Abstract:
:DNA methylation is the best-studied epigenetic modification and describes the conversion of cytosine to 5-methylcytosine. The importance of this phenomenon is that aberrant promoter hypermethylation is a common occurrence in cancer and is frequently associated with gene silencing. Various techniques are currently available for the analysis of DNA methylation. However, accurate and reproducible quantification of DNA methylation remains challenging. In this report, we describe Bio-COBRA (combined bisulfite restriction analysis coupled with the Agilent 2100 Bioanalyzer platform), as a novel approach to quantitative DNA methylation analysis. The combination of a well-established method, COBRA, which interrogates DNA methylation via the restriction enzyme analysis of PCR-amplified bisulfite treated DNAs, with the Bioanalyzer platform allows for the rapid and quantitative assessment of DNA methylation patterns in large sample sets. The sensitivity and reproducibility of Bio-COBRA make it a valuable tool for the analysis of DNA methylation in clinical samples, which could aid in the development of diagnostic and prognostic parameters with respect to disease detection and management.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Brena RM,Auer H,Kornacker K,Hackanson B,Raval A,Byrd JC,Plass Cdoi
10.1093/nar/gnj017keywords:
subject
Has Abstractpub_date
2006-02-07 00:00:00pages
e17issue
3eissn
0305-1048issn
1362-4962pii
34/3/e17journal_volume
34pub_type
杂志文章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::DNA mismatches that occur between vector homology arms and chromosomal target sequences reduce gene targeting frequencies in several species; however, this has not been reported in human cells. Here we demonstrate that even a single mismatched base pair can significantly decrease human gene targeting frequencies. In a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1303
更新日期:2014-03-01 00:00:00
abstract::An important model system for studying the process leading to productive transcription is provided by the superfamily of nuclear receptors, which are for the most part ligand-controlled transcription factors. Over the past years several 'orphan' nuclear receptors have been isolated for which no ligand has yet been ide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.16.3424
更新日期:2001-08-15 00:00:00
abstract::Mutations in the RecQ DNA helicase gene BLM give rise to Bloom's syndrome, which is a rare autosomal recessive disorder characterized by genetic instability and cancer predisposition. BLM helicase is highly active in binding and unwinding G-quadruplexes (G4s), which are physiological targets for BLM, as revealed by ge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv361
更新日期:2015-05-19 00:00:00
abstract::The unwinding of supercoiled phi X174 RFI DNA induced by the tumorigenic (+) and non-tumorigenic (-) enantiomers of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) has been investigated by agarose slab-gel and ethidium titration tube gel electrophoresis. The differences in adduct conformat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.23.6167
更新日期:1992-12-11 00:00:00
abstract::Robust estimation of allele frequencies in pools of DNA has the potential to reduce genotyping costs and/or increase the number of individuals contributing to a study where hundreds of thousands of genetic markers need to be genotyped in very large populations sample sets, such as genome wide association studies. In o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni142
更新日期:2005-09-30 00:00:00
abstract::The high-mobility-group A2 protein (HMGA2) plays important functional roles in transcriptional regulation, DNA replication and chromatin structure. In this study, the effect of histone deacetylase inhibition on the transcriptional activity of the Hmga2 gene was investigated in vivo both at the endogenous gene level an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg403
更新日期:2003-06-15 00:00:00
abstract::The Aspergillus nidulans sequence ans1, previously known to enhance transformation frequencies of pyr4-based vectors, was shown to enhance the efficiency of argB and trpC-based vectors. Increased efficiencies could be obtained by constructing vectors containing argB and ans1 or by cotransforming selectable plasmids (c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.22.9163
更新日期:1987-11-25 00:00:00
abstract::Hybridization solutions containing chaotropes may be used to modulate the thermal stability (Tm or Td) of oligodeoxynucleotide (ODN) duplexes or hybrids over a 90 degrees C range. Modulation of Td allows formulation of hybridization solutions that permit ambient temperature hybridization using most combinations of pro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.19.5143
更新日期:1991-10-11 00:00:00
abstract::For sophisticated gene targeting procedures requiring two sequential selective steps to operate efficiently it is essential that the marker genes used are not prone to position effects. The double replacement gene targeting procedure, to produce mice with subtle gene alterations, is based on the use of hypoxanthine ph...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.19.3937
更新日期:1997-10-01 00:00:00
abstract::Using a human interferon-alpha probe we have isolated recombinant phages containing murine interferon-alpha (Mu IFN-alpha) genes from a genomic library. One of these phages contained two complete Mu IFN-alpha genes and part of a third gene. The insert of a second phage held two IFN genes. This indicates that the Mu IF...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.3.791
更新日期:1985-02-11 00:00:00
abstract::Gel migration and uranyl photoprobing have been used to study the effects of inosine and 2,6-diaminopurine (2,6-DAP) substitution on adenine-tract (A-tract) induced DNA curvature. Using a 10mer repeated sequence including five inosines we show by uranyl photoprobing that a narrow minor groove varying in phase with the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.17.3497
更新日期:1997-09-01 00:00:00
