Sugar-Pucker Force-Induced Transition in Single-Stranded~DNA

TL;DR

This study uses optical tweezers to measure the elastic properties of ssDNA across a wide length range, revealing a force-induced sugar pucker transition that affects its elasticity.

Contribution

It provides experimental evidence of a force-induced conformational transition in ssDNA and clarifies how ssDNA elasticity varies with molecule length and force regime.

Findings

Persistence length nearly doubles for shorter ssDNA.

Two distinct elastic regimes at low and high forces.

Force induces a sugar pucker conformational transition.

Abstract

The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples range from DNA hybridization, DNA ligand binding, DNA unwinding by helicases, etc. To date, ssDNA elasticity has been studied with different methods in molecules of varying sequence and contour length. A dispersion of results has been reported and the value of the persistence length has been found to be larger for shorter ssDNA molecules. We carried out pulling experiments with optical tweezers to characterize the elastic response of ssDNA over three orders of magnitude in length (60-14 k bases). By fitting the force-extension curves (FECs) to the Worm-Like Chain model we confirmed the above trend:the persistence length nearly doubles for the shortest molecule (60 b) with respect to the longest one (14 kb). We demonstrate that the observed trend is due to the different force regimes fitted for long and short molecules, which translates into two distinct elastic regimes at low and high forces. We interpret this behavior in terms of a force-induced sugar pucker conformational transition (C3'-endo to C2'-endo) upon pulling ssDNA.