Conformation and flexibility of the 3'-end of trna

Abstract

A close examination of the crystal structure of tRNA^Phe proposed by various groups reveals a great deal of discrepancy in the secondary structure of its acceptor end. The technique of energy minimization has been employed to study the preferred conformations and the flexibility of the pCpCpA fragment. Starting from various structures proposed for the -C-C-A end in tRNA^Phe, the energy has been minimized as a function of 17 dihedral angles. A conformation where the terminal adenine is not stacked over the other two bases is found to be the most preferred conformation. This geometry is close to the refined structure proposed by the DUK group. Our results suggest a high degree of flexibility for the terminal adenosine unit in the -C-C-A segment. These findings are compared with the structure of -C-C-A in solution, as observed by nuclear magnetic resonance.