title: Sequence effects on the relative thermodynamic stabilities of B-Z junction-forming DNA oligomeric duplexes.
abstract: Circular dichroism (CD) and ultraviolet absorption techniques were employed in characterizing the sequence-dependent thermodynamic stabilities of B-Z junction-forming DNA duplexes. The Watson strand of the duplexes has the general sequence (5meC-G)4-NXYG-ACTG (where N = A or G and XY represents all permutations of pyrimidine bases). Duplexes were generated by mixing stoichiometric amounts of the complementary strands. Circular dichroism studies indicate that each duplex is fully right-handed at low salt (e.g., 115 mM Na+) but undergoes a salt-induced conformational transition to a structure that possesses both left- and right-handed conformations at high salt (4.5 M Na+), and hence a B-Z junction. Optical melting studies of the DNA duplexes at fixed DNA concentration with total Na+ concentration ranging from 15 mM to 5.0 M were determined. A nonlinear dependence of the melting temperature (Tm) on [Na+] was observed. Thermodynamic parameters at Na+ concentrations of 115 mM and 4.5 M with a wide range of DNA concentrations were determined from UV optical melting studies via construction of van't Hoff plots. A change of a single dinucleotide within these duplexes significantly affected the helix stabilities. The experimentally obtained free energies for the duplex to single-strand transitions were in close agreement with predicted values obtained from two different methods.
authors.affiliation: Department of Chemistry, Seton Hall University, South Orange, New Jersey 07079, USA.
authors.forename: E O
authors.initials: EO
authors.lastname: Otokiti
authors.forename: R D
authors.initials: RD
authors.lastname: Sheardy
mesh_terms: D001483:Base Sequence; D055592:Biophysical Phenomena; D001703:Biophysics; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D012965:Sodium Chloride; D013056:Spectrophotometry, Ultraviolet; D013816:Thermodynamics
chemical_list: D009838:Oligodeoxyribonucleotides; D012965:Sodium Chloride; D004247:DNA