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Cell Biochemistry and Biophysics

, Volume 61, Issue 3, pp 507–521 | Cite as

Conformational Preferences of Modified Nucleoside N2-methylguanosine (m2G) and Its Derivative N2, N2-dimethylguanosine (m 2 2 G) Occur at 26th Position (Hinge Region) in tRNA

  • Rohit S. Bavi
  • Asmita D. Kamble
  • Navanath M. Kumbhar
  • Bajarang V. Kumbhar
  • Kailas D. Sonawane
Original Paper

Abstract

Conformational preferences of the modified nucleosides N2-methylguanosine (m2G) and N2, N2-dimethylguanosine (m 2 2 G) 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 m 2 2 G26:C/A/U44. The glycosyl torsion angle prefers “syn” (χ = 286°) conformation for m2G and m 2 2 G 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 (m 2 2 G) prefers “distal” conformation that may allow base pairing with A/U instead of C at 44th position. Such orientations of m2G and m 2 2 G could play an important role in base-stacking interactions at the hinge region of tRNA during protein biosynthesis process.

Keywords

Transfer RNA Modified nucleosides m2m22PCILO 

Supplementary material

12013_2011_9233_MOESM1_ESM.doc (84 kb)
Supplementary material 1 (DOC 84 kb)

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Rohit S. Bavi
    • 1
  • Asmita D. Kamble
    • 1
  • Navanath M. Kumbhar
    • 2
  • Bajarang V. Kumbhar
    • 1
  • Kailas D. Sonawane
    • 1
    • 3
  1. 1.Department of BiochemistryShivaji UniversityKolhapurIndia
  2. 2.Department of BiotechnologyShivaji UniversityKolhapurIndia
  3. 3.Department of MicrobiologyShivaji UniversityKolhapurIndia

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