DNA Origami Force Balance

Abstract

Commonly used techniques to study conformational changes of interacting macromolecules such as atomic force microscopy and magnetic or optical tweezers today feature spatial resolutions of single nanometers and piconewton force sensitivity [1]. One of the limitations of these methods is the need to couple the molecules under investigation to a cantilever tip or micrometer-sized beads. By constructing molecular force spectroscopy tools with the help of DNA origami [2-4] we are trying to overcome this limitation. Our DNA origami-based force balance comprises a moveable lever on top of a base, which can exert defined forces in the regime between 1 pN and 10 pN between the lever and the base. The position of the lever can be detected with Transmission Electron Microscopy (TEM) and by Fluorescence Resonance Energy Transfer (FRET) in a dynamic fashion. Discrete and geometrically distinguishable conformations of our force balance can be observed when competing hybridizing DNA single-strands occupy their complementary counterparts on the structure on both sides of the lever. In model experiments where we tested different numbers of hybridizing strands on the two opposing ends of the lever, we observed surprisingly uniform populations of structures that were set in the “correct” conformation (∼ 90%).In a next step, we designed variants of the force balance with pre-stressed segments of DNA and investigated the dynamic switching of a Holliday junction under stress. In ongoing experiments we study the tension dependent bending behavior of DNA bending proteins.[1] C. Bustamante et al., Ten years of tension: single-molecule DNA mechanics, Nature (2003).[2] P. Rothemund, Folding DNA to create nanoscale shapes and patterns, Nature (2006).[3] H. Dietz et al., Folding DNA into twisted and curved nanoscale shapes, Nature (2009).[4] T. Liedl et al., Self-assembly of three-dimensional prestressed tensegrity structures from DNA, Nature Nanotechnology (2010).