Book of Abstracts: Albany 2011
June 14-18 2011
©Adenine Press (2010)
A-minor I vs A-minor 0 tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis
The second tertiary contact in RNA kink-turns is represented by A-minor interaction between adenine of the second A•G base pair in the NC-stem and the first canonical base pair of the C-stem. Known kink-turn structures possess either A-minor I (A-I) or A-minor 0 (A-0) interaction (Figure). Bioinformatics data show that kink-turns with A-I in the available X-ray structures keep primarily G=C pair in the first C-stem position during evolution while the inverted base pair (C=G) is basically not realized. In contrast, kink-turns with A-0 in the observed structures alternate G=C and C=G base pairs in sequences. Molecular dynamics simulations of X-ray structures of kink-turns reveal that the A-I interaction with G=C base pair (A-I/G=C triple) is stable while inversion of the canonical base pair (A-I/C=G) leads either to kink-turn disruption or rearrangement to A-0/C=G (1). The A-0/G=C initial configuration tends to transform to the A-I/G=C arrangement. Finally, simulations testing the A-0/C=G arrangement lead either to disruption of the structure (after unsuccessful transition to the A-I configuration) or are stable. Thus, the A-I/G=C arrangement appears to be intrinsically preferred by kink-turns while formation of the A-0 interaction is likely related to the context. In addition, as shown for ribosomal Kink-turn 15, A-0 may be supported by additional interactions that do not belong to the kink-turn signature interactions. Quantum-chemical calculations explain how a delicate balance of various intermolecular interactions plays a decisive role in determining the dynamic behavior and stability of the various A-minor patterns in kink-turns.
Figure: Tertiary interactions (A-0 and A-I) stabilizing kink-turn structures.