Abstract:
:A new thermodynamic database for normal and modified nucleic acids has been developed. This Thermodynamic Database for Nucleic Acids (NTDB) includes sequence, structure and thermodynamic information as well as experimental methods and conditions. In this release, there are 1851 sequences containing both normal and modified nucleic acids. A user-friendly web-based interface has been developed to allow data searching under different conditions. Useful thermodynamic tools for the study of nucleic acids have been collected and linked for easy usage. NTDB is available at http://ntdb.chem.cuhk.edu.hk.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Chiu WL,Sze CN,Ip LN,Chan SK,Au-Yeung SCdoi
10.1093/nar/29.1.230keywords:
subject
Has Abstractpub_date
2001-01-01 00:00:00pages
230-3issue
1eissn
0305-1048issn
1362-4962journal_volume
29pub_type
杂志文章abstract::We devised an indicator gene for retrotransposition based on an autocatalytic ribozyme element--the Tetrahymena thermophila 23S rRNA group I intron--which can self-splice in vitro and does not require--at variance with nuclear mRNA introns--any specific pathway and cellular component for the completion of the splicing...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.11.e49
更新日期:2002-06-01 00:00:00
abstract::One-Block CYRCA is an automated procedure for identifying multiple-block alignments from single block queries (http://bioinfo.weizmann.ac.il/blocks/OneCYRCA). It is based on the LAMA and CYRCA block-to-block alignment methods. The procedure identifies whether the query blocks can form new multiple-block alignments (bl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki488
更新日期:2005-07-01 00:00:00
abstract::Using a combination of bioinformatic and molecular biology approaches a Drosophila melanogaster protein, DmTTF, has been identified, which exhibits sequence and structural similarity with two mitochondrial transcription termination factors, mTERF (human) and mtDBP (sea urchin). Import/processing assays indicate that D...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg272
更新日期:2003-03-15 00:00:00
abstract::MicroRNAs (miRNAs) can group together along the human genome to form stable secondary structures made of several hairpins hosting miRNAs in their stems. The few known examples of such structures are all involved in cancer development. A large scale computational analysis of human chromosomes crossing sequence analysis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt112
更新日期:2013-04-01 00:00:00
abstract::Orthology is a widely used concept in comparative and evolutionary genomics. In addition to prokaryotic orthology, delineating eukaryotic orthology has provided insight into the evolution of higher organisms. Indeed, many eukaryotic ortholog databases have been established for this purpose. However, unlike prokaryotes...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn227
更新日期:2008-06-01 00:00:00
abstract::We have determined the DNA sequence surrounding the transcription terminator following rpoC, the gene that codes for the beta' subunit of RNA polymerase in E. coli K12. The 2044 bp sequence obtained contains the distal 335 codons of rpoC followed by a 212 bp non-coding region and a second open reading frame (ORFa) of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.24.6827
更新日期:1981-12-21 00:00:00
abstract::The genome of the cell is often exposed to DNA damaging agents and therefore requires an intricate well-regulated DNA damage response (DDR) to overcome its deleterious effects. The DDR needs proper regulation for its timely activation, repression, as well as appropriate choice of repair pathway. Studies in Saccharomyc...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkw1369
更新日期:2017-03-17 00:00:00
abstract::The nucleoside compositions of chloroplast and cytoplasmic tRNAPhe's from Euglena gracilis have been determined. The modified nucleoside compositions of these two tRNAs indicate that tRNAPheChl is more similar to procaryotic (E. coli) tRNAPhe than to either the Euglena cytoplasmic tRNAPhe or other eucaryotic cytoplasm...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.2.371
更新日期:1976-02-01 00:00:00
abstract::Insertion of the four major nucleotides at the 5'-side of the anticodon triplet of E. coli tRNAMetf was performed by joining of the half molecules obtained by limited digestion with RNase A and the chemically synthesized tetranucleotide pN-C-A-U using RNA ligase. Insertion of U-U at the 5'-side or A and A-A at the 3'-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.10.3685
更新日期:1985-05-24 00:00:00
abstract::A sixty base pair DNA duplex containing the nucleotide sequence of the bacteriophage T5 early (T5P25) promoter has been constructed using a combination of chemical synthesis and enzymatic methods. Subsequent to cloning into pBR322, the promoter has been demonstrated to be biologically active being capable of directing...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.17.5921
更新日期:1983-09-10 00:00:00
abstract::TAP/hNXF1 is a key factor that mediates general cellular mRNA export from the nucleus, and its orthologs are structurally and functionally conserved from yeast to humans. Metazoans encode additional proteins that share homology and domain organization with TAP/hNXF1, suggesting their participation in mRNA metabolism; ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki706
更新日期:2005-07-13 00:00:00
abstract::Calf lens messenger fractions have been purified on poly(dT)-cellulose. The purified RNA's have been analyzed as nucleosides by a method which can be used on a micro-scale with highly reproduceble results. Both the 10S and 14S lens mRNA contain poly A sequences. The poly A content found in 14S mRNA cannot account for ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.2.245
更新日期:1974-02-01 00:00:00
abstract::Fluoropyrimidines, such as 5-fluorouracil (5-FU), are used extensively in cancer therapy. In the cell, 5-FU is metabolized to 5-fluorodeoxyuridylate (5-FdUMP), a tight binding covalent inhibitor of thymidylate synthase (TS). In order to create 5-FdUMP resistant enzymes to protect chemosensitive normal cells and furthe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.18.3702
更新日期:1999-09-15 00:00:00
abstract::Correlation of motif occurrences with gene expression intensity is an effective strategy for elucidating transcriptional cis-regulatory logic. Here we demonstrate that this approach can also identify cis-regulatory elements for alternative pre-mRNA splicing. Using data from a human exon microarray, we identified 56 ca...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm485
