A CA( ) Pair Adjacent to a Sheared GA or AA Pair Stabilizes Size-Symmetric RNA Internal Loops

作者：Chen Gang; Kennedy Scott D; Turner Douglas H^*

来源：Biochemistry, 2009, 48(24): 5738-5752.

DOI：10.1021/bi8019405

RNA internal loops are often important sites for folding and function. Residues in internal loops can have pK(a) values shifted close to neutral pH because of the local structural environment. A series of RNA internal loops were studied at different pH by UV absorbance versus temperature melting experiments and imino proton nuclear magnetic resonance (NMR). A stabilizing CA pair forms at pH 7 in the CG/AA and CA/AA nearest neighbors when the CA pair is the first noncanonical pair (loop-terminal pair) in 3 x 3 nucleotide and larger size-symmetric internal loops. These CG/AA and CA/AA nearest neighbors, with CA adjacent to a closing Watson-Crick pair, are further stabilized when the pH is lowered from 7 to 5.5. The results are consistent with a significantly larger fraction (from similar to 20% at pH 7 to similar to 90% at pH 5.5) of adenines being protonated at the N1 position to form stabilizing wobble CA(+) pairs adjacent to a sheared GA or AA pair. The noncanonical pair adjacent to the GA pair in CG/AA can either stabilize or destabilize the loop, consistent with the sequence-dependent thermodynamics of GA pairs. No significant pH-dependent stabilization is found for most of the other nearest neighbor combinations involving CA pairs (e.g., CA/AG and AG/CA), which is consistent with the formation of various nonwobble pairs observed in different local sequence contexts in crystal and NMR structures. A revised free-energy model, including stabilization by wobble CA(+) pairs, is derived for predicting stabilities of medium-size RNA internal loops.

• 出版日期2009-6-23