Poor hydration enhances the activation energy of the exchange rate of the base-paired imino protons with water at the core part of the DNA duplex

Abstract

Here we report the exchange rates (k e x) of imino protons of d[ 5′p(T 1G 2T 3T 4T 5G 6G 7C 8) 3′]:d[ 3∼'(A 15C 14A 13A 12A 11C 10C 9)p 5′ ] (duplex I) with water at different pH and temperature to give the life-times ( τ o ) of the closed state of the base-pairs. The τ o of the closed state of the base-pairs is uniform (E a ≈ 25 ± 5 kcal/mol) in the duplex I, and varies between 0.2 – 4 ms. A plot of the natural log of various exchange rates of the imino protons of the base-pair of the duplex I within the pH range of 6.1 to 8.6 as a function of the inverse of temperature gave the activation energy (E a) of the exchange process of imino protons with the bound water (hydration). It has been found that although τ o are in the same range but the E a of the exchange processes of the open state of imino protons with the bound water are very different, and they are strongly dependent upon the location of the nucleotide residues along the DNA duplex: 22.3±3.3 kcal/mol for the core base-pair T 4-A 12, 16.2±2.4 kcal/mol for the base-pair T 5-A 11, 10.5±1.6 kcal/mol for the base-pair T 3-A 13. 12.3±1.8 kcal/mol for the base-pair G 6-C 10 and 2.4±0.4 kcal/mol for the base-pair G 2-C 14. The comparison of the activation energies of the exchange process of imino protons and water with that of the water abundance in the first spine of hydration between fully-matched duplex I and the analogous G 7-A 9 mismatched duplex II, (d[ 5′p(T 1G 2T 3T 4T 5G 6G 7C 8) 3′]: d[ 3′(A 15C 14A 13A 12A 11C 10A 9)p 5′], determined by a combination of NOESY and ROESY experiments, suggests for the first time that the relative exchange of imino protons of the base-pairs in the DNA duplex is more rapid when there is an abundance of water at the first spine of hydration. This result also showed unambiguously that the core of the DNA is by and large devoid of water and the energy penalty of water entering the core is very high. This is consistent with our earlier work which showed that as the water activity in the minor and major groove of DNA increases, the T m decreases (ref. 1), suggesting the water poisoning as the principal factor for base-pair mismatch, frame-shift and mutation in our DNA replication machinery.