DNA origami-based platform for multi-axial single-molecule force spectroscopy reveals hidden dynamics in Holliday junctions

In living cells, biomolecules operate in a crowded 3D milieu and are subjected to complex multi-axial stress environment. These mechanical forces are fundamental regulators of biomolecular structures and functions. However, most single-molecule force spectroscopy techniques primarily exert force along a single axis, thereby failing to recreate the mechanical environments experienced by biomolecules in cells. Here, we present a molecular tool comprising a multi-axial entropic spring tweezer along rigid DNA origami (MAESTRO), which utilizes ssDNA entropic springs to apply forces in the piconewton (pN) range and is designed to examine the dynamics of biomolecules under defined multi-axial tensions. Combining MAESTRO, single-molecule Förster resonance energy transfer (smFRET) and Bayesian non-parametric FRET (BNP-FRET) enables high-throughput study of biomolecules under different complexities of multi-axial tension forces. We demonstrate our tension-inducing molecular tool on Holliday junction (HJs)—intermediate DNA structures important in the homologous recombination process. Instead of faster kinetics under tension, we discovered ≥ 5× slower kinetics of the HJ conformations under multi-axial tension than under tension-free conditions, which in turn permits direct observations of intermediate open and unstacked HJ conformations. Notably, under four-way tension, we observed clear evidence of inter-conversion between several different kinetic patterns in many individual HJs, previously believed to be non-interconverting owing to the rugged energy landscape of the system. In addition to controlling conformational dynamics, we show that the tension experienced by HJ also mechanically tunes the functional outcome of T7 endonuclease I, a junction-resolving enzyme that recognizes HJ and catalyzes two cleavage sites within the junction. By overcoming the limitations of single-axial force spectroscopy, we envision that MAESTRO’s versatile multi-axial tension capability will enable high-throughput investigation of complex, previously unseen dynamics and probe the mechanoregulation of many biomolecules.