Abstract:
:The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics--indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Waldispühl J,Devadas S,Berger B,Clote Pdoi
10.1093/nar/gkp477subject
Has Abstractpub_date
2009-07-01 00:00:00pages
W281-6issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkp477journal_volume
37pub_type
杂志文章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::Transcription of RNA from the beta-globin (major) gene in nuclei from induced mouse erythroleukemia cells terminates within the region between 700 to 2000 bases downstream from the poly(A) addition site, but not at particularly favored sites. In addition we present the first analysis of in vivo labeled RNA from a cell...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.22.8723
更新日期:1984-11-26 00:00:00
abstract::In plants, small interfering RNAs (siRNAs) can trigger a silencing signal that may spread within a tissue to adjacent cells or even systemically to other organs. Movement of the signal is initially limited to a few cells, but in some cases the signal can be amplified and travel over larger distances. How far silencing...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1240
更新日期:2011-04-01 00:00:00
abstract::Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt030
更新日期:2013-04-01 00:00:00
abstract::Small interfering RNAs (siRNAs) are promising new active compounds in gene medicine but the induction of non-specific immune responses following their delivery continues to be a serious problem. With the purpose of avoiding such effects chemically modified siRNAs are tested in screening assay but often only examining ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks033
更新日期:2012-05-01 00:00:00
abstract::Dictyostelium intermediate repeat sequence 1 (DIRS-1) is the founding member of a poorly characterized class of retrotransposable elements that contain inverse long terminal repeats and tyrosine recombinase instead of DDE-type integrase enzymes. In Dictyostelium discoideum, DIRS-1 forms clusters that adopt the functio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1337
更新日期:2014-03-01 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
pub_type: 杂志文章
doi:10.1093/nar/gkl643
更新日期:2006-01-01 00:00:00
abstract::An adequate supply of nucleotides is essential for DNA replication and DNA repair. Moreover, inhibition of TTP synthesis can cause cell death by a poorly characterized mechanism called thymine-less death. In the yeast Saccharomyces cerevisiae, the genes encoding thymidylate synthetase (CDC21) and thymidylate kinase (C...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki219
更新日期:2005-01-28 00:00:00
abstract::We propose a novel mechanism of gene regulation in Mycobacterium tuberculosis where the protein Rv1222 inhibits transcription by anchoring RNA polymerase (RNAP) onto DNA. In contrast to our existing knowledge that transcriptional repressors function either by binding to DNA at specific sequences or by binding to RNAP,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv516
更新日期:2015-07-13 00:00:00
abstract::The nucleotide sequence of the Anacystis nidulans 23S rRNA gene, including the 5'- and 3'-flanking regions has been determined. The gene is 2876 nucleotides long and shows higher primary sequence homology to the 23S rRNAs of plastids (84.5%) than to that of E. coli (79%). The predicted rRNA transcript also shares many...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.7.3373
更新日期:1984-04-11 00:00:00
abstract::Replication Protein A (RPA) is a critical complex that acts in replication and promotes homologous recombination by allowing recombinase recruitment to processed DSB ends. Most organisms possess three RPA subunits (RPA1, RPA2, RPA3) that form a trimeric complex critical for viability. The Caenorhabditis elegans genome...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1293
更新日期:2021-01-21 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::Large-scale sequencing studies discovered substantial genetic variants occurring in enhancers which regulate genes via long range chromatin interactions. Importantly, such variants could affect enhancer regulation by changing transcription factor bindings or enhancer hijacking, and in turn, make an essential contribut...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx920
更新日期:2018-01-04 00:00:00
abstract::In this study, we show that silencing of CITED2 using small-hairpin RNA (shCITED2) induced DNA damage and reduction of ERCC1 gene expression in HEK293, HeLa and H1299 cells, even in the absence of cisplatin. In contrast, ectopic expression of ERCC1 significantly reduced intrinsic and induced DNA damage levels, and res...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv934
更新日期:2015-12-15 00:00:00
abstract::Analysis of the human VK (ref. 2) gene locus led to the detection of a new sequence family (L sequences). Its copy number is in the range of 10(2). The L sequences, which are about 500 bp long, are found as part of the 3' flanking regions of a clustered set of human VKI genes but they occur also separate from the gene...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.13.5265
更新日期:1984-07-11 00:00:00
abstract::Tcf/Lef family transcription factors are the downstream effectors of the Wingless/Wnt signal transduction pathway. Upon Wingless/Wnt signalling, beta-catenin translocates to the nucleus, interacts with Tcf (1-3) and thus activates transcription of target genes (4,5). Tcf factors also interact with members of the Grouc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.7.1410
