Exact theory of kinkable elastic polymers.

Division of Physics, Mathematics, and Astronomy, California Institute of Technology, Pasadena, California 91125, USA.
Physical Review E (Impact Factor: 2.33). 03/2005; 71(2 Pt 1):021909. DOI: 10.1103/PhysRevE.71.021909
Source: PubMed

ABSTRACT The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection angles, many rod systems exhibit a high-curvature softening. The signature behavior of these rod systems is a kinking transition in which the bending is localized. Recent DNA cyclization experiments by Cloutier and Widom have offered evidence that the linear-elastic bending theory fails to describe the high-curvature mechanics of DNA. Motivated by this recent experimental work, we develop a simple and exact theory of the statistical mechanics of linear-elastic polymer chains that can undergo a kinking transition. We characterize the kinking behavior with a single parameter and show that the resulting theory reproduces both the low-curvature linear-elastic behavior which is already well described by the worm-like chain model, as well as the high-curvature softening observed in recent cyclization experiments.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The helical structure of double-stranded DNA is destabilized by increasing temperature. Above a critical temperature (the melting temperature), the two strands in duplex DNA become fully separated. Below this temperature, the structural effects are localized. Using tethered particle motion in a temperature-controlled sample chamber, we systematically investigated the effect of increasing temperature on DNA structure and the interplay between this effect and protein binding. Our measurements revealed that (1) increasing temperature enhances DNA flexibility, effectively leading to more compact folding of the double-stranded DNA chain, and (2) temperature differentially affects different types of DNA-bending chromatin proteins from mesophilic and thermophilic organisms. Thus, our findings aid in understanding genome organization in organisms thriving at moderate as well as extreme temperatures. Moreover, our results underscore the importance of carefully controlling and measuring temperature in single-molecule DNA (micromanipulation) experiments.
    Biochemistry 10/2014; 53(41). DOI:10.1021/bi500344j · 3.19 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding.
    Biochimica et Biophysica Acta (BBA) - General Subjects 08/2014; 1850(5). DOI:10.1016/j.bbagen.2014.08.009 · 3.83 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The apparently anomalous flexibility of DNA on short length scales has attracted a lot of attention in recent years. We use atomic force microscopy (AFM) in solution to directly study the DNA bending statistics for small lengths down to one helical turn. The accuracy of experimental estimates could be improved due to a large data volume and a refined algorithm for image processing and measuring bend angles. It is found that, at length scales beyond two helical turns (7 nm), DNA is well described by the harmonic worm-like chain (WLC) model with the bending persistence length of 56 nm. Below this threshold, the AFM data are also described by the WLC model assuming that the accuracy of measured bend angles is limited by the physical width of the double helix. We conclude that the double helical DNA behaves as a uniform elastic rod even at very short length scales. Strong bends due to kinks, melting bubbles and other deviations from the WLC model are statistically negligible. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
    Nucleic Acids Research 11/2014; 42(22). DOI:10.1093/nar/gku1192 · 8.81 Impact Factor


Available from