title: Thermodynamic analysis of conformational transitions in oligonucleotide complexes in presence of Na(+) and Mg(2+) ions, using "staggering zipper" model.
abstract: Curves of transitions in double (2-->1 transition) and triple (3-->2 transition) complexes of oligonucleotides dA(N1)with dT(N2) in solutions with Na(+) and Mg(2+) are calculated for the case of oligomer lengths from 10 to 500 nucleotides in the wide range of ion concentrations. The calculated curves of transitions and their differential analogs reflect rather exactly the position and form of experimental curves and describe dependences of transition temperatures on the length of molecules, their concentration, and ionic conditions. Values of the nucleation parameter beta for the systems studied are determined by comparison of the calculated and experimental data obtained in a number of works. The average beta value equal to 10(-3) l/mole is in an agreement with values reported for similar systems earlier. It is shown that disordering of duplex and triplex ends ("end fraying") has an essential influence on the form of melting curves, their asymmetry and the increase of the transition interval.
authors.affiliation: B.I.Verkin Institute for Low Temperature Physics and Engineering, National Academy of Science of Ukraine, 47 Lenin Avenue, Kharkov 61103, Ukraine. BLAGOI@ilt.kharkov.ua
authors.forename: Yurii
authors.initials: Y
authors.lastname: Blagoi
authors.forename: Victor
authors.initials: V
authors.lastname: Zozulya
authors.forename: Sergey
authors.initials: S
authors.lastname: Egupov
authors.forename: Vladimir
authors.initials: V
authors.lastname: Onishchenko
authors.forename: Galina
authors.initials: G
authors.lastname: Gladchenko
mesh_terms: D002412:Cations; D008274:Magnesium / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D012964:Sodium / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
chemical_list: D002412:Cations; D009841:Oligonucleotides; D012964:Sodium; D008274:Magnesium