Hyperstretching DNA

Koen Schakenraad,Iddo Heller,Erwin J G Peterman,Cornelis Storm,Paul Van Der Schoot,Brian Ten Bensel,Andreas S Biebricher,Maarten Sebregts,Gijs J L Wuite

doi:10.1038/s41467-017-02396-1

Abstract

The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely used in biophysical/chemical assays and drug treatments. We present single-molecule experiments and a three-state statistical mechanical model that provide a quantitative understanding of the interplay between B-DNA, overstretched DNA and intercalated DNA. The predictions of this model include a hitherto unconfirmed hyperstretched state, twice the length of B-DNA. Our force-fluorescence experiments confirm this hyperstretched state and reveal its sequence dependence. These results pin down the physical principles that govern DNA mechanics under the influence of tension and biochemical reactions. A predictive understanding of the possibilities and limitations of DNA extension can guide refined exploitation of DNA in, e.g., programmable soft materials and DNA origami applications.

Highlights

The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro
The interplay between DNA mechanics and structure is evident in stretching experiments[2,3]
While the bond lengths in the backbone of DNA permit a maximum extension of 0.7 nm per base pair, the native helical B-form of DNA has a length of only 0.34 nm per bp[4]

Summary

Introduction

The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. Dense stacking interactions of the aromatic systems of typical planar mono-intercalators such as YO-PRO-1 and Sytox Orange and bis-intercalators such as YOYO-1 and POPO with neighbouring base pairs result in an extension of DNA by 0.34 nm per intercalated moiety[12,13,14]. Because binding of such intercalators locally extends DNA by 100% to 0.68 nm per bp, intercalation is not commensurate with the natural local geometry of the dsDNA. We demonstrate that this is the case due to the combined effect of mechanical and mass action

Methods

Results

Conclusion