Fidelity of binding of the guanidinium nucleic acid (DNG) d(Tg)(4)-T-azido with short strand DNA oligomers (A(5)G(3)A(5), GA(4)G(3)A(4)G, G(2)A(3)G(3)A(3)G(2), G(2)A(2)G(5)A(2)G(2)). A kinetic and thermodynamic study

Short strand DNA oligomers (A(5)G(3)A(5), GA(4)G(3)A(4)G, G(2)A(3)G(3)A(3)G(2), and G(2)A(2)G(5)A(2)G(2)) and the guanidinium (g) linked thymidyl nucleoside d(Tg)(T)-azido associate as triplexes, The melting temperatures, T-m, the association and dissociation kinetic and thermodynamic parameters and activation energies for the triplexes were determined by UV thermal analysis, The hypochromic shift and T-m for tripler formation increases with increase in concentration and decreases with the number of mismatches. The melting temperatures are between 35 and 55 degrees C in the range of ionic strength of 0.06-0.24 and decrease with increase in ionic strength at 100 deg/(ionic strength unit). The melting and cooling curves exhibit hysteresis behavior in the temperature range 5-95 degrees 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 second-order rate constants, k(on), for the tripler formation at 288 K are between 10 and 500 M-1 s(-1). Values of k(on) increase with the decrease in the ionic strength. The first order rate constants for the dissociation, k(off), at 288 K are between 10(-6) and 40 x 10(-6) s(-1) and increase with increase in ionic strength, The energies of activation for the association and dissociation processes are in the range -22 to -9 kcal/mol and 8 to 29 kcal/mol, respectively. At 6.3 x 10(-5) M/base and at the physiological ionic strength (0.15-0.30) and below, the tripler structures formed with d(Tg)(4)-T-azido and A(5)G(3)A(5) and GA(4)G(3)A(4)G have well-defined T-m values. The melting curves with G(2)A(3)G(3)A(3)G(2) and G(2)A(2)G(5)A(2)G(2) are very shallow with small hypochromic shifts denoting negligible binding at physiological ionic strength. Therefore, with the increase in the G content (mismatched base pairs) at a certain concentration (e.g., 6.3 x 10(-5) M/base), discrimination (change in fidelity) occurs in the formation and strength of binding of d(Tg)(4)-T-azido to d(pA(n)pG(m)) oligomers. The standard molar enthalpies for tripler formation have in general larger negative values at low ionic strength than al high ionic strength, indicating that at lower mu values the formation of triplexes of d(Tg)(4)-T-azido with d(pA(n)pG(m)) are more favorable. The values of Delta H degrees(288) calculated from the activation parameters are between -17 and -49 kcal/mol, and the values of Delta G degrees(288) are between -7.5 and -11.8 kcal/mol for A(5)G(3)A(5), GA(4)G(3)A(4)G, G(2)A(3)G(3)A(3)G(2), and G(2)A(2)G(5)A(2)G(2), respectively. There is a linear relationship in the enthalpy-entropy compensation for the tripler melting thermodynamics.