Origin of Overstretching Transitions in Single-Stranded Nucleic Acids

Zackary N. Scholl, Mahir Rabbi, David Lee, Laura Manson, Hanna S-Gracz, and Piotr E. Marszalek

Phys. Rev. Lett. 111, 188302 – Published 31 October 2013

Abstract

We combined single-molecule force spectroscopy with nuclear magnetic resonance measurements and molecular mechanics simulations to examine overstretching transitions in single-stranded nucleic acids. In single-stranded DNA and single-stranded RNA there is a low-force transition that involves unwinding of the helical structure, along with base unstacking. We determined that the high-force transition that occurs in polydeoxyadenylic acid single-stranded DNA is caused by the cooperative forced flipping of the dihedral angle formed between four atoms, O5’-C5’-C4’-C3’ ( $γ$ torsion), in the nucleic acid backbone within the canonical $B$ -type helix. The $γ$ torsion also flips under force in $A$ -type helices, where the helix is shorter and wider as compared to the $B$ -type helix, but this transition is less cooperative than in the $B$ type and does not generate a high-force plateau in the force spectrums of $A$ -type helices. We find that a similar high-force transition can be induced in polyadenylic acid single-stranded RNA by urea, presumably due to disrupting the intramolecular hydrogen bonding in the backbone. We hypothesize that a pronounced high-force transition observed for $B$ -type helices of double stranded DNA also involves a cooperative flip of the $γ$ torsion. These observations suggest new fundamental relationships between the canonical structures of single-and double-stranded DNA and the mechanism of their molecular elasticity.

Received 19 July 2011

DOI:https://doi.org/10.1103/PhysRevLett.111.188302

Authors & Affiliations

Zackary N. Scholl¹, Mahir Rabbi², David Lee², Laura Manson², Hanna S-Gracz³, and Piotr E. Marszalek^2,*

¹Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA
²Department of Mechanical Engineering and Materials Science, Center for Biologically Inspired Materials and Material Systems, Duke University, Durham, North Carolina 27708, USA
³Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27708, USA

^*Corresponding author. pemar@duke.edu

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Vol. 111, Iss. 18 — 1 November 2013

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Images

Figure 1
Force spectra of poly(A) (red) and poly(dA) (blue). Superimposed force extensions of poly(A) and poly(dA) normalized to the highest force. Poly(A) force spectrum exhibits a force plateau of $19.7 \pm 3.9 pN$ ( $mean \pm s . d .$ , $n = 95$ experiments on 27 molecules) followed by a quasilinear force region to $\sim 200 pN$ . Poly(dA) force spectrum exhibits two force plateaus of $21.7 \pm 5.0 pN$ and $125.3 \pm 25.1 pN$ ( $mean \pm s . d .$ , $n = 70$ experiments on 23 molecules).Reuse & Permissions
Figure 2
Force spectra of different single-stranded nucleic acids. (a) Superimposed normalized force spectra of poly(C) (magenta) and poly(A) (red). Poly(C) force spectrum exhibits a force plateau of $24.3 \pm 4.4 pN$ ( $mean \pm s . d .$ , 53 force curves on 14 molecules). (b) Superimposed normalized force spectra of poly(dT) (gray) and poly(dC) (pink). Both behave as unstructured, freely jointed, polymers.Reuse & Permissions
Figure 3
The effect of 1M urea on poly(A) elasticity. Superimposed normalized force spectra of poly(dA) with 1M urea and poly(A) with 1M urea. $Poly (A) + 1 M$ urea has two force plateaus of $19.9 \pm 4.0 pN$ and $69.6 \pm 7.3 pN$ ( $mean \pm s . d .$ , $n = 65$ experiments on 6 different molecules). The low-force plateau occurs at an identical force as the low-force plateau in poly(A) without urea (see Supplemental Material, Fig. 11 [7]). Poly(dA) with 1M urea does not show any significant difference from poly(dA) without urea (see Supplemental Material, Fig. 12 [7]).Reuse & Permissions
Figure 4
Results of molecular mechanic simulations of poly(A) and poly(dA) 12mers. Poly(A) starting configurations were from the $A$ -type single-stranded RNA helix and poly(dA) starting configurations were from the $B$ -type single-stranded DNA helix. (a) Changes in the $γ$ torsion during the extension of nucleic acids which shows an abrupt change from cis to trans conformation. (b) Kernel density estimated probability density function (PDF) for the extension at which a $γ$ torsion flips to trans conformation.Reuse & Permissions
Figure 5
The atomic representation of the flipping of a $γ$ torsion in poly(A) [similar for poly(dA)]. (a) Shows the locations of the torsion angles in the nucleic acid backbone labeled by Greek letters. Relevant atoms are also labeled. (b) Shows a representative snapshot of the $γ$ torsion (gray highlight) before (left) and after flipping (right) and the consequential increase in the phosphate distances for poly(A) [averaged from trajectories, similar for poly(dA)], as described in main text.Reuse & Permissions

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