Effect of 5-bromo- and 5-methyldeoxycytosine on duplex stability and discrimination of the NotI octadeoxynucleotide. Quantitative measurements using thin-layer chromatography.

Octadeoxynucleotides based on the recognition sequence of the restriction endonuclease NotI were synthesized containing unmodified nucleotides and nucleotides with methyl and bromide additions at the C5 position of the pyrimidine ring of deoxycytosine. On annealing to single-stranded DNA bearing one NotI site, thin-layer chromatography (TLC) of the different oligonucleotides was used quantitatively to determine differences in dissociation temperature (Td) and binding equilibrium. Buffers used in filter hybridization experiments could be used in this TLC system. In addition, actual hybridizations were carried out to filter-bound DNA with and without a NotI site. The incorporation of 5-methyldeoxycytosine and 5-bromodeoxycytosine led to a significant increase in stability of homoduplex formation during hybridization, due to a shift in the binding equilibrium and an increase of the Td, thereby improving discrimination considerably. Some implications of the results for several techniques involving oligomer hybridization are discussed.

• Publication year

  1990

• Venue

  Journal of Biological Chemistry

• Publication date

  1990-09-25

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1016/s0021-9258(17)46271-5PMID 2398067
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Ordering of cosmid clones covering the herpes simplex virus type I (HSV-I) genome: a test case for fingerprinting by hybridisation.

  1990cited by this paper
• Labelling oligonucleotides to high specific activity (I).

  1989cited by this paper
• An oligonucleotide hybridization approach to DNA sequencing

  1989cited by this paper
• A strategy for high-volume sequencing of cosmid DNAs: random and directed priming with a library of oligonucleotides.

  1989cited by this paper
• Sequencing of megabase plus DNA by hybridization: theory of the method.

  1989cited by this paper
• A cassette with seven unique restriction sites, including octanucleotide sequences: extension of multiple-cloning-site plasmids.

  1989cited by this paper
• Generation of cDNA probes directed by amino acid sequence: cloning of urate oxidase.

  1988cited by this paper
• A simple DNA diagnostic method for human genetic disorders

  1987cited by this paper
• A rapid method to identify cosmids containing rare restriction sites.

  1987cited by this paper
• Molecular approaches to genome analysis: a strategy for the construction of ordered overlapping clone libraries

  1987cited by this paper
• CpG-rich islands and the function of DNA methylation

  1986cited by this paper
• Simplified preparation of unidirectional deletion clones.

  1986cited by this paper
• Single-stranded DNA 'blue' T7 promoter plasmids: a versatile tandem promoter system for cloning and protein engineering.

  1986cited by this paper
• Discrimination among the transcripts of the allelic human beta-globin genes beta A, beta S and beta C using oligodeoxynucleotide hybridization probes.

  1986cited by this paper
• Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia.

  1985cited by this paper
• Base composition-independent hybridization in tetramethylammonium chloride: a method for oligonucleotide screening of highly complex gene libraries.

  1985cited by this paper
• Genomic sequencing.

  1984cited by this paper
• Synthesis and use of synthetic oligonucleotides.

  1984cited by this paper
• Temperature dependence of the activity of DNA-modifying enzymes: endonucleases and DNA ligase.

  1982cited by this paper
• DNA N-glycosidases: properties of uracil-DNA glycosidase from Escherichia coli.

  1977cited by this paper
• DNA sequencing with chain-terminating inhibitors.

  1977cited by this paper
• Stereochemistry of nucleic acids and their constituents. X. solid‐slate base‐slacking patterns in nucleic acid constituents and polynucleotides

  1971cited by this paper
• Interaction of poly-5-bromocytidylic acid with polyinosinic acid. A study of helix stability and spectroscopic properties.

  1969cited by this paper
• Conformation and thermodynamic properties of oligocytidylic acids.

  1967cited by this paper
• Polynucleotide analogues. VI. Physical studies on 5-substituted pyrimidine polynucleotides.

  1966cited by this paper

• Effect of DNA Methylation on the 3′→5′ Exonuclease Activity of Major Human Abasic Site Endonuclease APEX1

  2022cites this paper
• DNA modification readers and writers and their interplay.

  2019cites this paper
• Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation

  2018cites this paper
• 5-Mercuricytosine: An Organometallic Janus Nucleobase.

  2016cites this paper
• Impact of cytosine 5-halogens on the interaction of DNA with restriction endonucleases and methyltransferase.

  2006cites this paper
• Quantitative assessment of the use of modified nucleoside triphosphates in expression profiling: differential effects on signal intensities and impacts on expression ratios

  2002cites this paper
• Influence of 5-bromodeoxycytosine substitution on triplex DNA stability and conformation.

  1999cites this paper
• Synthesis of 5-substituted 2'-deoxycytidine 5'-(alpha-P-borano)triphosphates, their incorporationinto DNA and effects on exonuclease.

  1999cites this paper
• Present and Future Detection Formats for PCR Quantitation of Nucleic Acids

  1998cites this paper
• Theoretical studies on intratriplex DNA with 5-bromocytosine

  1998cites this paper
• A New Phosphoramidite Reagent for the Incorporation of Diazaphenoxazinone Nucleoside With Enhanced Base-Pairing Properties into Oligodeoxynucleotides

  1997cites this paper
• Synthesis and DNA Duplex Stabilities of Oligonucleotides Containing C-5-(3-Methoxypropynyl)-2′-deoxyuridine Residues

  1997cites this paper
• The effects of internal primer-template mismatches on RT-PCR: HIV-1 model studies.

  1997cites this paper
• Sequence-independent and linear variation of oligonucleotide DNA binding stabilities.

  1996cites this paper
• Oligonucleotides containing 2-aminoadenine and 5-methylcytosine are more effective as primers for PCR amplification than their nonmodified counterparts.

  1996cites this paper
• Substitution of 2-aminoadenine and 5-methylcytosine for adenine and cytosine in hybridization probes increases the sensitivity of DNA fingerprinting.

  1994cites this paper
• Relational genome analysis using reference libraries and hybridisation fingerprinting.

  1994cites this paper
• A guide to the design and use of mismatched and degenerate primers.

  1994cites this paper
• High resolution cosmid and P1 maps spanning the 14 Mb genome of the fission yeast S. pombe.

  1993cites this paper
• [Oligonucleotides forming highly stable, specific duplexes, their use as primers in sequencing and in the polymerase chain reaction].

  1993cites this paper
• Strings of contiguous modified pentanucleotides with increased DNA-binding affinity can be used for DNA sequencing by primer walking.

  1993cites this paper
• Nonradioactive detection of DNA using dioxetane chemiluminescence.

  1992cites this paper
• Use of high coverage reference libraries of Drosophila melanogaster for relational data analysis. A step towards mapping and sequencing of the genome.

  1991cites this paper
• Quantitative measurements on the duplex stability of 2,6‐diaminopurine and 5‐chloro‐uracil nucleotides using enzymatically synthesized oligomers

  1990cites this paper