Rohit Bavi, A. D. Kamble, Navanath M. Kumbhar
Jul 7, 2011
Citations
1
Influential Citations
18
Citations
Journal
Cell Biochemistry and Biophysics
Abstract
Conformational preferences of the modified nucleosides N2-methylguanosine (m2G) and N2, N2-dimethylguanosine (m22G) have been studied theoretically by using quantum chemical perturbative configuration interaction with localized orbitals (PCILO) method. Automated complete geometry optimization using semiempirical quantum chemical RM1, along with ab initio molecular orbital Hartree–Fock (HF-SCF), and density functional theory (DFT) calculations has also been made to compare the salient features. Single-point energy calculation studies have been made on various models of m2G26:C/A/U44 and m22G26:C/A/U44. The glycosyl torsion angle prefers “syn” (χ = 286°) conformation for m2G and m22G molecules. These conformations are stabilized by N(3)–HC2′ and N(3)–HC3′ by replacing weak interaction between O5′–HC(8). The N2-methyl substituent of (m2G26) prefers “proximal” or s-trans conformation. It may also prefer “distal” or s-cis conformation that allows base pairing with A/U44 instead of C at the hinge region. Thus, N2-methyl group of m2G may have energetically two stable s-trans m2G:C/A/U or s-cis m2G:A/U rotamers. This could be because of free rotations around C–N bond. Similarly, N2, N2-dimethyl substituent of (m22G) prefers “distal” conformation that may allow base pairing with A/U instead of C at 44th position. Such orientations of m2G and m22G could play an important role in base-stacking interactions at the hinge region of tRNA during protein biosynthesis process.