Stretching of macromolecules and proteins

Abstract

In this paper we review the biophysics revealed by stretching single biopolymers. During the last decade various techniques have emerged allowing micromanipulation of single molecules and simultaneous measurements of their elasticity. Using such techniques, it has been possible to investigate some of the interactions playing a role in biology. We shall first review the simplest case of a non-interacting polymer and then present the structural transitions in DNA, RNA and proteins that have been studied by single-molecule techniques. We shall explain how these techniques permit a new approach to the protein folding/unfolding transition.

Platinum-Based Drugs and DNA Interactions Studied by Single-Molecule and Bulk Measurements

“…2 A provide key information that is directly extracted from standard MT measurements for positive n t , namely, the values of the buckling transition, n b , and the slope, dL e =dn t (56). In considering the behavior of bare DNA in this study, according to a standard model for bare DNA (56), n b and dL e =dn t are predicted to display power-law dependence as a function of the imposed force, F. In the standard model, doublestranded DNA can be simply represented as an elastic rod with a torsional constant, C, and a bending constant, B ¼ k B TL P .…”

Single-Molecule Study of the DNA Denaturation Phase Transition in the Force-Torsion Space

“…We find that large temporal fluctuations of extension arise at one of the boundaries of the denaturation region. Finally, we interpret the experimental data with a simple mechanical model obtained by considering a denaturation term to the classical energy [17] used to describe the buckling transition.Several MT apparatuses have already been reported in the literature and, in our set up [12], we generally follow the most classically proposed schemes [8,19]. The technique is based on the following procedure: one end of the DNA is connected by standard biochemical techniques [8] to a commercial micron-sized superparamagnetic bead and the other DNA end is fixed to the inner wall of a squared capillary tube [20,21].…”

“…The initial pioneering MT studies focused on the topology of DNA molecules and showed that torsion can produce a so-called "plectoneme", which reduces DNA extension [15,16]. For modeling plectoneme formation, the DNA can be simply described as an elastic rod [17]. The experiments showed that the plectonemes disappear when the force becomes sufficiently high and the direction of the torsion is toward the unwinding of the DNA double helix [8].…”

“…We find that large temporal fluctuations of extension arise at one of the boundaries of the denaturation region. Finally, we interpret the experimental data with a simple mechanical model obtained by considering a denaturation term to the classical energy [17] used to describe the buckling transition.…”

“…2 confirming the existence of a fluctuation increase at a characteristic value of the force F char and deriving an original relation between F char and DNA nanomechanical constants (bending constant B and the binding energy between the DNA bases (denaturation energy)). The model is an extension of the classical theory of plectoneme formation [17] considering the denaturation energy. Indeed, when twisted by the magnetic bead, the DNA molecule relaxes the applied work in three different ways: by twisting (twisting energy: E twist ), by forming plectonemes (plectonemic energy: E plect ) and by partially denaturating (denaturation energy: E den ).…”