title: DNA-duplexes containing abasic sites: correlation between thermostability and acoustic wave properties.
abstract: Aldehydic apurinic or apyrimidinic sites that lack a nucleobase moiety are one of the most common forms of toxic lesions in DNA. In the present study, a close structural analog of such a site, the 2-(hydroxymethyl) tetrahydrofuranyl residue, was synthesized in order to act as a model for damaged nucleic acid probes. Prepared oligodeoxyribonucleotides containing one, two or three abasic sites were hybridized to complementary sequences immobilized on a gold surface using the neutravidin-biotin interaction for study by thickness shear mode acoustic wave detector. Measurement of the complex electrical impedance of an AT-cut quartz device with immobilized biotinylated nucleotide allowed the detection of changes of series resonance frequency, Deltafs, and motional resistance, Rm, associated with duplex formation. The changes as detected by the acoustic wave method correlated well with the thermostability of DNA duplexes in solution. With respect to the latter, UV-monitored melting curves indicate that both the number of sites and their localization in the double-stranded structure influence the amount by which a 19 b.p. duplex is destabilized. The presence of 3 abasic sites completely destabilized the DNA duplex.
authors.affiliation: Laboratory of Biophysics, Faculty of Mathematics, Physics and Computer Science, Comenius University, Mlynská dolina F1, 842 48 Bratislava, Slovak Republic.
authors.forename: T
authors.initials: T
authors.lastname: Hianik
authors.forename: X
authors.initials: X
authors.lastname: Wang
authors.forename: S
authors.initials: S
authors.lastname: Andreev
authors.forename: N
authors.initials: N
authors.lastname: Dolinnaya
authors.forename: T
authors.initials: T
authors.lastname: Oretskaya
authors.forename: M
authors.initials: M
authors.lastname: Thompson
mesh_terms: D000162:Acoustics; D004247:DNA / Q000737:chemistry*; D004249:DNA Damage; D015342:DNA Probes; D004260:DNA Repair; D006358:Hot Temperature; D008956:Models, Chemical; D009692:Nucleic Acid Heteroduplexes; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D013056:Spectrophotometry, Ultraviolet / Q000379:methods
chemical_list: D015342:DNA Probes; D009692:Nucleic Acid Heteroduplexes; D009838:Oligodeoxyribonucleotides; D004247:DNA