更新日期:2007-01-01 00:00:00
abstract::The availability of protein fluorophores with appropriate spectral properties has made it possible to employ fluorescence resonance energy transfer (FRET) to assess interactions between three proteins microscopically. Flow cytometry offers excellent sensitivity, effective signal separation and the capacity to assess a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni057
更新日期:2005-04-01 00:00:00
abstract::Dramatic improvements in ribozyme mimics have been achieved by employing the principles of small molecule catalysis to the design of macromolecular, biomimetic reagents. Ribozyme mimics derived from the ligand 2,9-dimethylphenanthroline (neocuproine) show at least 30-fold improvements in efficiency at sequence-specifi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.10.2199
更新日期:2001-05-15 00:00:00
abstract::Linkage analysis is a successful procedure to associate diseases with specific genomic regions. These regions are often large, containing hundreds of genes, which make experimental methods employed to identify the disease gene arduous and expensive. We present two methods to prioritize candidates for further experimen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl707
更新日期:2006-01-01 00:00:00
abstract::Abasic sites are common DNA lesions resulting from spontaneous depurination and excision of damaged nucleobases by DNA repair enzymes. However, the influence of the local sequence context on the structure of the abasic site and ultimately, its recognition and repair, remains elusive. In the present study, duplex DNAs ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm622
更新日期:2008-01-01 00:00:00
abstract::Coralyne is a small crescent-shaped molecule known to intercalate duplex and triplex DNA. We report that coralyne can cause the complete and irreversible disproportionation of duplex poly(dT)*poly(dA). That is, coralyne causes the strands of duplex poly(dT)*poly(dA) to repartition into equal molar equivalents of tripl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.4.983
更新日期:2002-02-15 00:00:00
abstract::Here, we present an update of Breast Cancer Now Tissue Bank bioinformatics, a rich platform for the sharing, mining, integration and analysis of breast cancer data. Its modalities provide researchers with access to a centralised information gateway from which they can access a network of bioinformatic resources to que...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx913
更新日期:2018-01-04 00:00:00
abstract::G-DNA, a polymorphic family of four-stranded DNA structures, has been proposed to play roles in a variety of biological processes including telomere function, meiotic recombination and gene regulation. Here we report the purification and cloning of TGP1, a G-DNA specific binding protein from Tetrahymena thermophila. T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.7.1613
更新日期:1998-04-01 00:00:00
abstract::We searched for nucleotide excision repair in human cell-free extracts using two assays: damage-specific incision of DNA (the nicking assay) and damage-stimulated DNA synthesis (the repair synthesis assay). HeLa cell-free extract prepared by the method of Manley et al. (1980) has a weak nicking activity on UV irradiat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.12.4471
更新日期:1989-06-26 00:00:00
abstract::Biological networks are a topic of great current interest, particularly with the publication of a number of large genome-wide interaction datasets. They are globally characterized by a variety of graph-theoretic statistics, such as the degree distribution, clustering coefficient, characteristic path length and diamete...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh164
更新日期:2004-01-14 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
pub_type: 杂志文章
doi:10.1093/nar/gkg340
更新日期:2003-05-01 00:00:00
abstract::Transcription of the human adenovirus 5 genome in transformed rat embryo cells (DFK3) was investigated using two different approaches. Preferential digestion of transcribed viral sequences by DNase I was analysed using kinetics of renaturation of 32P-labeled Ad5 HpaI restriction fragments in the presence of material w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.1.1
更新日期:1978-01-01 00:00:00
abstract::Plant mitochondrial genomes show much more evolutionary plasticity than those of animals. We analysed the first mitochondrial DNA (mtDNA) of a lycophyte, the quillwort Isoetes engelmannii, which is separated from seed plants by more than 350 million years of evolution. The Isoetes mtDNA is particularly rich in recombi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp532
更新日期:2009-08-01 00:00:00
abstract::The expression of the nicotinic acetylcholine receptor alpha 2 subunit gene is highly restricted to the Spiriform lateralis nucleus of the Chick diencephalon. As a first step toward understanding the molecular mechanism underlying this regulation, we have investigated the structural and regulatory properties of the 5'...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.9.2185
更新日期:1993-05-11 00:00:00
abstract::PrimPol is a primase-polymerase involved in nuclear and mitochondrial DNA replication in eukaryotic cells. Although PrimPol is predicted to possess an archaeo-eukaryotic primase and a UL52-like zinc finger domain, the role of these domains has not been established. Here, we report that the proposed zinc finger domain ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku214
更新日期:2014-05-01 00:00:00
abstract::We have developed efficient methods for creating artificial transposons and inserting these transposons into plasmid targets in vitro, primarily for the purpose of DNA mapping and sequencing. A novel plasmid has been engineered to convert virtually any DNA sequence, or combination of sequences, into an artificial tran...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.18.3765
更新日期:1994-09-11 00:00:00
abstract::mRNA differential display RT-PCR has been extensively used for the isolation of genes differentially expressed between RNA populations. We have assessed its utility for the identification of developmentally regulated genes in plasmid cDNA libraries derived from individual tissues dissected from early mouse embryos. Us...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.19.4538
更新日期:1998-10-01 00:00:00