Structural transitions and elasticity from torque measurements on DNA

Abstract

Knowledge of the elastic properties of DNA is required to understand the structural dynamics of cellular processes such as replication and transcription. Measurements of force and extension on single molecules of DNA have allowed direct determination of the molecule's mechanical properties, provided rigorous tests of theories of polymer elasticity, revealed unforeseen structural transitions induced by mechanical stresses, and established an experimental and conceptual framework for mechanical assays of enzymes that act on DNA. However, a complete description of DNA mechanics must also consider the effects of torque, a quantity that has hitherto not been directly measured in micromanipulation experiments. We have measured torque as a function of twist for stretched DNA--torsional strain in over- or underwound molecules was used to power the rotation of submicrometre beads serving as calibrated loads. Here we report tests of the linearity of DNA's twist elasticity, direct measurements of the torsional modulus (finding a value approximately 40% higher than generally accepted), characterization of torque-induced structural transitions, and the establishment of a framework for future assays of torque and twist generation by DNA-dependent enzymes. We also show that cooperative structural transitions in DNA can be exploited to construct constant-torque wind-up motors and force-torque converters.

Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation

“…In this work, we take the twist persistence length to be 70 nm, which agrees with experimental measurements based on topoisomer distributions generated by ligation (44), but is slightly smaller than the value of z100 nm measured in single-molecule mechanics studies (24). The second form of Eq.…”

“…Although supercoiled DNA has been extensively studied theoretically (10)(11)(12)(13)(14)(15)(16)(17)(18) as well as experimentally (19)(20)(21)(22)(23)(24)(25)(26), both simulation and experimental studies that directly investigate the large-scale organization of supercoiled DNA are typically limited to supercoiling densities up to the average supercoiling density in E. coli (s~À0.06). However, the topological state of the bacterial chromosome is highly dynamic (27), and both DNA gyrase and RNA polymerase are capable of generating negative supercoiling densities far in excess of average supercoiling levels (28)(29)(30).…”

“…Furthermore, although complementary experimental single-molecule mechanics studies have reported the behavior of underwound DNA over a broad range of linking deficits (24,26,(39)(40)(41), experimental data at degrees of underwinding with s < À0.07 have been restricted to sufficiently large extensional forces where supercoiled plectoneme formation is suppressed. At lower tensions (<0.4 pN), where plectoneme formation is favored, the experimental phase diagram of supercoiled DNA cannot be extracted from the extension versus winding behavior for s < À0.07 (40).…”

Mechanisms of DNA binding determined in optical tweezers experiments

“…Though the bead is usually free to unwind, some magnetic and optical tweezers experiments have constrained the bead to examine the effect of applied torques upon the double helix. [14][15][16] Additionally, transient decreases in the force at these low to mid force extensions have been observed in constructs displaying secondary structure common to RNA hairpins and DNA loops. 9,17,18 At $65 pN, an abrupt transition occurs, as the DNA may be extended to nearly double its length without a strong increase in force.…”

Anomalous Conductance Response of DNA Wires under Stretching

“…is the stretch modulus [13][14][15][16] and nm pN 100 200 ⋅ ± = g is the stretch-twist coupling. 15,[17][18][19][20][21] The stretching distance is…”