The rate of intramolecular loop formation in DNA and polypeptides: the absence of the diffusion-controlled limit and fractional power-law viscosity dependence.
The problem of determining the rate of end-to-end collisions for polymer chains has attracted the attention of theorists and experimentalists for more than three decades. The typical theoretical approach to this problem has focused on the case where a collision is defined as any instantaneous fluctuation that brings the chain ends to within a specific capture distance. In this paper, we study the more experimentally relevant case, where the end-to-end collision dynamics are probed by measuring the excited state lifetime of a fluorophore (or other lumiphore) attached to one chain end and quenched by a quencher group attached to the other end. Under this regime, a "contact" is defined not by the chain ends approach to within some sharp cutoff but, instead, typically by an exponentially distance-dependent process. Previous theoretical models predict that, if quenching is sufficiently rapid, a diffusion-controlled limit is attained, where such measurements report on the probe-independent, intrinsic end-to-end collision rate. In contrast, our theoretical considerations, simulations, and an analysis of experimental measurements of loop closure rates in single-stranded DNA molecules all indicate that no such limit exists, and that the measured effective collision rate has a nontrivial, fractional power-law dependence on both the intrinsic quenching rate of the fluorophore and the solvent viscosity. We propose a simple scaling formula describing the effective loop closure rate and its dependence on the viscosity, chain length, and properties of the probes. Previous theoretical results are limiting cases of this more general formula.
Department of Chemistry and Biochemistry and Institute for Theoretical Chemistry, University of Texas at Austin, Austin, Texas 78712, USA.
Ryan R
RR
Cheng
Takanori
T
Uzawa
Kevin W
KW
Plaxco
Dmitrii E
DE
Makarov
D004277:DNA, Single-Stranded / Q000737:chemistry*; D004058:Diffusion; D007700:Kinetics; D010455:Peptides / Q000737:chemistry*; D014783:Viscosity
D004277:DNA, Single-Stranded; D010455:Peptides