DNA Calorimetric Force Spectroscopy at Single Base Pair Resolution

Abstract

DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have been done in melting experiments in bulk, of limited resolution due to ensemble averaging. In contrast, single-molecule methods have reached the maturity to derive DNA thermodynamics with unprecedented accuracy. We combine single-DNA mechanical unzipping experiments using a temperature jump optical trap with machine learning methods and derive the temperature-dependent DNA energy parameters of the NN model. In particular, we measure the previously unknown ten heat-capacity change parameters $\Delta C_p$, relevant for thermodynamical predictions throughout the DNA stability range. Calorimetric force spectroscopy establishes a groundbreaking methodology to accurately study nucleic acids, from chemically modified DNA to RNA and DNA/RNA hybrid structures.