How does a protein search for the specific site on DNA: The role of disorder.
Proteins can locate their specific targets on DNA up to two orders of magnitude faster than the Smoluchowski three-dimensional diffusion rate. This happens due to nonspecific adsorption of proteins to DNA and subsequent one-dimensional sliding along DNA. We call such a one-dimensional route towards the target an "antenna." We studied the role of the dispersion of nonspecific binding energies within the antenna due to a quasirandom sequence of natural DNA. A random energy profile for sliding proteins slows the searching rate for the target. We show that this slowdown is different for macroscopic and mesoscopic antennas.
Hu
Tao
T
Department of Physics, University of Minnesota, 116 Church Street SE, Minneapolis, Minnesota 55455, USA.
Shklovskii
B I
BI
D000327:Adsorption; D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding
D004268:DNA-Binding Proteins; D004247:DNA