abstract::Giant viruses have extraordinarily large dsDNA genomes, and exceptionally, they encode various components of the translation apparatus, including tRNAs, aminoacyl-tRNA synthetases and translation factors. Here, we focused on the elongation factor 1 (EF1) family of viral translational GTPases (trGTPases), using computa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz296
更新日期:2019-06-20 00:00:00
abstract::In the most extensive examination to date of the relationship between the pausing of reverse transcrip-tase (RT) and RNA secondary structures, pause events were found to be correlated to inverted repeats both ahead of, and behind the catalytic site in vitro. In addition pausing events were strongly associated with pol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.14.3433
更新日期:1998-07-15 00:00:00
abstract::Specific guanine-rich regions in human genome can form higher-order DNA structures called G-quadruplexes, which regulate many relevant biological processes. For instance, the formation of G-quadruplex at telomeres can alter cellular functions, inducing apoptosis. Thus, developing small molecules that are able to bind ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku247
更新日期:2014-05-01 00:00:00
abstract::Current literature describes several methods for the design of efficient siRNAs with 19 perfectly matched base pairs and 2 nt overhangs. Using four independent databases totaling 3336 experimentally verified siRNAs, we compared how well several of these methods predict siRNA cleavage efficiency. According to receiver ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm088
更新日期:2007-01-01 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::Protein synthesis elongation factor 2 (EF-2) from all archaebacteria so far analysed, is susceptible to inactivation by diphtheria toxin, a property which it shares with EF-2 from the eukaryotic 8OS translation system. To resolve the structural basis of diphtheria toxin susceptibility, the structural gene for the EF-2...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.16.7817
更新日期:1988-08-25 00:00:00
abstract::We developed a framework for quick and reliable construction of complex gene circuits for genetically engineering mammalian cells. Our hierarchical framework is based on a novel nucleotide addressing system for defining the position of each part in an overall circuit. With this framework, we demonstrate construction o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt605
更新日期:2013-09-01 00:00:00
abstract::Herein, we describe a case study into the population dynamics of in vitro selection, using RNA-cleaving DNAzymes as a model system. We sought to understand how the composition of the population can change over time in response to different levels of selection pressure, and how well these changes are correlated with se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp222
更新日期:2009-06-01 00:00:00
abstract::Accurate maps and DNA sequences for human subtelomere regions, along with detailed knowledge of subtelomere variation and long-range telomere-terminal haplotypes in individuals, are critical for understanding telomere function and its roles in human biology. Here, we use a highly automated whole genome mapping technol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx017
更新日期:2017-05-19 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::Unoxidized crystalline silicon, characterized by high purity, high homogeneity, sturdiness and an atomically flat surface, offers many advantages for the construction of electronic miniaturized biosensor arrays upon attachment of biomolecules (DNA, proteins or small organic compounds). This allows to study the inciden...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnj034
更新日期:2006-02-28 00:00:00
abstract::Translin is a single-stranded RNA- and DNA-binding protein, which has been highly conserved in eukaryotes, from man to Schizosaccharomyces pombe. TRAX is a Translin paralog associated with Translin, which has coevolved with it. We generated structural models of the S. pombe Translin (spTranslin), based on the solved 3...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1230
更新日期:2010-05-01 00:00:00
abstract::FIMM database (http://sdmc.krdl.org.sg:8080/fimm) contains data relevant to functional molecular immunology, focusing on cellular immunology. It contains fully referenced data on protein antigens, major histocompatibility complex (MHC) molecules, MHC-associated peptides and relevant disease associations. FIMM has a se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.226
更新日期:2002-01-01 00:00:00
abstract::The wobble uridine of certain bacterial and mitochondrial tRNAs is modified, at position 5, through an unknown reaction pathway that utilizes the evolutionarily conserved MnmE and GidA proteins. The resulting modification (a methyluridine derivative) plays a critical role in decoding NNG/A codons and reading frame mai...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp762
更新日期:2009-11-01 00:00:00
abstract::We have analyzed the molecular mechanism that makes translation of the MS2 replicase cistron dependent on the translation of the upstream coat cistron. Deletion mapping on cloned cDNA of the phage shows that the ribosomal binding site of the replicase cistron is masked by a long distance basepairing to an internal coa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.19.6955
更新日期:1985-10-11 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::Homopolyribonucleotides and E. coli DNA wer spin labeled with an iodoacetamide-nitroxide compound. The extent of labeling is highly dependent upon the nature of the base and the secondary structure of the nucleic acid. This spin label-polymer linkage is unstable at high temperatures and in phosphate buffers. In order ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.4.847
更新日期:1976-04-01 00:00:00
abstract::Fully protected diastereoisomers of deoxyguanylyl (3' leads to 5') deoxyadenosine stereospecifically labelled on phosphorus with oxygen-18 have been synthesized by oxidation of phosphite triester intermediates in the presence of 18O-labelled water. The diastereoisomers have been chromatographically separated and their...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.20.7087
更新日期:1983-10-25 00:00:00