Abstract:
:The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently offers prediction of secondary structure from a single sequence, prediction of the consensus secondary structure for a set of aligned sequences and the design of sequences that will fold into a predefined structure. All three services can be accessed via the Vienna RNA web server at http://rna.tbi.univie.ac.at/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Hofacker ILdoi
10.1093/nar/gkg599keywords:
subject
Has Abstractpub_date
2003-07-01 00:00:00pages
3429-31issue
13eissn
0305-1048issn
1362-4962journal_volume
31pub_type
杂志文章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
pub_type: 杂志文章
doi:10.1093/nar/gkw042
更新日期:2016-06-02 00:00:00
abstract::The Homeodomain Resource is a comprehensive collection of sequence, structure and genomic information on the homeodomain protein family. Available through the Resource are both full-length and domain-only sequence data, as well as X-ray and NMR structural data for proteins and protein-DNA complexes. Also available is ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.1.336
更新日期:1999-01-01 00:00:00
abstract::The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw432
更新日期:2016-07-27 00:00:00
abstract::The sequence GCGCGCGCGC contains three overlapping, mutually exclusive, BssHII restriction sites, each corresponding to one of the three different reading frames. When inserted into a plasmid and digested with BssHII, the three sites in this sequence are cleaved at an approximate ratio of 2:1:2. Consequently, this sys...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.8.3107
更新日期:1989-04-25 00:00:00
abstract::I show that the recognition sequences of Type II restriction systems are correlated with the G + C content of the host bacterial DNA. Almost all restriction systems with G + C rich tetranucleotide recognition sequences are found in species with A + T rich genomes, whereas G + C rich hexanucleotide and octanucleotide r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.5.2283
更新日期:1988-03-25 00:00:00
abstract::A newly discovered group of spherical plant viruses contains a bipartite genome consisting of a single-strand linear RNA molecule (RNA 1, Mr 1.5 x 10(6) ), and a single-strand, covalently closed circular viroid-like RNA molecule (RNA 2, Mr approximately 125,000). The nucleotide sequences of the RNA 2 of two of these, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.12.3681
更新日期:1982-06-25 00:00:00
abstract::The ciliate Tetrahymena thermophila is an important eukaryotic model organism that has been used in pioneering studies of general phenomena, such as ribozymes, telomeres, chromatin structure and genome reorganization. Recent work has shown that Tetrahymena has many classes of small RNA molecules expressed during veget...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr792
更新日期:2012-02-01 00:00:00
abstract::The interaction specificity of salmon sperm DNA with 2-hydroxyethanethionlato(2,2',2''-terpyridine)platinum(II),PtTS has been studied. The results of 1H and 13C nuclear magnetic resonance, flow dichroism and circular dichroism studies are found to be consistent with an intercalation mode of binding as has been propose...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.4.1081
更新日期:1979-10-25 00:00:00
abstract::The catalytic function of the hairpin ribozyme has been investigated by modification-interference analysis of both ribozyme and substrate, using ribonucleoside phosphorothioates. Thiophosphate substitutions in two ribozyme domains were examined by using a novel and highly efficient two-piece ribozyme assembled from tw...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.11.2835
更新日期:1992-06-11 00:00:00
abstract::Melibiose uptake and hydrolysis in E.coli is performed by the MelB and MelA proteins, respectively. We report the cloning and sequencing of the melA gene. The nucleotide sequence data showed that melA codes for a 450 amino acid long protein with a molecular weight of 50.6 kd. The sequence data also supported the assum...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.5.2213
更新日期:1987-03-11 00:00:00
abstract::Perturbation and time-course data sets, in combination with computational approaches, can be used to infer transcriptional regulatory networks which ultimately govern the developmental pathways and responses of cells. Here, we individually knocked down the four transcription factors PU.1, IRF8, MYB and SP1 in the huma...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq729
更新日期:2010-12-01 00:00:00
abstract::A cDNA that encodes a transcription factor able to recognize the thyroglobulin gene promoter in vitro was isolated from a dog thyroid cDNA expression library in lambda gt11. The library was screened with a multimerized 20 bp-oligonucleotide probe corresponding to the -126 to -107 bp region of the bovine thyroglobulin ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.5.1121
更新日期:1991-03-11 00:00:00
abstract::Expressed Sequence Tag-based gene expression profiling can be used to discover functionally associated genes on a large scale. Currently available web servers and tools focus on finding differentially expressed genes in different samples or tissues rather than finding co-expressed genes. To fill this gap, we have deve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki480
更新日期:2005-07-01 00:00:00
abstract::Using a genetic selection for suppressors of a UGA nonsense mutation in trpA, we have isolated a G to A transition mutation at position 1491 in the decoding region of 16S rRNA. This suppressor displayed no codon specificity, suppressing UGA, UAG and UAA nonsense mutations and +1 and -1 frameshift mutations in lacZ. Su...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.21.4234
更新日期:1995-11-11 00:00:00
abstract::Recent studies have shown that homologous recombination (HR) requires chromatin repression as well as relaxation at DNA double strand breaks (DSBs). HP1 and SUV39H1/2 are repressive factors essential for HR. Here, we identify SETDB1 as an additional compacting factor promoting HR. Depletion of HP1, SUV39, SETDB1 or BR...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv722
