Preparation and analysis of oligonucleotides containing lesions resulting from C5'-oxidation.
[reaction: see text] Hydrogen atom abstraction from the C5'-position of nucleotides in DNA results in direct strand scission. The newly formed 5'-termini of the cleaved DNA consists of alkali-labile fragments of the oxidized nucleotide. One terminus contains a 5'-aldehyde as part of an otherwise undamaged nucleotide (T-al). A second more structurally distinct product that is produced in lower yields results from cleavage of the C4'-C5' carbon-carbon bond. The 1,4-dioxo-2-phosphorylbutane (DOB) is a precursor of the alkylating agent but-2-ene-1,4-dial. To facilitate studies on these lesions, methods for synthesizing oligodeoxynucleotides containing DOB or T-al at their 5'-termini were developed. The effects of these lesions on the UV-melting temperatures of duplex DNA, and their cleavage labilities were determined. T-al cleaves very slowly (t(1/2) = 100.7 h), whereas DOB has a half-life at 37 degrees C (pH 7.2) of less than 11 h. In addition, DOB forms a stable adduct very efficiently with Tris, which protects the abasic site against cleavage.
Kodama
Tetsuya
T
Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, USA.
Greenberg
Marc M
MM
D015394:Molecular Structure; D009841:Oligonucleotides / Q000032:analysis* / Q000138:chemical synthesis* / Q000737:chemistry; D010084:Oxidation-Reduction; D013997:Time Factors
D009841:Oligonucleotides