Critical Torque for Kink Formation in Double-Stranded DNA

Abstract

We measure the bending energy of double-stranded DNA in the nonlinear (sharply bent) regime. The measurements are obtained from the melting curves of stressed DNA ring molecules. The nonlinear elastic behavior is captured by a single parameter: the critical torque c at which the molecule develops a kink. In this regime, the elastic energy is linear in the kink angle. This phenomenology is the same as for the previously reported case of nicked DNA. For the sequences examined, we find c ¼ 31 pN Â nm. This critical torque corresponds to a characteristic energy scale ð =2Þ c ¼ 12 kT room relevant for molecular biology processes associated with DNA bending.

Phase diagram of the ground states of DNA condensates

“…The model provides a simple explanation for the results of prior experimental and computational studies and makes predictions for the specific geometries of the ground states. The results underscore the impact of the form of the microscopic bending energy at macroscopic observable scales.The non-linear elasticity of DNA at short length scales, probed by non-equilibrium DNA cyclization experiments [1,2], AFM imaging on surfaces [3], as well as by equilibrium mechanically constrained DNA experiments [4][5][6], is still not well understood. While the conclusions regarding the first two methods for probing non-linear ds-DNA elasticity have been criticized [7], the experiments on stressed DNA ring molecules are performed by a different methodology based on thermodynamic methods via DNA high-curvature states through partial hybridization of a ss-DNA loop with a linear complementary strand [6].…”

“…While the conclusions regarding the first two methods for probing non-linear ds-DNA elasticity have been criticized [7], the experiments on stressed DNA ring molecules are performed by a different methodology based on thermodynamic methods via DNA high-curvature states through partial hybridization of a ss-DNA loop with a linear complementary strand [6]. This methodology does not depend on thermal fluctuations to realize high-curvature states and thus appears to have a far better accuracy and reliability.…”

EcoRV catalysis with a pre-bent substrate

“…2(a) as a flexible rod with bending modulus B = 200 pN × nm 2 (the so called worm-like-chain or WLC approach) which develops a (constant torque) kink at a critical value of the internal bending torque τ c ≈ 30 pN × nm. 18,22 It is straightforward to obtain, from the equations in Ref. 18, the elastic energy, the kink angle, and the other parameters of the DNA constructs for different values of N d and N s .…”

“…The DNA substrate was prepared by hybridizing two complementary linear strands of DNA of different lengths, in the molar ratio 1:1. 18,[22][23][24][25] There is therefore a nick, positioned at the center of the ds part of the molecule. The recognition sequence of EcoRV, 5-GATATC-3, was positioned at the nick of the constrained DNA molecules such that the center TA-sequence resides at the apex of the nick.…”

“…1) comprises the restriction enzyme EcoRV, which cuts ds DNA at a specific site defined by the base sequence 5' -GATATC, [19][20][21] and a DNA construction (the substrate for the enzyme) with built in stress (Fig. 2) which we have exhaustively characterized in previous work 18,[22][23][24][25] . Briefly, these DNA molecules are obtained by hybridizing two linear DNA single strands of different lengths, where the shorter strand is complementary to the ends of the longer strand ( Fig.…”