Mechanism of RNA Double Helix-Propagation at Atomic Resolution

Abstract

The conversion of a nucleic acid from single strands to double strands is thought to involve slow nucleation followed by fast double-strand propagation. Here, for RNA double-strand propagation, we propose an atomic resolution reaction mechanism. This mechanism, called the stack-ratchet, is based on data-mining of three-dimensional structures and on available thermodynamic information. The stack-ratchet mechanism extends and adds detail to the classic zipper model proposed by Porschke (Porschke, D. Biophysical Chemistry 1974, 2, pp. 97-101). Porschke's zipper model describes the addition of a base pair to a nucleated helix in terms of a single type of elementary reaction; a concerted process in which the two bases, one from each strand, participate in the transition state. In the stack-ratchet mechanism proposed here a net base-pairing step consists of two elementary reactions. Motions of only one strand are required to achieve a given transition state. One elementary reaction preorganizes and stacks the 3' single-strand, driven by base--base stacking interactions. A second elementary reaction stacks the 5' strand and pairs it with the preorganized 3' strand. In the stack-ratchet mechanism, a variable length 3' stack leads the single-strand/double-strand junction. The stack-ratchet mechanism is not a two-state process. A base can be (i) unstacked and unpaired, (ii) stacked and paired, or (ii) stacked and unpaired (only on the 3' strand). The data suggests that helices of DNA and of RNA do not propagate by similar mechanisms.

RNA Unwinding from Reweighted Pulling Simulations

“…43 In particular, we found the most stable 3´-dangling end in construct 1 ( 5´-C G.. 3´-GC.. ), which has also been counted as the most common dangling end pattern in rRNA crystal structures. 16 Further agreement can be found considering dsRNA optical melting experiments which have shown that single-nucleotides overhanging at 3´-ends of an RNA helix increase the stability of the duplex in a sequence-dependent manner. Notably, such a stabilization has been interpreted as the capability of the 3´dangling ends to stack over the hydrogen bonds of the closing base pair protecting them from water exchange.…”

“…16 Our computations link experimental data from different fields creating a common reading frame among them. Taken together, these results suggest that RNA unwinding occurs by a stepwise process in which the probability of unbinding of the base on the 5´strand is significantly higher than that on the 3´strand.…”

Mechanisms of StpA-mediated RNA remodeling

“…52 The formation of the final duplex evolving from the transition state is assumed to be very fast. [63][64][65] The annealing rate constants of complementary RNAs are very small and in the conformationally-controlled RNA annealing. So far, three different, but not necessarily mutually exclusive, mechanisms for the acceleration of complementary RNA annealing have been proposed: (a) the active attraction of RNA molecules to increase the encounter frequency between them, (b) stabilization of the annealing transition state by shielding the negative RNA backbone charges (often referred to as 'matchmaker activity') and (c) 'conversion' of the RNA into an annealing-prone conformation.…”

Base-pair Ambiguity and the Kinetics of RNA Folding

“…One way to look at this is that larger numbers of partial matches for a given sequence in or around a stem would likely interfere with the nucleation of the native stem structure, and nucleation appears to be a critical and perhaps even rate-limiting step. Indeed, the experimental literature [30][31][32][33] has long suggested that stem formation in RNA molecules is a two-step process. When forming a stem, there is usually a slow nucleation step, resulting in a few consecutive base pairs at a nucleation point, followed by a fast zipping step.…”