DNA Dynamics under Nano-Confinement

Abstract

DNA polymer dynamics are fundamental to the function of biological systems. Examples include gene regulation, cell division, threading and transport through pores. We studied the dynamics of DNA molecules ranging in length from 40bp to 20kbp both in solution and under confinement in nano-slits. DNA molecules were 2-color end labeled and their internal polymer dynamics were observed by fluorescence microscopy and fluorescence cross correlation spectroscopy. We also present a modified fitting model for FCCS results taking into account confocal volume overlap imperfection and nano-slit confinement. We experimentally determined the diffusion coefficients of a range of different weight DNA molecules. Better understanding internal polymer dynamics under nano-confinement has potential applications in genomic sequencing, single biomolecule manipulation, and separations as well as the ability to address fundamental research questions in biophysics and molecular biology.