3did: a catalog of domain-based interactions of known three-dimensional structure.

abstract：:Equilibrative nucleoside transporters (ENTs) are a recently characterized and poorly understood group of membrane proteins that are important in the uptake of endogenous nucleosides required for nucleic acid and nucleoside triphosphate synthesis. Despite their central importance in cellular metabolism and nucleoside a...

journal_title：Nucleic acids research

authors： Sankar N,Machado J,Abdulla P,Hilliker AJ,Coe IR

更新日期：2002-10-15 00:00:00

abstract：:Targeted modulation of gene expression represents a valuable approach to understand the mechanisms governing gene regulation. In a therapeutic context, it can be exploited to selectively modify the aberrant expression of a disease-causing gene or to provide the target cells with a new function. Here, we have establish...

journal_title：Nucleic acids research

authors： Mlambo T,Nitsch S,Hildenbeutel M,Romito M,Müller M,Bossen C,Diederichs S,Cornu TI,Cathomen T,Mussolino C

更新日期：2018-05-18 00:00:00

abstract：:Biophysical properties of DNA such as its longitudinal and torsional persistence length govern many processes and phenomena in biology, DNA nanotechnology and biotechnology. It has, for example, long been known that the circularization efficiency of short DNA fragments shows a periodic pattern where fragments with int...

journal_title：Nucleic acids research

authors： Joffroy B,Uca YO,Prešern D,Doye JPK,Schmidt TL

更新日期：2018-01-25 00:00:00

abstract：:In a recent paper we have estimated the total number of protein coding open reading frames (ORFs) in the Saccharomyces cerevisiae genome, based on their properties, at about 4800. This number is much smaller than the 5800-6000 which is widely accepted. In this paper we analyse differences between the set of ORFs with ...

journal_title：Nucleic acids research

authors： Mackiewicz P,Kowalczuk M,Gierlik A,Dudek MR,Cebrat S

更新日期：1999-09-01 00:00:00

abstract：:The G- and U-specific reagent, carbodiimide was used to probe the solution structure of aminoacylated yeast phenylalanine tRNA. Both quantitative and qualitative changes in modification were observed when the modification patterns of tRNA-CCA(3'OH), tRNA-CCA(3'NH2) and phe-tRNA-CCA(3'NH2) were compared. Five nucleotid...

journal_title：Nucleic acids research

authors： Fritzinger DC,Fournier MJ

更新日期：1982-04-10 00:00:00

abstract：:Isolated yeast mitochondria incorporate added UTP into RNA. Amongst the products formed are the two rRNAs, 4S RNA and several components presumed to be mRNAs. In omega+ strains (containing an intervening sequence in the 21S rRNA gene) besides mature 21S rRNA a transcript could be detected still containing nucleotide s...

journal_title：Nucleic acids research

authors： Groot GS,van Harten-Loosbroek N,van Ommen GJ,Pijst HL

更新日期：1981-12-11 00:00:00

abstract：:A segment of 1160 nucleotides of the FMDV genome has been sequenced using three overlapping fragments of cloned cDNA from FMDV strain O1K. This sequence contains the coding sequence for the viral capsid protein VP1 as shown by its homology to known and newly determined amino acid sequences from this man antigenic poly...

journal_title：Nucleic acids research

authors： Kurz C,Forss S,Küpper H,Strohmaier K,Schaller H

更新日期：1981-04-24 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：:Binding of the DnaA protein to oriC leads to DNA melting within the DNA unwinding element (DUE) and initiates replication of the bacterial chromosome. Helicobacter pylori oriC was previously identified as a region localized upstream of dnaA and containing a cluster of DnaA boxes bound by DnaA protein with a high affin...

journal_title：Nucleic acids research

authors： Donczew R,Weigel C,Lurz R,Zakrzewska-Czerwinska J,Zawilak-Pawlik A

更新日期：2012-10-01 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：:We have amplified the large subunit ribosomal DNA (LSUrDNA) of the 12 described Naegleria spp. and of 34 other Naegleria lineages that might be distinct species. Two strains yielded a product that is longer than 3 kb, which is the length of the LSUrDNA of all described Naegleria spp. Sequencing data revealed that the ...

journal_title：Nucleic acids research

authors： De Jonckheere JF,Brown S

更新日期：1998-01-15 00:00:00

abstract：:In Euplotes crassus millions of telomeres are synthesized during the sexual phase of the life cycle. Since these newly synthesized telomeres are longer than normal macronuclear telomeres, they must be trimmed to the mature size. We have examined the timing and mechanism of this trimming step. We have shown that a sudd...

journal_title：Nucleic acids research

authors： Vermeesch JR,Williams D,Price CM

更新日期：1993-11-25 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：:Hexokinase 2 is an essential factor for signalling repression through the Saccharomyces cerevisiae high-glucose sensing pathway. The main regulatory mechanism that controls the HXK2 gene expression in yeast is mediated by the Rgt1 and Med8 transcription factors, which repress HXK2 expression in low-glucose containing ...

journal_title：Nucleic acids research

authors： Palomino A,Herrero P,Moreno F

更新日期：2006-03-09 00:00:00

abstract：:The RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of nucleic acid polymerases. RdRPs are essential in virus life cycle due to their central role in viral genome replication/transcription processes. However, their contribution in host adaption has not been well documented. By sol...

