Triple-helix formation of DNA oligomers with methylthiourea-linked nucleosides (DNmt): A kinetic and thermodynamic analysis

Complementary short-strand DNA homooligomers and methylthiourea-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)(10)–d(pA)(23)] and poly(dA) with the methylthiourea-linked nucleoside [5′-NH(3)(+)-d(Tmt)(4)-T-OH {DNmt(5)}]. Circular dichroism studies show evidence of triple-helical association dependent on the length of the target homooligomer. The melting and cooling curves exhibit hysteresis behavior in the temperature range of 10–95°C at 0.13 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)) were obtained. T(m) decreases with the ionic strength and increases with increase in length of the monomers. The rate constants k(on) and k(off) at a given temperature (288 K–310 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 −18 to −38 kcal/mol and 3 to 18 kcal/mol, respectively. The equilibrium constant for the formation of the triplexes [5′-NH(3)(+)-d(Tmt)(4)-T-OH)(2)⋅d(pA)(x), x = 10–23] is several orders of magnitude greater when compared with the triplexes of DNA. The number of base triplets in the nucleus of the DNmt(2)⋅DNA triple-helix (nucleation–zipping model) increases with decreased DNA oligomer length and with increased ionic strength. The values of ΔH° calculated from the activation parameters are between −30 and −50 kcal/(mol base) and the values of ΔG° are between −6 and −11 kcal/(mol base) for short-strand DNA.