Twist–stretch coupling and phase transition during DNA supercoiling

Abstract

As a single DNA molecule is positively supercoiled under constant tension, its extension initially increases due to a negative twist-stretch coupling1, 2. The subsequent attainment of an extension maximum has previously been assumed to be indicative of the onset of a phase transition from B- to scP-DNA2. Here we show that an extension maximum in fact does not coincide with the onset of a phase transition. This transition is evidenced by a direct observation of a torque plateau using an angular optical trap. Instead we find that the shape of the extension curve can be well explained with a theory by John Marko3 that incorporates both DNA twist-stretch coupling and bending fluctuations. This theory also provides a more accurate method of determining the value of the twist-stretch coupling modulus, which has possibly been underestimated in previous studies that did not take into consideration the bending fluctuations2. Our study demonstrates the importance of torque detection in the correct identification of phase transitions as well as the contribution of the twist-stretch coupling and bending fluctuations to DNA extension.

Double-stranded RNA under force and torque: Similarities to and striking differences from double-stranded DNA

“…4 B and C), in good agreement with previous measurements (38)(39)(40)(41). Our measurements suggest that dsRNA has a positive twist-stretch coupling equal to D RNA = -S RNA ·(dΔL/dN) RNA /(2π·k B T) = +11.5 ± 3.3 (assuming S RNA = 350 pN; SI Appendix, Materials and Methods), in contrast to the negative twist-stretch coupling of dsDNA (38)(39)(40)(41), D DNA = -17 ± 5.…”

DNA supercoiling during transcription

“…Since its invention, the AOT has been successfully used to study transcription under DNA supercoiling, as well as torsional properties of various other biological systems (Forth et al. 2011; Forth et al 2008; Forth et al 2013; Ma et al 2013; Sheinin et al 2011; Sheinin et al 2013; Sheinin and Wang 2009). …”

“…(a) A schematic of an angular optical trap (AOT) setup (Forth et al 2011; Forth et al 2008; Forth et al 2013; Inman et al 2010; La Porta and Wang 2004; Ma et al 2013; Sheinin et al 2011; Sheinin et al 2013; Sheinin and Wang 2009). A DNA molecule is torsionally anchored at one end to the surface of a coverglass and at the other end to a nanofabricated quartz cylinder held in an optical trap of linear polarization.…”

“…Phase transitions between specific states of DNA are represented by solid black lines (Bryant et al 2003; Marko 2007; Sarkar et al 2001). Red points indicate torque values measured during phase transitions using an angular optical trap (Deufel et al 2007; Forth et al 2008; Sheinin et al 2011; Sheinin and Wang 2009). Adapted from (Forth et al 2013) with permission.…”

Torque Measurement at the Single-Molecule Level

“…Interestingly, C eff has been observed to increase with force and approach C at ~ 3 pN (65, 76); this behavior has been explained by taking into account the writhe fluctuations of the DNA molecule (75). While a harmonic approximation describes the torsional response of B-DNA rather well, sensitive experiments have detected nonzero coupling between twist and tension (39, 63, 99), leading to a more precise formulation of the torsional energy $E_{\text{twist}}=\frac{C{\theta }^2}{2L}+g\theta \frac{z}{L}$. Here, z is the DNA extension and g is the so called twist-stretch coupling.…”