Site-specific intercalation at the triplex-duplex junction induces a conformational change which is detectable by hypersensitivity to diethylpyrocarbonate.

Abstract

Using site-specific intercalation directed by intermolecular triplex formation, the conformation of an intercalation site in DNA was examined by footprinting with the purine-specific (A much greater than G) reagent diethylpyrocarbonate. Site specific intercalation was achieved by covalently linking an intercalator to the 5' end of a homopyrimidine oligodeoxynucleotide, which bound to a homopurinehomopyrimidine stretch in a recombinant plasmid via intermolecular triplex formation. This directs intercalation to a single site in 3kb of DNA at the 5' triplex-duplex junction. Footprinting with diethylpyrocarbonate and dimethylsulphate revealed strong protection from modification of adenine residues within the triple-helix in concordance with their Hoogsteen pairing with the third strand, and a strong hypersensitivity to diethylpyrocarbonate at the first adenine of the duplex. This result indicates that intercalation at this site induces a conformational change at the 5' triplex-duplex junction. Furthermore, the same diethlypyrocarbonate hypersensitivity was observed with an unmodified triple-strand forming oligonucleotide and a range of intercalating molecules present in solution. Thus the 5' triplex-duplex junction is a strong binding site for some intercalating molecules and the junction undergoes a conformational change which is sensitive to diethylpyrocarbonate upon insertion of the planar aromatic chromophore. This conformational change can be used to direct a single-strand cut in duplex DNA to a defined site.

• Authors: D A Collier, J L Mergny, N T Thuong, C Helene
• Journal: Nucleic acids research (Nucleic Acids Res) Vol. 19 Issue 15 Pg. 4219-24 (Aug 11 1991) ISSN: 0305-1048 [Print] England
• PMID: 1870975 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• Acridines
• Oligonucleotides
• Purines
• Pyrimidines
• Sulfuric Acid Esters
• DNA
• Adenine
• dimethyl sulfate
• Diethyl Pyrocarbonate

Topics

• Acridines (chemistry)
• Adenine (chemistry)
• Base Sequence
• DNA (chemistry)
• Diethyl Pyrocarbonate (chemistry)
• Molecular Sequence Data
• Nucleic Acid Conformation
• Nucleotide Mapping
• Oligonucleotides (chemistry)
• Purines (chemistry)
• Pyrimidines (chemistry)
• Spectrophotometry, Ultraviolet
• Sulfuric Acid Esters (chemistry)