E

更新日期：2002-01-01 00:00:00

abstract：:A formaldehyde denaturation map of the replicative form of phiX174 DNA is obtained. The RFI DNA was converted into a linear state by restriction endonuclease pst I which introduces into this DNA a single double-stranded break. The map has four clear-cut peaks. Their positions excellently correlate with the peak positi...

journal_title：Nucleic acids research

authors： Karataev GI,Permogorov VI,Vologodskii AV,Frank-Kamenetskii MD

更新日期：1978-07-01 00:00:00

abstract：:Comparison of the nucleotide sequence of mRNAs coding for several vertebrate actins revealed a high degree of sequence homology in the 3' untranslated region (3' UTR) between those mRNAs coding for homologous (isotypic) actins in different organisms but not between mRNAs coding for very similar isoforms differing in t...

journal_title：Nucleic acids research

authors： Yaffe D,Nudel U,Mayer Y,Neuman S

更新日期：1985-05-24 00:00:00

abstract：:Double-strand breaks (DSBs) are dangerous chromosomal lesions that must be efficiently repaired in order to avoid loss of genetic information or cell death. In all organisms studied to date, two different mechanisms are used to repair DSBs: homologous recombination (HR) and non-homologous end joining (NHEJ). Previous ...

journal_title：Nucleic acids research

authors： Haviv-Chesner A,Kobayashi Y,Gabriel A,Kupiec M

更新日期：2007-01-01 00:00:00

abstract：:Bile acid biosynthesis is subjected to feedback regulation whereby bile acids down-regulate their own synthesis. The major point of this regulation is at the level of cholesterol 7alpha-hydroxylase (7alpha-hydroxylase), which controls bile acid output from the classic pathway. This regulation is at the level of transc...

journal_title：Nucleic acids research

authors： del Castillo-Olivares A,Gil G

更新日期：2000-09-15 00:00:00

abstract：:The attachment of replicating DNA to a rapidly sedimenting nuclear structure was investigated by digestion with various nucleases. When DNA was gradually removed by DNase I, pulse label incorporated during either 1 min or during 1 hour in the presence of arabinosylcytosine, remained preferentially attached to the nucl...

journal_title：Nucleic acids research

authors： Dijkwel PA,Mullenders LH,Wanka F

更新日期：1979-01-01 00:00:00

abstract：:Translin and translin-associated factor-x are highly conserved in eukaroytes; they can form heteromeric complexes (known as C3POs) and participate in various nucleic acid metabolism pathways. In humans and Drosophila, C3POs cleave the fragmented siRNA passenger strands and facilitate the activation of RNA-induced sile...

journal_title：Nucleic acids research

authors： Zhang J,Liu H,Yao Q,Yu X,Chen Y,Cui R,Wu B,Zheng L,Zuo J,Huang Z,Ma J,Gan J

更新日期：2016-11-02 00:00:00

abstract：:Genetic therapy holds great promise for the treatment of inherited or acquired genetic diseases; however, its breakthrough is hampered by the lack of suitable gene delivery systems. Dumbbell-shaped DNA minimal vectors represent an attractive, safe alternative to the commonly used viral vectors which are fraught with r...

journal_title：Nucleic acids research

authors： Yu H,Jiang X,Tan KT,Hang L,Patzel V

更新日期：2015-10-15 00:00:00

abstract：:The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa;...

journal_title：Nucleic acids research

authors： Lefkowitz EJ,Dempsey DM,Hendrickson RC,Orton RJ,Siddell SG,Smith DB

更新日期：2018-01-04 00:00:00

abstract：:DNA adenine methyltransferase (Dam) is widespread and conserved among the γ-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. Dam also controls virulence in many pathogenic Gram-negative bacteria. ...

journal_title：Nucleic acids research

authors： Horton JR,Zhang X,Blumenthal RM,Cheng X

更新日期：2015-04-30 00:00:00

abstract：:DNA-PKcs and Ku are essential components of the complex that catalyzes non-homologous end joining (NHEJ) of DNA double-strand breaks (DSBs). Ku, a heterodimeric protein, binds to DNA ends and facilitates recruitment of the catalytic subunit, DNA-PKcs. We have investigated the effect of DNA strand orientation and seque...

journal_title：Nucleic acids research

authors： Pawelczak KS,Andrews BJ,Turchi JJ

更新日期：2005-01-07 00:00:00

abstract：:The three-dimensional structures of two DNA duplexes d(CATGAGTAC). d(GTACXCATG) (1) and d(CATGAGTAC).d(GTACTCATG) (2), where X represents 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole, were solved using high resolution nuclear magnetic resonance spectroscopy and restrained molecular dynamics. Good convergence was o...

