Association of Short-Strand DNA Oligomers with Guanidinium-Linked Nucleosides. A Kinetic and Thermodynamic Study

• Published in: Journal of the American Chemical Society 1996-08, Vol.118 (34), p.7892-7899
• Main Authors: Blaskó, Andrei, Dempcy, Robert O, Minyat, Elvira E, Bruice, Thomas C
• Format: Article
• Language: English
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja961308m

Complementary short-strand DNA homooligomers and guanidinium-linked homonucleosides associate and form triplexes in solution. The melting temperatures, T m, the association and dissociation kinetic and thermodynamic parameters, and activation energies were determined by UV thermal analysis for the triplexes of short strand DNA homooligomers {d(pA)5-d(pA)12 - 18} and poly(dA) with the guanidinium-linked nucleoside d(Tg)4-T-azido {DNG5}. The melting and cooling curves exhibit hysteresis behavior in the temperature range of 5−95 °C at 0.2 deg/min thermal rate. From these curves the rate constants and the energies of activation for association (k on, E on) and dissociation (k off, E off) processes were obtained. The T m decreases with the ionic strength and increases slightly with increase in concentration of the monomers. A greater increase in the T m results from an increase in the length of the DNA strand d(pA) x . In the case of d(pA)5 and d(pA)6, triplexes are formed, with T m = 34 and 39 °C, respectively, only above 0.063 mM/(adenine base) concentration when ionic strength is 0.08. The rate constants k on and k off at a reference temperature (288 K) are dependent on the DNA strand length and also decrease and increase respectively with the ionic strength. The energies of activation for the association and dissociation processes are in the range of −10 to −50 and 17 to 44 kcal/mol, respectively. The equilibrium for the formation of the triplexes {(d(Tg)4-T-azido)2·d(pA) x , x = 5−10)} is favored by several orders of magnitude when compared to the triplexes of DNA. The standard molar enthalpies for triplex formation have larger negative values at low ionic strength than at high ionic strength indicating that at lower μ values the formation of triplexes of d(Tg)4-T-azido with d(pA) x is more favored. The values of ΔH°(288) calculated from the activation parameters are between −30 and −60 kcal/(mol base) and the values of ΔG°(288) are between −8 and −13 kcal/(mol base) for short-strand DNA. There is a linear relationship in the enthalpy−entropy compensation for the triplex-melting thermodynamics.