Ab initio and DFT studies on nucleobase radicals of nucleotides

The nucleobase radicals are known for their role in producing nucleic acid strand break, and it is important to identify the radical formation at particular atomic site in the nucleobase centered radicals so that the major pathway for the nucleic acid damage may be trapped. Ab initio and DFT calculations of several nucleobase radicals formed at specific atomic site of nucleobases of a nucleotide segment have been performed. The radicals such as a type and 71 type formed at different atomic sites of adenosine, guanosine, thymidine and cytidine occur at different energy levels, and also the pi radicals are formed at lower energy level than the sigma radicals. Among the nucleobase radicals the C6 radical of thymidine is found to be the most stable as shown from the results of ROHF/6-31G** route. But the results obtained from DFT method do not show similar trend in energy values of ab initio calculations. Again the radical formation is monitored with respect to the location of radical center within Watson Crick (WC) and non Watson Crick (NWC) hydrogen bonding atomic sites of nucleobases. The nucleobase radicals formed at the atomic sites of non Watson Crick region are more stable than those of Watson Crick sites. The puckering of sugar and non-planarity of adenosine and guanosine nucleobases due to radical formation are found. The energies of forming the most stable radicals in nucleobases range from similar to-25 to -29 kcal/mol for ROHF/6-31G** route, whereas the energy values from DFT study range from -32 to -40 kcal/mol. (c) 2006 Elsevier B.V. All rights reserved.