DNA Calorimetric Force Spectroscopy at Single Base Pair Resolution

TL;DR

This paper introduces a novel single-molecule calorimetric force spectroscopy technique that accurately measures DNA thermodynamics, including previously unknown heat capacity parameters, enhancing understanding of nucleic acid stability.

Contribution

It combines single-DNA unzipping experiments with machine learning to derive temperature-dependent DNA energy parameters, including new heat capacity change measurements.

Findings

Measured ten heat-capacity change parameters $C_p$ for DNA.

Demonstrated high-resolution thermodynamic profiling of DNA.

Established a new methodology applicable to various nucleic acid structures.

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.