Structure of aggregates of water and Li+, Na+, or K+ counterions with nucleic acid in solution

Abstract

The position and orientation of water molecules hydrating fragments of DNA in the B and Z conformations are analyzed with the help of computer simulations. Monte Carlo studies are carried out at room temperature, high relative humidity (500 water molecules per pitch) and in the presence of counterions such as Li+, Na+, and K+. Differences in hydration patterns and in the counterionic structures were found by compairing B-DNA with Z-DNA double helices and B-DNA helices with different base-pair distributions. The present extension of our similations to Z-DNA and to Li+ and K+ counterions permits some general conclusions concerning nucleic acids in solution.