Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes

Abstract

A-tracts are A:T rich DNA sequences that exhibit unique structural and mechanical properties associated with several functions i n v i vo . The crystallographic structure of A-tracts has been well characterized. However, the mechanical properties of these sequences is controversial and their response to force remains unexplored. Here, we rationalize the mechanical properties of in-phase A-tracts present in the C a e n o r h a b d i t i s e l e g a n s genome over a wide range of external forces, using single-molecule experiments and theoretical polymer models. Atomic Force Microscopy imaging shows that A-tracts induce long-range (∼200 nm) bending, which originates from an intrinsically bent structure rather than from larger bending flexibility. These data are well described with a theoretical model based on the worm-like chain model that includes intrinsic bending. Magnetic tweezers experiments show that the mechanical response of A-tracts and arbitrary DNA sequences have a similar dependence with monovalent salt supporting that the observed A-tract bend is intrinsic to the sequence. Optical tweezers experiments reveal a high stretch modulus of the A-tract sequences in the enthalpic regime. Our work rationalizes the complex multiscale flexibility of A-tracts, providing a physical basis for the versatile character of these sequences inside the cell.The authors acknowledge the computer resources, technical expertise and assistance provided by the Red Española de Supercomputacion at the Minotauro Supercomputer (BSC, Barcelona). We thank Andrew Fire (Stanford University, USA) and Ralf Seidel (University of Leipzig, Germany) for providing us biological material required for the fabrication of the DNA molecules.Peer reviewe