Microfluidic Cantilever Dynamics and Thermomechanics of DNA Melting Transitions

Abstract

The unravelling of a double stranded DNA into separate strands is crucial to DNA transcription, the integral basis of life, and thus remains a well explored bio-physics problem. In a double stranded DNA, the nucleotides are stacked and held together by hydrogen bonds in paired A-T and G-C sequence. With increasing temperature, the hydrogen bonds break and the strands separate base by base over a narrow temperature range. Melting of DNA samples causes measurable changes in their physical properties such as viscosity, buoyant density, UV260 nm absorption, optical rotation, etc. At molecular level unravelling of a dsDNA into individual strands when heated, occurs through an entropy-driven conformational transition. The unravelling typically proceeds through conformations that have locally denatured single stranded bubbles bound in-between double stranded helical segments. Investigations carried out using pico-liter solutions of micro molar concentrations of DNA molecules confined in a resonating microfluidic cantilever reveal interesting mechanical characteristics of denaturation process. As the strands unravel, the nanomechanical dissipation response sensitively follows the base-pair binding-unbinding energy landscape, revealing the characteristics of a two-stage transition curve. The fluctuation mediated transition pathway suggests an intermediate nucleation stage to the two-principal DNA denaturation pathways: the molecular zipper transition and the bubble state cooperativity. In fact, for both melting and pre-melting states, the cantilever response provides a framework to calculate the specific heat capacity and the storage and loss modulus the cantilever-DNA solution system, thereby establishing a platform for quantifying thermomechanical behavior of confined DNA molecules. Extremely small sample volume a hollow channel cantilever together with its high thermal sensitivity due to bi-material effect may open further avenues for studying fluctuation kinetics in DNA transcription and other complex bio-molecular phenomena.