Simulation of DNA Bases in Water: Comparison of the Monte Carlo Algorithm with Molecular Mechanics Force Fields

---

M. Monajjemi^1*, S. Ketabi², M. Hashemian Zadeh³, and A. Amiri⁴

¹Department of Chemistry, Science and Research Campus, Islamic Azad University, P.O. Box 14155-775, Tehran, Iran; E-mail: m_monajjemi@yahoo.com

²Department of Chemistry, Central Tehran Campus (East Tehran-Ghiam Dasht), Islamic Azad University, Tehran, Iran

³Department of Chemistry, University of Science and Technology of Iran, Tehran, Iran

⁴Department of Chemistry, Central Tehran Campus, Islamic Azad University, Tehran, Iran

^* To whom correspondence should be addressed.

Received September 1, 2004

---

The interaction between the nucleic acid bases and solvent molecules has an important effect in various biochemical processes. We have calculated total energy and free energy of the solvation of DNA bases in water by Monte Carlo simulation. Adenine, guanine, cytosine, and thymine were first optimized in the gas phase and then placed in a cubic box of water. We have used the TIP3 model for water and OPLS for the nucleic acid bases. The canonical (T, V, N) ensemble at 25°C and Metropolis sampling technique have been used. Good agreement with other available computational data was obtained. Radial distribution functions of water around each site of adenine, guanine, cytosine, and thymine have been computed and the results have shown the ability of the sites for hydrogen bonding and other interactions. The computations have shown that guanine has the highest value of solvation free energy and N7 and N6 in adenine and guanine, N3 in cytosine, and N3 and O4 in thymine have the largest radial distribution function. Monte Carlo simulation has also been performed using the CHARMM program under the same conditions, and the results of two procedures are compared.

---

KEY WORDS: Monte Carlo simulation, radial distribution function, force field, hydration, adenine, guanine, cytosine, thymine

DOI: 10.1134/S0006297906130013

---