INTRUSION OF COUNTERIONS INTO THE SPINE OF HYDRATION IN THE MINOR-GROOVE OF B-DNA - FRACTIONAL OCCUPANCY OF ELECTRONEGATIVE POCKETS

A sequence of ordered solvent peaks in the electron density map of the minor groove region of ApT-rich tracts of the double helix is a chara cteristic of B-form DNA well established from crystallography. This fe ature, termed the ''spine of hydration'', has been discussed as a stab ilizing feature of B-DNA, the structure of which is known to be sensit ive to environmental effects. Nanosecond-range molecular dynamics simu lations on the DNA duplex of sequence d(CGCGAATTCGCG) have been carrie d out, including explicit consideration of similar to 4000 water molec ules and 22 Na+ counterions, and based on the new AMBER 4.1 force fiel d with the particle mesh Ewald summation used in the treatment of long -range interactions. The calculations support a dynamical model of B-D NA closer to the B form than any previously reported. Analysis of the dynamical structure of the solvent revealed that, in over half of the trajectory, a Na+ ion is found in the minor groove localized at the Ap T step. This position, termed herein the ''ApT pocket'', was noted pre viously (Lavery, R.; Pullman, B. J. Biomol. Struct. Dyn. 1985, 5, 1021 ) to be of uniquely low negative electrostatic potential relative to o ther positions of the groove, a result supported by the location of a Na+ ion in the crystal structure of the dApU miniduplex [Seeman, N.; e t al J. Mol. Biol. 1976, 104, 109) and by additional calculations desc ribed herein based on continuum electrostatics. The Na+ ion in the ApT pocket interacts favorably with the thymine O2 atom on opposite stran ds of the duplex and is well articulated with the water molecules whic h constitute the remainder of the minor groove spine. This result indi cates that counterions may intrude on the minor groove spine of hydrat ion on B-form DNA and subsequently influence the environmental structu re and thermodynamics in a sequence-dependent manner. The observed nar rowing of the minor groove in the AATT region of the d(CGCGAATTCGCG) s tructure may be due to direct binding effects and also to indirect mod ulation of the electrostatic repulsions that occur when a counterion r esides in the minor groove ''AT pocket''. The idea of localized comple xation of otherwise mobile counterions in electronegative pockets in t he grooves of DNA helices introduces a heretofore mostly unappreciated source of sequence-dependent effects on local conformational, helicoi dal, and morphological structure and may have important implications i n understanding the functional energetics and specificity of the inter actions of DNA and RNA with regulatory proteins, pharmaceutical agents , and other ligands.