Equilibrium dynamics of single DNA molecules confined to nanopit structures

Abstract

Introduction: of great interest in the physical sciences today, is the study of single molecules in nano-fluidic devices. These ‘labs-on-a-chip’ can provide the basic framework for quantifying the behavior of molecules, such as polymers, under confinement. This study is an investigation of a theoretical free-energy model used to predict thermodynamic properties of DNA molecules situated in a device called a nanopit array. Two parameters in the model, molecule length and nanopit width, are varied and tested against experimental data. Methods: Video-fluorescence microscopy was used to image single DNA molecules in the nanopit array; analysis consisted of determining the average number of nanopits occupied by a single DNA molecule over time. results: good qualitative agreement was reached between theory and experiment for the nanopit width variation, but molecule-length variation predictions were shown to still need improvement. A least-squares fit of the theory to the data suggested that the entropic parameter, A, and the excluded volume term, b, have a modified dependence on nanoslit height and nanopit depth than what is currently predicted by the model. discussion: These experiments confirm that the theoretical model is adequate under certain regimes and predicts conditions under which theory and experiment may significantly diverge. Modifications to the theory are proposed.