更新日期:2001-04-01 00:00:00
abstract::Transfection of a human estrogen receptor cDNA expression vector (HEO) into cultured Xenopus kidney cells confers estrogen responsiveness to the recipient cells as demonstrated by the hormone dependent expression of co-transfected Xenopus vitellogenin-CAT chimeric genes. The estrogen stimulation of these vit-CAT genes...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.17.8291
更新日期:1988-09-12 00:00:00
abstract::A series of unusual folding regions (UFR) immediately 3' to the cleavage site of the outer membrane protein (OMP) and transmembrane protein (TMP) were detected in the envelope gene RNA of the human immunodeficiency virus (HIV-1, HIV-2) and simian immunodeficiency virus (SIV) by an extensive Monte Carlo simulation. The...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.6.1613
更新日期:1990-03-25 00:00:00
abstract::Herpes simplex type 1 virus (HSV-1) and bacteriophage λ capsids undergo considerable structural changes during self-assembly and DNA packaging. The initial steps of viral capsid self-assembly require weak, non-covalent interactions between the capsid subunits to ensure free energy minimization and error-free assembly....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku634
更新日期:2014-08-01 00:00:00
abstract::Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw077
更新日期:2016-04-20 00:00:00
abstract::Oligoamines (spermidine, dipropylenetriamine and propylenediamine) were covalently attached to acridine via a hexamethylene linker. These oligoamine-acridine conjugates were efficiently bound to gap sites in substrate DNA, and promoted the DNA hydrolysis by a homogeneous Ce(IV)/ethylenediamine-N,N,N',N'-tetraacetate (...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg634
更新日期:2003-08-01 00:00:00
abstract::The cDNA of human DNA polymerase delta was cloned. The cDNA had a length of 3.5 kb and encoded a protein of 1107 amino acid residues with a calculated molecular mass of 124 kDa. Northern blot analysis showed that the cDNA hybridized to a mRNA of 3.4 kb. Monoclonal and polyclonal antibodies to the C-terminal 20 residue...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.4.735
更新日期:1992-02-25 00:00:00
abstract::Gene rewiring is a common evolutionary phenomenon in nature that may lead to extinction for living organisms. Recent studies on synthetic biology demonstrate that cells can survive genetic rewiring. This survival (adaptation) is often linked to the stochastic expression of rewired genes with random transcriptional cha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1366
更新日期:2015-01-01 00:00:00
abstract::Core members of the MBD protein family (MeCP2, MBD1, MBD2 and MBD4) share a methyl-CpG-binding domain that has a specific affinity for methylated CpG sites in double-stranded DNA. By multimerizing the MDB domain of Mbd1, we engineered a poly-MBD protein that displays methyl-CpG-specific binding in vitro with a dissoci...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl527
更新日期:2006-08-07 00:00:00
abstract::By introduction of recombinant plasmids into monkey CV1 cells, we have unambiguously demonstrated that sequences entirely within the 72 bp repeat, which is located upstream of the SV40 early region, are crucial for T-antigen expression in vivo. We have also shown that a DNA fragment containing the 72 bp repeat, insert...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.22.6047
更新日期:1981-11-25 00:00:00
abstract::High mobility group protein B1 (HMGB1) binds to the internucleosomal linker DNA in chromatin and abuts the nucleosome. Bending and untwisting of the linker DNA results in transmission of strain to the nucleosome core, disrupting histone/DNA contacts. An interaction between H3 and HMGB1 has been reported. Here we confi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt950
更新日期:2014-01-01 00:00:00
abstract::This study unveils Mycobacterium smegmatis DinB2 as the founder of a clade of Y-family DNA polymerase that is naturally adept at incorporating ribonucleotides by virtue of a leucine in lieu of a canonical aromatic steric gate. DinB2 efficiently scavenges limiting dNTP and rNTP substrates in the presence of manganese. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku752
更新日期:2014-01-01 00:00:00
abstract::Yeast two-hybrid (Y2H) screenings result in identification of many out-of-frame (OOF) clones that code for short (2-100 amino acids) peptides with no sequence homology to known proteins. We hypothesize that these peptides can reveal common short linear motifs (SLiMs) responsible for their selection. We present a new p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr600
更新日期:2011-10-01 00:00:00
abstract::The RecQL4 helicase is involved in the maintenance of genome integrity and DNA replication. Mutations in the human RecQL4 gene cause the Rothmund-Thomson, RAPADILINO and Baller-Gerold syndromes. Mouse models and experiments in human and Xenopus have proven the N-terminal part of RecQL4 to be vital for cell growth. We ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks591
更新日期:2012-09-01 00:00:00
abstract::DNA methylation and chromatin DNaseI sensitivity were analyzed in and adjacent to D4Z4 repeat arrays, which consist of 1 to approximately 100 tandem 3.3-kb units at subtelomeric 4q and 10q. D4Z4 displayed hypomethylation in some cancers and hypermethylation in others relative to normal tissues. Surprisingly, in cancer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn055
更新日期:2008-04-01 00:00:00