Journal of Chemical Physics, Vol.118, No.18, 8513-8520, 2003
Effect of the intermediate state on the loop-to-coil transition of a telechelic chain
The kinetics of conformational fluctuations of a telechelic chain with two binding sites at both ends is studied by Monte Carlo simulations. The site-to-site binding energy is -epsilon. An example of the telechelic biopolymer is RNA or ssDNA made of a homogeneous sequence such as poly(T) with complementary bases at both ends. The conformation of such a chain fluctuate from loop (closed) to coil (open) state and the probability of the coil state depends on the temperature. An all-or-none transition between open and closed states is often adopted to depict the melting curves. It is found that the two-state model fails due to the existence of the intermediate state. A three-state model including open, intermediate, and closed states is proposed. The melting curves obtained from such a scenario agree quite well with the simulation results and there are two characteristic temperatures. The rate constants from closed to intermediate states k(c,i) and from intermediate to open states k(i,o) are independent of chain length but proportional to e(-epsilon/kT). In contrast, the rate constants from open to intermediate states k(o,i) is independent of temperature and that from intermediate to closed states k(i,c) is essentially constant. (C) 2003 American Institute of Physics.