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 in vivo. 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 Caenorhabditis elegans 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.

SerraNA: a program to determine nucleic acids elasticity from simulation data

“…6), so local bends can couple for building up a significant curvature. Our results are in the same line of others that highlighted the importance of periodicity 32,72,73 for understanding the special mechanical properties of A-tracts 19 or nucleosome-positioning sequences. [74][75][76] Protein-DNA and sequence mismatch SerraNA has the capacity to deal with perturbed DNA molecules caused by a series of factors like sequence mismatch or protein binding.…”

“…16,17 In addition, it has been very difficult to identify the mechanisms through which some short sequence motifs, like A-tracts, originate extraordinary bending. 18,19 On these matters, molecular dynamics (MD) simulations at atomic resolution have become an impressive source of new important information, 20 that have provided (i) systematic analysis at the dinucleotide level, 21,22 (ii) an evaluation of the influence of nearest flanking base-pairs (bp) up to the tetranucleotide level 23,24 and, among others, (iii) an explanation of contradictory stiffness data on A-tracts. 25 On a more coarse-grained level, Monte Carlo (MC) simulations have found that most of sequence-dependence variability is originated at the level of static curvature.…”

Double-stranded RNA bending by AU-tract sequences

“…Consistent with the presence of intrinsic bending, our AU-tracts also presented significant deviations from the WLC in the data. Moreover, the shape of the plot for the phased AU-tract studied here is remarkably similar to an intrinsically-bent A-tract dsDNA that we recently reported (24). Finally, we checked whether the AU-tracts caused anomalous migration of dsRNA in agarose gels, as occurs for A-tracts in dsDNA molecules.…”

“…Further analysis of our data in terms of the cosines of the tangents provided a more stringent test to the WLC model (24) (39). For the control molecule, the cosines of the tangents reasonably fitted to the WLC model (Eq.…”

“…In contrast to dsRNA, sequence-induced bending in the canonical DNA double-helix (dsDNA) is wellcharacterized. A prime example of such sequence-dependent deformations are the so-called A-tracts, runs of adenines and thymines without a TA step that, when in phase with the helical pitch yield a significant global curvature of the dsDNA (18) (19) (20) (21) (22) (23) (24). Besides their bending character, A-tracts show a peculiar conformation at the molecular level, with a characteristic narrow minor groove (25).…”