Strong deformations of DNA: Effect on the persistence length

Kyryło A Simonov

doi:10.1140/epje/i2018-11722-8

Abstract

.Extreme deformations of the DNA double helix attracted a lot of attention during the past decades. Particularly, the determination of the persistence length of DNA with extreme local disruptions, or kinks, has become a crucial problem in the studies of many important biological processes. In this paper we review an approach to calculate the persistence length of the double helix by taking into account the formation of kinks of arbitrary configuration. The reviewed approach improves the Kratky-Porod model to determine the type and nature of kinks that occur in the double helix, by measuring a reduction of the persistence length of the kinkable DNA.Graphical abstract

Highlights

Many biological functions are intimately connected to the conformational deformability of DNA which can essentially influence its genetic activity
The recent view on the problem of strong bending and kink formation in the double helix was refreshed by Cloutier and Widom who found that the short DNA fragments of 94 base pairs cyclise much more than one would expect from the theory [9]
Wiggins and colleagues proposed an extension of the WLC model —the kinkable WLC model (KWLC), which includes sharp kinks characterised by a probability of such a kink occurring per unit length [24]

Summary

Introduction

Many biological functions are intimately connected to the conformational deformability of DNA which can essentially influence its genetic activity. The Kratky-Porod model (and its continuous version —the worm-like chain, WLC) [16] is considered as a basic mechanical model of DNA which can well describe a wide range of its mechanical properties [17]. The Kratky-Porod model is expected to describe only the smooth deformations of the double helix with relatively small changes between the bonds In this way, this model should be improved to include the configurations of the double helix with kinks of various nature, since corresponding approaches are still not completely developed. Wiggins and colleagues proposed an extension of the WLC model —the kinkable WLC model (KWLC), which includes sharp kinks characterised by a probability of such a kink occurring per unit length [24] These approaches consider the kinks to be of one type only, which is rather idealised.

Kinks in the Kratky-Porod model

Bending of DNA by multivalent cations

Summary and outlook