Kinetic analysis of sequence-specific alkylation of DNA by pyrimidine oligodeoxyribonucleotide-directed triple-helix formation

Bioconjugate Chemistry
M J Taylor, P B Dervan

Abstract

Attachment of a nondiffusible bromoacetyl electrophile to the 5-position of a thymine at the 5'-end of a pyrimidine oligodeoxyribonucleotide affords sequence-specific alkylation of a guanine base in duplex DNA two base pairs to the 5'-side of a local triple-helical complex. Products resulting from reaction of 5'-ETTTTMeCTTTTMeCMeCTTTMeCTTTT-3' at 37 degrees C with a 29 base pair target duplex are determined by a gel mobility analysis to be oligonucleotides terminating in 5'- and 3' -phosphate functional groups, consistent with a mechanism involving alkylation, glycosidic bond cleavage, and base-promoted strand cleavage. The guanine-(linker)-oligonucleotide conjugate formed upon triple-helix-mediated alkylation at the N7 position of a guanine base in a 60 base pair duplex was identified by enzymatic phosphodiester hydrolysis of the alkylation products followed by reversed phase HPLC analysis. To determine the rate enhancement achieved by oligonucleotide-directed alkylation of duplex DNA, a comparison of rates of alkylation at N7 of guanine in double-stranded DNA by the N-bromoacetyloligonucleotide and 2-bromoacetamide was performed by a polyacrylamide gel assay. The reaction within the triple-helical complex on a restriction fra...Continue Reading

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Citations

Apr 8, 2009·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Meghan A Campbell, Paul S Miller
May 12, 2000·Biochimica Et Biophysica Acta·D PraseuthC Hélène
Dec 3, 2009·Bioconjugate Chemistry·Meghan A Campbell, Paul S Miller
Jan 22, 2011·Chemical Research in Toxicology·Mostafa I FekryKent S Gates
Dec 20, 2002·Nucleic Acids Research·Patrizia AlbertiJian-Sheng Sun
Jan 30, 2015·Chembiochem : a European Journal of Chemical Biology·Ellen GysselsAnnemieke Madder

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