Folding energy and kinetics of mutually interacting DNA Hairpins

Abstract

The Szilard engine is a Maxwell demon thought experiment where information is converted into work. We propose a novel DNA molecule with two hairpins in serial that could act as a complex four-state Szilard engine using optical tweezers to apply a force. We synthesized the molecule with identical hairpins to perform two different experiments with optical tweezers, passive mode and pulling. Only 3 different states were observed as the intermediate state is degenerated. Their energy levels were obtained from kinetic rates measured in passive mode and work measured in pulling cycles. We conclude that the molecule follows well the uctuation theorems and the Bell-Evans theory, with the exception of a Chevron type curvature in the kinetic rates due to the degeneration. The obtained data will help in the development and study of a Szilard engine with this molecule.