Work

Evidence of a Three-State Mechanism in DNA Hairpin Folding

Year: 2025

Type: article

Abstract: DNA hairpins are a model system for biomolecule folding as well as key structures in biology and nanotechnology. However, limitations in traditional solution-phase spectroscopy shorten the window of observable kinetics and cannot account for static heterogeneity. Here, we show that the application of two-dimensional fluorescence lifetime correlation spectroscopy (2DFLCS) to a solution-phase molecule trapped in an anti-Brownian electrokinetic (ABEL) trap bypasses those limitations, enabling kinetic analysis of the dynamics of single solution-phase molecules on a broad range of time scales down to microseconds. The analysis unambiguously shows that DNA hairpin folding proceeds via a three-state system, where hairpins fold initially on the scale of tens to hundreds of microseconds from a random coil to a partially closed intermediate and then form a stable fully closed state.

Source: Journal of the American Chemical Society

DOI: 10.1021/jacs.4c17471

Authors: Brendan Cullinane, Kunihiko Ishii, Simi Kaur, Tahei Tahara, Randall H. Goldsmith

Institutions: University of Wisconsin–Madison, RIKEN, RIKEN Center for Advanced Photonics

Language: English

Topic: DNA and Nucleic Acid Chemistry

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Institutes of Health, Japan Society for the Promotion of Science, National Institute of General Medical Sciences

Awards: Elucidation of heterogeneity and hierarchy of biomacromolecular dynamics by novel fluorescence correlation methods, Development of Cavity-Enhanced Single-Molecule Electronic and Vibrational Spectroscopy for Mechanistic Studies of Biomolecules, G8745028046