End-to-surface reaction dynamics of a single surface-attached DNA or polypeptide.
The dynamics of surface-attached polymers play a key role in the operation of a number of biological sensors, yet its current understanding is rather limited. Here we use computer simulations to study the dynamics of a reaction between the free end of a polymer chain and a surface, to which its other end has been attached. We consider two limiting cases, the diffusion-controlled limit, where the reaction is accomplished whenever the free chain end diffuses to within a specified distance from the surface, and the reaction-controlled limit, where slow, intrinsic reaction kinetics rather than diffusion of the chain is rate limiting. In the diffusion-controlled limit, we find that the overall rate scales as N(-b), where N is the number of monomers in the chain and b approximately = 2.2 for excluded volume chains. This value of the scaling exponent b is close to that derived from a simple approximate theory treating the dynamics of the chain end relative to the surface as one-dimensional diffusion in an effective potential. In the reaction-controlled limit, the value of the scaling exponent b is close to 1. We compare our findings with those for the related (and better studied) problem of end-to-end reactions within an unconstrained polymer chain and discuss their implications for electrochemical DNA sensors.
Department of Chemistry and Biochemistry and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA.
Ryan R
RR
Cheng
Dmitrii E
DE
Makarov
D015374:Biosensing Techniques; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D007700:Kinetics; D010455:Peptides / Q000737:chemistry*; D011108:Polymers / Q000737:chemistry*; D013499:Surface Properties
D010455:Peptides; D011108:Polymers; D004247:DNA