Article

# Diffusion-controlled first contact of the ends of a polymer: crossover between two scaling regimes.

Department of Physics, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1.

Physical Review E (Impact Factor: 2.31). 10/2005; 72(3 Pt 1):031804. DOI: 10.1103/PhysRevE.72.031804 Source: PubMed

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**ABSTRACT:**A common theoretical approach to calculating reaction kinetics is to approximate a high-dimensional conformational search with a one-dimensional diffusion along an effective reaction coordinate. We employed Brownian dynamics simulations to test the validity of this approximation for loop formation kinetics in the worm-like chain polymer model. This model is often used to describe polymers that exhibit backbone stiffness beyond the monomer length scale. We find that one-dimensional diffusion models overestimate the looping time and do not predict the quantitatively correct dependence of looping time on chain length or capture radius. Our findings highlight the difficulty of describing high-dimensional polymers with simple kinetic theories.The Journal of Chemical Physics 05/2013; 138(17):174908. · 3.12 Impact Factor - [Show abstract] [Hide abstract]

**ABSTRACT:**Is it possible to extract the size and structure of chromosomal territories (confined domain) from the encounter frequencies of chromosomal loci? To answer this question, we estimate the mean time for two monomers located on the same polymer to encounter, which we call the mean first encounter time in a confined microdomain (MFETC). We approximate the confined domain geometry by a harmonic potential well and obtain an asymptotic expression that agrees with Brownian simulations for the MFETC as a function of the polymer length, the radius of the confined domain, and the activation distance radius ε at which the two searching monomers meet. We illustrate the present approach using chromosome capture data for the encounter rate distribution of two loci depending on their distances along the DNA. We estimate the domain size that restricts the motion of one of these loci for chromosome II in yeast.Physical Review Letters 06/2013; 110(24). · 7.73 Impact Factor -
##### Article: Sequence and Temperature Dependence of the End-to-End Collision Dynamics of Single-Stranded DNA.

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**ABSTRACT:**Intramolecular collision dynamics play an essential role in biomolecular folding and function and, increasingly, in the performance of biomimetic technologies. To date, however, the quantitative studies of dynamics of single-stranded nucleic acids have been limited. Thus motivated, here we investigate the sequence composition, chain-length, viscosity, and temperature dependencies of the end-to-end collision dynamics of single-stranded DNAs. We find that both the absolute collision rate and the temperature dependencies of these dynamics are base-composition dependent, suggesting that base stacking interactions are a significant contributor. For example, whereas the end-to-end collision dynamics of poly-thymine exhibit simple, linear Arrhenius behavior, the behavior of longer poly-adenine constructs is more complicated. Specifically, 20- and 25-adenine constructs exhibit biphasic temperature dependencies, with their temperature dependences becoming effectively indistinguishable from that of poly-thymine above 335 K for 20-adenines and 328 K for 25-adenines. The differing Arrhenius behaviors of poly-thymine and poly-adenine and the chain-length dependence of the temperature at which poly-adenine crosses over to behave like poly-thymine can be explained by a barrier friction mechanism in which, at low temperatures, the energy barrier for the local rearrangement of poly-adenine becomes the dominant contributor to its end-to-end collision dynamics.Biophysical Journal 06/2013; 104(11):2485-92. · 3.67 Impact Factor

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