Abstract
Single-molecule tweezers measurements of double-stranded nucleic acids (dsDNA and dsRNA) provide unprecedented opportunities to dissect how these fundamental molecules respond to forces and torques analogous to those applied by topoisomerases, viral capsids, and other biological partners. However, tweezers data are still most commonly interpreted post facto in the framework of simple analytical models. Testing falsifiable predictions of state-of-the-art nucleic acid models would be more illuminating but has not been performed. Here we describe a blind challenge in which numerical predictions of nucleic acid mechanical properties were compared to experimental data obtained recently for dsRNA under applied force and torque. The predictions were enabled by the HelixMC package, first presented in this paper. HelixMC advances crystallography-derived base-pair level models (BPLMs) to simulate kilobase-length dsDNAs and dsRNAs under external forces and torques, including their global linking numbers. These calculations recovered the experimental bending persistence length of dsRNA within the error of the simulations and accurately predicted that dsRNA's “spring-like” conformation would give a two-fold decrease of stretch modulus relative to dsDNA. Further blind predictions of helix torsional properties, however, exposed inaccuracies in current BPLM theory, including three-fold discrepancies in torsional persistence length at the high force limit and the incorrect sign of dsRNA link-extension (twist-stretch) coupling. Beyond these experiments, HelixMC predicted that ‘nucleosome-excluding’ poly(A)/poly(T) is at least two-fold stiffer than random-sequence dsDNA in bending, stretching, and torsional behaviors; Z-DNA to be at least three-fold stiffer than random-sequence dsDNA, with a near-zero link-extension coupling; and non-negligible effects from base pair step correlations. We propose that experimentally testing these predictions should be powerful next steps for understanding the flexibility of dsDNA and dsRNA in sequence contexts and under mechanical stresses relevant to their biology.
Highlights
Nucleic acids play central roles in biological processes including transcription, translation, catalysis and regulation of gene expression [1,2]
We present the first such blind challenge, involving recent dsRNA tweezers data that were kept hidden from modelers and a new HelixMC toolkit that resolves challenges in simulating long double helices from basepair level models
HelixMC predicted that poly(A)/poly(T) and Z-DNA–biologically important variants whose elastic responses have not been studied with tweezers–will have distinct mechanical properties
Summary
Nucleic acids play central roles in biological processes including transcription, translation, catalysis and regulation of gene expression [1,2]. High precision experimental data are becoming increasingly available from measurements using optical and magnetic tweezers [8,9,10,11,12,13,14,15,16,17,18,19,20] that measure end-toend lengths and linking numbers of kilobase-length single molecules upon variation of solution condition, sequence, applied force and torque In principle, these data offer rigorous challenges that can falsify or validate – and thereby advance – models of nucleic acid flexibility. Such direct comparison of model predictions and experimental observables remains incomplete
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