MODELING DNA IN AQUEOUS-SOLUTIONS

A surge in theoretical and computer simulation studies on DNA has been witnessed during the last few years. These are focused on addressing problems concerning the molecular basis of conformational transitions of DNA, base sequence specific structural modulations (fine structure) of DNA and structural and thermodynamic aspects of recognition in pro tein-DNA and drug-DNA systems. Computer modelling of DNA is now becomi ng increasingly popular in the research and developmental activity in pharmaceutical industry. Several models of DNA have been put forth to describe DNA. These range from very simple descriptions, such as a lin e of charge, uniformly charged cylinder, to more complex models of DNA , with water and supporting electrolyte considered explicitly at an at omic level. The techniques employed include the more common molecular mechanics and quantum and statistical mechanical methods. This article presents the progress attained via the diverse theoretical and comput er simulation studies on DNA with a special emphasis on the methodolog ical issues involved in modelling DNA in aqueous solutions.