Leila Esmaeili Sereshki

Persian

Role of DNA conformation in Gene regulation.

Essentially all the biological functions of DNA rely on site-specific DNA-binding proteins finding their targets (cognate sites), and therefore searching through mega bases of non-target DNA in a very efficient manner. The most prominent example is the process of gene regulation, during which a particular binding protein needs to find its specific binding sequence on the DNA.We analyze the polymeric conformations of DNA molecules under topological constraints, such as looped DNA or DNA-knots. These polymeric degrees of freedom of a DNA chain also influence the search of DNA binding proteins for their specific binding site on the DNA, a prerequisite to genetic regulation. We are interested in generic aspects of search strategies, in particular, the effect of scale-free search mechanisms. These provide searching agents with a means to escape the central limit theorem and avoid oversampling, which is the major shortcoming of Brownian search strategies in one and two dimensions. Our studies on search go hand in hand with the investigation of anomalous stochastic processes such as Lévy flights and subdiffusion.

M. Neek-Amal, G. Tayebirad, M. Molayem, M. E. Foulaadvand, L. Esmaeili Sereshki, A. Namiranian:
“Ground state study of simple atoms within a nano-scale box”
Solid State Communications, 145, 594 (2008)