We performed a molecular dynamics simulation to study the binding process between DNA and the third DNA binding region of HMG-I(Y) in explicit water. Starting from a configuration where the two biomolecules were positioned spatially apart to each other, they approached and bound to each other during the simulation. In this process, a solvent site-dipole field was formed in the inter-biomolecular zone, as if the field connects the biomolecules. This indicates that the directional motions of water molecules were restrained in the zone, and suggests that the solvent site-dipole field may mediate the molecular binding. (c) 2006 Elsevier B.V. All rights reserved.