Structures and stabilities of sugar radical nucleotides

Abstract

The structures and energies of forming C1′, C2′, C3′ and C4′ radicals in sugar, and C5′ radical in various nucleotides have been studied by ab initio and DFT methods. Among these radicals, the radical at C1 position of sugar forms at lower energy level, and the efficiency of generating this radical will be more than other radicals. The puckering of sugar in 2-deoxy adenosine 5-monophosphate and 2-deoxy thymidine 5-monophosphate after radical formation at C1 is significant, herein C2 endo is observed in C1′ sugar radical compared to the C3 endo structure in its non-radical counterpart. In the case of 2-deoxy guanosine 5-monophosphate and 2-deoxy cystidine 5-monophosphate, C2 endo structures in sugar are found and distinct flattening of C3 center occurs after radical formation. There are intramolecular hydrogen bonds in the non-radical and radical structures of 2-deoxy guanosine 5-monophosphate and 2-deoxy adenosine 5-monophosphate nucleotides. In addition, significant variation of puckering amplitudes and phase angles between non-radical and C1′ sugar radical are also found.