title: Conformational transitions of alternating purine-pyrimidine DNAs in perchlorate ethanol solutions.
abstract: Conformational transitions of poly(dA-dC).poly(dG-dT), poly(dA-dT).poly(dA-dT), and other alternating purine-pyrimidine DNAs were studied in aqueous ethanol solutions containing molar concentrations of sodium perchlorate, which is a novel solvent stabilizing non-B duplexes of DNA. Using CD and UV absorption spectroscopies, we show that this solvent unstacks bases and unwinds the B-forms of the DNAs to transform them into the A-form or Z-form. In the absence of divalent cations poly(dA-dC).poly(dG-dT) can adopt both of these conformations. Its transition into the Z-form is induced at higher salt and lower ethanol concentrations, and at higher temperatures than the transition into the A-form. Submillimolar concentrations of NiCl2 induce a highly cooperative and slow A-Z transition or Z-Z' transition, which is fast and displays low cooperativity. Poly(dA-dT).poly(dA-dT) easily isomerizes into the A-form in perchlorate-ethanol solutions, whereas high perchlorate concentrations denature the polynucleotide, which then cannot adopt the Z-form. At low temperatures, however, NiCl2 also cooperatively induces the Z'-form in poly(dA-dT).poly(dA-dT). Poly(dI-dC).poly(dI-dC) is known to adopt an unusual B-form in low-salt aqueous solution, which is transformed into a standard B-form by the combination of perchlorate and ethanol. NiCl2 then transforms poly(dI-dC).poly(dI-dC) into the Z'-form, which is also adopted by poly(dI-br5dC).poly(dI-br5dC).
authors.affiliation: Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic.
authors.forename: M
authors.initials: M
authors.lastname: Vorlícková
mesh_terms: D001483:Base Sequence; D055592:Biophysical Phenomena; D001703:Biophysics; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D000431:Ethanol; D066298:In Vitro Techniques; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D010472:Perchlorates; D011067:Poly dA-dT / Q000737:chemistry; D011089:Polydeoxyribonucleotides / Q000737:chemistry; D017670:Sodium Compounds; D012996:Solutions; D013056:Spectrophotometry, Ultraviolet
chemical_list: D010472:Perchlorates; D011089:Polydeoxyribonucleotides; D017670:Sodium Compounds; D012996:Solutions; D011067:Poly dA-dT; D000431:Ethanol; C044165:poly(d(G-T).d(C-A)); D004247:DNA; C031068:sodium perchlorate