Topology matters: Some aspects of DNA physics

Ralf Metzler,
NORDITA - Nordic Institute for Theoretical Physics, Copenhagen, Denmark

Abstract:
Double-stranded DNA is one of the best known realisations of a self-avoiding polymer due to its small ratio between effective diameter and persistence length; moreover, it can be perfectly copied. Thus, DNA is of high interest to polymer physics, in particular, given the possibility of performing single molecule experiments on DNA strands. However, due to its heterogeneous character and the specific binding strengths (`kT-physics'), as well as its interaction with certain enzymes occurring in its natural biochemical environment, this biological macromolecule instigates the investigation of additional properties of (bio)polymers:

(1) DNA knots and other entangled states: The enzyme topoisomerase II is able to detect knotted states in DNA and to actively reduce the degree of knottedness under consumption of ATP-energy. Given its necessarily local probing, how can the enzyme be so efficient in reducing the knottedness? It will be shown that tightening of the knot due to thermal fluctuations may facilitate this detection.

(2) Single-stranded loops in double-stranded DNA: Already at physiological temperatures, short stretches of DNA open up due to fluctuations, to form flexible single-stranded loops (`DNA breathing'). Upon heating, the typical size of these fluctuation bubbles increases, until at the melting tempera- ture, the two strands seperate fully. Recent single molecule experiments reveal the processive character of the breathing dynamics. A simple phenomenological model based on statistical mechanical properties of the DNA will be introduced to explain the details of the bubble dynamics. An analysis similar to the investigation of DNA knots allows modifications of the traditional DNA-melting models to explain the sharp melting transition of double-stranded DNA.

References:
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[4] A. Hanke and R. Metzler, eprint cond-mat/0305049.