title: Contribution of loops and nicks to the formation of DNA dumbbells: melting behavior and ligand binding.
abstract: We have evaluated the thermodynamic contribution of thymine loops and nicks to the overall stability of double-helical DNA by investigating (1) the melting behavior of two unligated DNA dumbbells and their corresponding core duplexes and (2) the association of netropsin to the central core of four A.T base pairs of these molecules. Temperature-dependent UV absorption and differential scanning calorimetry techniques have been used to characterize the helix-coil transitions of all four deoxyoligonucleotide duplexes. In 10 mM NaP(i) buffer at pH 7.0, all transitions were monophasic. The dumbbells melt with transition temperatures, Tm, independent of strand concentration, while each duplex melts with transition temperature dependence on strand concentration, characteristic of mono- and bimolecular processes, respectively. The Tm's for the dumbbells correspond to those of single hairpins containing only four base pairs in the stem. We obtain dTm/d log [Na+] values of 10.9-12.5 degrees C for these molecules, which correspond to similar counterion releases and suggest helical structures with similar charge densities and helical strandedness. Standard thermodynamics profiles at 5 degrees C reveal that the favorable free energy of forming these ordered structures results from the partial compensation of favorable enthalpies with unfavorable entropies. The stabilization of the dumbbells relative to the core duplexes is enthalpic, due to extra stacking of the nearest loop thymines on the G.C base pairs at both ends of the stem.(ABSTRACT TRUNCATED AT 250 WORDS)
authors.affiliation: Department of Chemistry, New York University, New York 10003.
authors.forename: D
authors.initials: D
authors.lastname: Rentzeperis
authors.forename: J
authors.initials: J
authors.lastname: Ho
authors.forename: L A
authors.initials: LA
authors.lastname: Marky
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002151:Calorimetry; D004247:DNA / Q000737:chemistry*; D008024:Ligands; D008433:Mathematics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D009994:Osmolar Concentration; D013056:Spectrophotometry, Ultraviolet; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D008024:Ligands; D009838:Oligodeoxyribonucleotides; D004247:DNA