Autochemophoretic DNA Motors Generate 100+ Piconewton Forces

Abstract

DNA walkers, which “walk” along linear or planar tracks via burnt-bridge hybridization interactions, are promising synthetic analogs of motor proteins such as kinesin, myosin, and dynein. DNA walkers can precisely transport nanoscale cargo but cannot generate piconewton-scale force. This primary function of motor proteins is necessary for countless processes including muscle contraction, clotting, immunosensing, embryogenesis, and mechanosensation. We present progress towards the design of force-generating nanomachines by showing that highly polyvalent DNA motors (HPDMs) generate 100+ piconewtons of force via a novel mechanism that we term autochemophoresis. HPDMs are DNA-coated microparticles that connect to planar RNA-functionalized surfaces via DNA-RNA hybridization (Yehl & Salaita et. al., Nature Nanotechnology 2016). Ribonuclease H enables translocation by cleaving the RNA-DNA duplexes, resulting in an RNA depletion track in the HPDM's wake. Translocating for hours at micron/minute speeds, HPDMs are the fastest, most processive DNA-based motors reported to date. To test HPDMs’ force generation capability we designed a single molecule fluorescence microscopy experiment which enables direct visualization of mechanically-ruptured molecular bonds. Surprisingly, we found that HPDMs generate forces that mechanically rupture 25 basepair DNA duplexes and biotin-streptavidin bonds (the strongest noncovalent bonds found in nature with 100+ pN force thresholds). HPDMs lack directed tracks and conformational switching such as ATP-fueled powerstrokes, thus underscoring the novelty of this result. To study this fundamental mechanism of force-generation, we developed a simulation method that accurately reproduces most properties of HPDM motion via direct modeling of the distance-dependant biophysics of DNA-RNA interactions. These simulations highlight the mechanism of HPDM force generation and demonstrate that motion is driven by autochemophoresis, which has been observed in biological systems (Sugawara & Kaneko, Biophysics 2011). Our work suggests that autochemophoresis may be a third fundamental method of force generation in molecular motors and living systems.