journal_title：Nucleic acids research

authors： Yang J,Jing X,Yi W,Li XD,Yao C,Zhang B,Zheng Z,Wang H,Gong P

更新日期：2021-01-06 00:00:00

abstract：:The B-subunits associated with the replicative DNA polymerases are conserved from Archaea to humans, whereas the corresponding catalytic subunits are not related. The latter belong to the B and D DNA polymerase families in eukaryotes and archaea, respectively. Sequence analysis places the B-subunits within the calcine...

journal_title：Nucleic acids research

authors： Jokela M,Eskelinen A,Pospiech H,Rouvinen J,Syväoja JE

更新日期：2004-04-30 00:00:00

abstract：:The distribution patterns of shared short repetitive motifs in the expansion segments of the large subunit rRNA genes of different species show that these segments are coevolving as a set and that in two examined vertebrate species the RNA secondary structures are conserved as a consequence of runs of motifs in one re...

journal_title：Nucleic acids research

authors： Hancock JM,Dover GA

更新日期：1990-10-25 00:00:00

abstract：:Identification of common sub-sequences for a group of functionally related DNA sequences can shed light on the role of such elements in cell-specific gene expression. In the megakaryocytic lineage, no one single unique transcription factor was described as linage specific, raising the possibility that a cluster of gen...

journal_title：Nucleic acids research

authors： Hazony Y,Lu J,St Hilaire C,Ravid K

更新日期：2006-01-01 00:00:00

abstract：:Self-cleaving ribozymes associated with the glmS genes of many Gram-positive bacteria are activated by binding to glucosamine-6-phosphate (GlcN6P). Representatives of the glmS ribozyme class function as metabolite-sensing riboswitches whose self-cleavage activities down-regulate the expression of GlmS enzymes that syn...

journal_title：Nucleic acids research

authors： Link KH,Guo L,Breaker RR

更新日期：2006-01-01 00:00:00

abstract：:Sequences preceding the minimal promoter play a role in the differential expression of the Xenopus somatic and oocyte-type 5S RNA genes. In this report, the somatic sequences between -32 and +37 are shown to increase transcriptional activity in microinjected embryos, yet have little to no effect in microinjected oocyt...

journal_title：Nucleic acids research

authors： Reynolds WF

更新日期：1989-11-25 00:00:00

abstract：:Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers...

journal_title：Nucleic acids research

authors： Zheng X,Yang J,Zhou C,Zhang C,Zhang Q,Wei X

更新日期：2019-02-20 00:00:00

abstract：:FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger stand...

journal_title：Nucleic acids research

authors： Cock PJ,Fields CJ,Goto N,Heuer ML,Rice PM

更新日期：2010-04-01 00:00:00

abstract：:The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are hierarchically classified into families, superfamilies, folds and classes. The continual accumulation of se...

journal_title：Nucleic acids research

authors： Andreeva A,Howorth D,Brenner SE,Hubbard TJ,Chothia C,Murzin AG

更新日期：2004-01-01 00:00:00

abstract：:NRPS-PKS is web-based software for analysing large multi-enzymatic, multi-domain megasynthases that are involved in the biosynthesis of pharmaceutically important natural products such as cyclosporin, rifamycin and erythromycin. NRPS-PKS has been developed based on a comprehensive analysis of the sequence and structur...

journal_title：Nucleic acids research

authors： Ansari MZ,Yadav G,Gokhale RS,Mohanty D

更新日期：2004-07-01 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 novel cytoplasmic gene expression system has been developed. This system differs from other expression systems in that it relies on the co-delivery of plasmid DNA and T7 RNA polymerase (RNAP) during transfection. The plasmid contains a T7 RNAP gene driven by the T7 promoter (T7 autogene) and a functional/reporter ge...

journal_title：Nucleic acids research

authors： Chen X,Li Y,Xiong K,Wagner TE

更新日期：1994-06-11 00:00:00

abstract：:We describe a method for the formation of hybrid genes by in vivo recombination between two genes with partial sequence homology. DNA structures consisting of plasmid vector sequences, flanked by the alpha 2 interferon gene on the one side and a portion of the alpha 1 interferon gene (homology about 80%) on the other,...

journal_title：Nucleic acids research

authors： Weber H,Weissmann C

更新日期：1983-08-25 00:00:00

abstract：:The remarkable selectivity of N-methyl mesoporphyrin IX (NMM) for G-quadruplexes (GQs) is long known, however its ability to stabilize and bind GQs has not been investigated in detail. Through the use of circular dichroism, UV-visible spectroscopy and fluorescence resonance energy transfer (FRET) melting assay we have...

journal_title：Nucleic acids research

authors： Nicoludis JM,Barrett SP,Mergny JL,Yatsunyk LA

更新日期：2012-07-01 00:00:00

abstract：:Eucaryotic ribosome biogenesis involves many cis-acting sequences and trans-acting factors, including snoRNAS: We have used directed mutagenesis of rDNA plasmids in yeast to identify critical sequence and structural elements within and flanking the ITS2-proximal stem. This base paired structure, present in the mature ...

journal_title：Nucleic acids research

authors： Côté CA,Peculis BA

更新日期：2001-05-15 00:00:00

abstract：:RNA levels in a cell are regulated by the relative rates of RNA synthesis and decay. We recently developed a new approach for measuring both RNA synthesis and decay in a single experimental setting by biosynthetic labeling of newly transcribed RNA. Here, we show that this provides measurements of RNA half-lives from m...

journal_title：Nucleic acids research

authors： Friedel CC,Dölken L,Ruzsics Z,Koszinowski UH,Zimmer R

更新日期：2009-09-01 00:00:00