Theoretical method for full ab Initio calculation of DNA/RNA-ligand interaction energy

The molecular fractionation with conjugate caps (MFCC) for ab initio calculation of DNA/RNA-ligand interaction energy was analyzed. The dinucleotide dCG/water, trinucleotide dCGT/water and Watson-Crick paired DNA segment were also studied for calculating DNA/RNA-ligand interaction energy. Investigations show that the interaction energies calculated by MFCC method were in excellent agreement with the results obtained from ab initio calculations. The results suggested an extension of the applications of the MFCC method to ab initio calculations for DNA/RNA-ligand interaction energies.