High flexibility of DNA on short length scales probed by atomic force microscopy

Abstract

Because of thermal fluctuations, a polymer chain at room temperature will be bent. WLC and our model both predict that the molecule's observed conformations will be drawn from a certain probability distribution of shapes, obtained by combining bends distributed according to Boltzmann statistics with some energy function E(θ). Our task is to evaluate E(θ) from data.A comprehensive theory of DNA bending on short length scales must also include the twist degrees of freedom [1], as well as inhomogeneities from sequence [2,3]. Indeed, recent cyclization experiments suggest that the harmonic-elasticity model for the twist response of DNA also overstates the energetic cost of twist when curvature is high [4]. Thus, it seems likely that the twist energy function must be modified in a manner analogous to the one we have proposed for the bending energy. We leave this generalization to future work. For the random sequences studied here, we expect bending anisotropy to be a small effect for behavior on length scales greater than the helical pitch of 3.5 nm. Sequence dependent curvature, in natural DNA and in modified constructs with nonstandard bases, has been observed in AFM studies [5,6]; again we leave the extension of our model to include sequence to future work. A.2 Scale dependence in equilibrium statistical physicsHere we briefly elaborate on some ideas of scale dependence in equilibrium statistical physics, applied to our problem.The conformation of a macromolecule like DNA can usefully be described on any of several length scales. That is, when describing the molecule's behavior on a length scale ℓ exp larger than the size of individual atoms, we can often simplify our description by imagining the macromolecule to be composed

Critical Torque for Kink Formation in Double-Stranded DNA

“…The measured elastic energies for sharp bending are quantitatively reproduced by assuming a kinked state of the DNA in this regime, with a constant (independent of EED x) torque c at the kink, i.e., the elastic energy is linear in the kink angle, as was suggested in [11]. The same conclusion was arrived at for the case of nicked DNA [20].…”

“…This form of the energy must break down for R sufficiently small, but this is not seen in the DNA stretching experiments where the highcurvature configurations are irrelevant [11]. In contrast, cyclization experiments initially suggested [12] that the high-curvature states of DNA are much more flexible than predicted by (1).…”

“…If we write this range of validity as R > Cl p =ð2 Þ, where C is a numerical factor (of order 1), then the initial suggestion from cyclization experiments [12] was C % 0:7, whereas Du et al argued that C is lower [13]; using DNA minicircles the study [14] found that C % 0:5. Other studies also reported softening of the DNA at small scales [15]; in particular, the Atomic Force Microscopy (AFM) study [11] reported that the measured correlation functions are best described by a linear (rather than quadratic) dependence of the energy on the bending angle. The structural transition responsible for this softening is likely to involve formation of a small bubble (single-stranded or ss region) in the DNA, as pointed out by Yan and Marko [16].…”

“…The structural transition responsible for this softening is likely to involve formation of a small bubble (single-stranded or ss region) in the DNA, as pointed out by Yan and Marko [16]. Cyclization experiments [12] and AFM imaging experiments [11] rely on thermal fluctuations to realize the highcurvature states; one difficulty is then that the probability of these states is small. In our approach, the high-curvature states are designed into a mechanically constrained molecule [17], and the elastic energy is measured by thermodynamics methods [18,19].…”

Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity

“…Interestingly, recent in vitro experiments also suggest short-length scale anomalies in DNA mechanics, 4,75,155,156 even though no consensus has been reached. 133 To fully understand the role of tightly bent DNA in transcriptional regulation the contribution of the different molecular players (intrinsic DNA mechanics, architectural proteins, transcription factors, supercoiling) has to be decoupled.…”