Biomedical subjects

Jae-Hyung Jeon

Publications and source records attributed to Jae-Hyung Jeon.

3 recordsLinked to original sources

PubMed2006

The effect of sequence correlation on bubble statistics in double-stranded DNA.

DNA exists stably in the double-stranded structure at physiological temperatures, but base pairs are observed to unbind locally, giving way to bubbles (i.e., locally denatured states) due to thermal fluctuation. In this study, we consider the effect of sequence on the bubble statistics. On the basis of the Edwards equation description [W. Sung and J.-H. Jeons, Phys. Rev. E 69, 031902 (2004) ], we develop a stochastic model incorporating the sequence randomness as a dichotomic noise, where the bubble and its size are identified as a returning random walk and its first passage time, respectively. By simulating the model Langevin equation, we obtain the bubble size distribution and show how it is affected by the sequence correlation. We find that the bubble size distribution of DNA with finite sequence correlation deviates from the Poland-Scheraga-type distribution. In particular, the formation of large bubbles is dramatically enhanced as sequence correlation length gets longer.

Base Sequence↗

PubMed2006

A semiflexible chain model of local denaturation in double-stranded DNA.

Double-stranded DNA (dsDNA) is known to form a locally denatured structure ("bubble") below its denaturation temperature (T(c)). We have investigated the physical behavior of the bubbles using a model of dsDNA as two wormlike chains containing interacting complementary base pairs. The model incorporates two biologically relevant features, i.e., semiflexibility of the strand and overdamping nature of aqueous background. Computer simulations using the Langevin equation are performed to examine the size distribution and dynamics of bubbles. The results show that the entropy associated with semiflexibility of DNA sensitively affects the size distribution and lifetime of bubble. In particular, the lifetime grows with bubble size m as m(2.7) at temperature close to T(c), which is consistent with our analysis based on a stochastic model of bubble size dynamics.

Algorithms↗

PubMed2004

Conformation of local denaturation in double-stranded DNA.

Double-stranded DNA (dsDNA) undergoes a denaturing transition above which the strands unbind completely. At temperatures (including the physiological temperature) below the transition the base pairs tend to unbind locally, giving way to loops, i.e., locally denatured states. In the flexible-chain model, the imaginary time Schrödinger equation describes the interstrand distance distribution of dsDNA with the time variable replaced by the sequence number. We transform the equation to the Fokker-Planck equation (FPE), which provides a convenient and powerful analytical method and, via the equivalent Langevin equation, a simulation scheme. The temperature-dependent potential that emerges in the FPE manifests how the DNA conformation changes dramatically near the transition temperature. We present several simulation plots along with analytical results illustrating the order parameter (concentration of bound base pairs), base pair distance correlation function, and loop size distribution at different temperatures.

Base Pairing↗