更新日期:2015-09-18 00:00:00
abstract::Small RNA (sRNA)-mediated gene silencing phenomena, exemplified by RNA interference (RNAi), require a unique class of proteins called Argonautes (AGOs). An AGO protein typically forms a protein-sRNA complex that contributes to gene silencing using the loaded sRNA as a specificity determinant. Here, we show that MoAGO2...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1301
更新日期:2018-03-16 00:00:00
abstract::The nucleotide sequence of a Pseudomonas trans-zeatin producing gene (ptz) from the pCK1 plasmid of Pseudomonas syringae pv. savastanoi strain 1006 has been determined. This gene confers upon E. coli the ability to synthesize and secrete several cytokinins including trans-zeatin, iso-pentenyladenine and their respecti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.6.2555
更新日期:1986-03-25 00:00:00
abstract::Non-structural protein 3 (NS3) of hepatitis C virus (HCV) has two distinct activities, protease and helicase, which are essential for HCV proliferation. In previous work, we obtained RNA aptamers (G9-I, II and III) which specifically bound the NS3 protease domain (DeltaNS3), efficiently inhibiting protease activity in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg291
更新日期:2003-04-01 00:00:00
abstract::We characterize a component of the E. coli bacterial nucleoid H1a, which accumulates in stationary phase. This protein, identical with the major component of a plasmid-protein complex previously isolated in our laboratory, has a pI close to 7.5. Acrylamide gel electrophoresis and sedimentation in sucrose gradient have...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.13.5321
更新日期:1984-07-11 00:00:00
abstract::Many multimeric transcription factors recognize DNA sequence patterns by cooperatively binding to bipartite elements composed of half sites separated by a flexible spacer. We developed a novel bipartite algorithm, bipartite pattern discovery (Bipad), which produces a mathematical model based on information maximizatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh825
更新日期:2004-09-23 00:00:00
abstract::ADGO 2.0 is a web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. Some other tools also incorporate composite annotations solely for interpreting lists of genes but usually provide highly redund...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr392
更新日期:2011-07-01 00:00:00
abstract::We have investigated the attachment of the DNA to the nuclear matrix during the division cycle of the plasmodial slime mold Physarum polycephalum. The DNA of plasmodia was pulse labelled at different times during the S phase and the label distribution was studied by graded DNase digestion of the matrix-DNA complexes p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.4.1181
更新日期:1983-02-25 00:00:00
abstract::In order to investigate the possible role of RNA secondary structure in determining the efficiency and specificity of mRNA splicing, the structures of sequences at three acceptor splice sites in adenovirus were studied. Transcripts spanning intron-exon junctions were synthesized using SP6 RNA polymerase and analyzed u...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.22.8437
更新日期:1984-11-26 00:00:00
abstract::A fluoride-cleavable phosphoramidite for biotinylation was designed, synthesized and coupled efficiently to the 5'-end of DNA on an automatic synthesizer. The diisopropylsilyl acetal functionality was used to link the biotin moiety through a tertiary hydroxide group to the 5'-end of DNA. This linkage proved to be comp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg130
更新日期:2003-01-15 00:00:00
abstract::The stable intermediates formed in the reaction of cytosine, cytidine and adenosine with chloracetaldehyde were isolated. The -CH2CH/OH/- bridge between the exo and endo nitrogen atoms of the parent base was found in these compounds by means of PMR spectroscopy. Their acid-induced dehydration resulted in formation of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.3.789
更新日期:1978-03-01 00:00:00
abstract::Protein-protein interactions regulate many essential enzymatic processes in the cell. Somatic mutations outside of an enzyme active site can therefore impact cellular function by disruption of critical protein-protein interactions. In our investigation of the cellular impact of the T304I cancer mutation of DNA Polymer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz293
更新日期:2019-07-09 00:00:00
abstract::We have previously described programs for a variety of types of sequence analysis (1-4). These programs have now been integrated into a single package. They are written in the standard C programming language and run on virtually any computer system with a C compiler, such as the IBM/PC and other computers running unde...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.1.443
更新日期:1986-01-10 00:00:00
abstract::The role of Ribonuclease H1 (RNase H1) during primer removal and ligation at the mitochondrial origin of light-strand DNA synthesis (OriL) is a key, yet poorly understood, step in mitochondrial DNA maintenance. Here, we reconstitute the replication cycle of L-strand synthesis in vitro using recombinant mitochondrial p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky708
更新日期:2018-10-12 00:00:00
abstract::We present a new coarse grained method for the simulation of duplex DNA. The algorithm uses a generalized multi-harmonic model that can represent any multi-normal distribution of helical parameters, thus avoiding caveats of current mesoscopic models for DNA simulation and representing a breakthrough in the field. The ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa015
更新日期:2020-03-18 00:00:00
abstract::Site-specific mutation was demonstrated in a shuttle vector system using nitrogen mustard-conjugated oligodeoxyribonucleotides (ODNs). Plasmid DNA was modified in vitro by ODNs containing all four DNA bases in the presence of Escherichia coli RecA protein. Up to 50% of plasmid molecules were alkylated in the targeted ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.24.e38
更新日期:1999-12-15 00:00:00