journal_title：Nucleic acids research

authors： Klewer DA,Hoskins A,Zhang P,Davisson VJ,Bergstrom DE,LiWang AC

更新日期：2000-11-15 00:00:00

abstract：:In neural stem cells (NSCs), the balance between stem cell maintenance and neuronal differentiation depends on cell-fate determinants such as TRIM32. Previously, we have shown that TRIM32 associates with the RNA-induced silencing complex and increases the activity of microRNAs such as Let-7a. However, the exact mechan...

journal_title：Nucleic acids research

authors： Nicklas S,Okawa S,Hillje AL,González-Cano L,Del Sol A,Schwamborn JC

更新日期：2015-03-11 00:00:00

abstract：:Members of the pentatricopeptide repeat domain (PPR) protein family bind RNA and are important for post-transcriptional control of organelle gene expression in unicellular eukaryotes, metazoans and plants. They also have a role in human pathology, as mutations in the leucine-rich PPR-containing (LRPPRC) gene cause sev...

journal_title：Nucleic acids research

authors： Baggio F,Bratic A,Mourier A,Kauppila TE,Tain LS,Kukat C,Habermann B,Partridge L,Larsson NG

更新日期：2014-12-16 00:00:00

abstract：:The modulation of GLI2, an oncogenic transcription factor commonly upregulated in cancer, is in many cases not due to genetic defects, suggesting dysregulation through alternative mechanisms. The identity of these molecular events remains for the most part unknown. Here, we identified TFII-I as a novel repressor of GL...

journal_title：Nucleic acids research

authors： McCleary-Wheeler AL,Paradise BD,Almada LL,Carlson AJ,Marks DL,Vrabel A,Vera RE,Sigafoos AN,Olson RL,Fernandez-Zapico ME

更新日期：2020-07-27 00:00:00

abstract：:Sequence heterogeneity is a common characteristic of RNA viruses that is often referred to as sub-populations or quasispecies. Traditional techniques used for assembly of short sequence reads produced by deep sequencing, such as de-novo assemblers, ignore the underlying diversity. Here, we introduce a novel algorithm ...

journal_title：Nucleic acids research

authors： Karagiannis K,Simonyan V,Chumakov K,Mazumder R

更新日期：2017-11-02 00:00:00

abstract：:The development of genetic switches and their integrated forms (genetic circuits) with desired specifications/functions is key for success in synthetic biology. Due to the difficulty in rational design, genetic switches and circuits with desirable specifications are mostly obtained by directed evolution. Based on a vi...

journal_title：Nucleic acids research

authors： Tashiro Y,Fukutomi H,Terakubo K,Saito K,Umeno D

更新日期：2011-02-01 00:00:00

abstract：:The gene, rpb1, encoding the largest subunit of RNA polymerase II has been cloned from Schizosaccharomyces pombe using the corresponding gene, RPB1, of Saccharomyces cerevisiae as a cross-hybridization probe. We have determined the complete sequence of this gene, and parts of PCR-amplified rpb1 cDNA. The predicted cod...

journal_title：Nucleic acids research

authors： Azuma Y,Yamagishi M,Ueshima R,Ishihama A

更新日期：1991-02-11 00:00:00

abstract：:Twenty AdoMet-dependent methyltransferases (MTases) have been characterized structurally by X-ray crystallography and NMR. These include seven DNA MTases, five RNA MTases, four protein MTases and four small molecule MTases acting on the carbon, oxygen or nitrogen atoms of their substrates. The MTases share a common co...

journal_title：Nucleic acids research

authors： Cheng X,Roberts RJ

更新日期：2001-09-15 00:00:00

abstract：:The P0 scaffold protein of the ribosomal stalk is mainly incorporated into pre-ribosomes in the cytoplasm where it replaces the assembly factor Mrt4. In analyzing the role of the P0 carboxyl terminal domain (CTD) during ribosomal stalk assembly, we found that its complete removal yields a protein that is functionally ...

journal_title：Nucleic acids research

authors： Francisco-Velilla R,Remacha M,Ballesta JP

更新日期：2013-10-01 00:00:00

abstract：:Different helical conformations of DNA (D), RNA (R), and DNA.RNA (DR) hybrid double and triple helices have been detected using affinity cleavage analysis. Synthetic methods were developed to attach EDTA.Fe to a single nucleotide on RNA as well as DNA oligonucleotides. Cleavage patterns generated by a localized diffus...

journal_title：Nucleic acids research

authors： Han H,Dervan PB

更新日期：1994-07-25 00:00:00