The Mechanical Properties of Double-Stranded RNA in Response to Force and Torque

While the response of double-stranded DNA to applied forces and torques has been measured with exquisite precision, much less is known about double-stranded RNA (dsRNA). We have recently developed a “polymerase-stall” labeling method that allows us to generate fully double-stranded RNA constructs carrying multiple biotin and digoxygenin labels at opposite ends. Using the functionalized dsRNA constructs in a range of a complementary magnetic tweezers assays, we have probed the elastic properties of dsRNA and, in addition, determined force and torque induced structural transitions that go beyond linear response behavior. Using conventional magnetic tweezers, we have determined the bending persistence length and the stretch (or Young's) modulus of dsRNA. Employing our novel magnetic torque tweezers[1] and freely-orbiting tweezers [2] assays, we have probed the torsional persistence length of dsRNA and its twist-stretch coupling. While the elastic properties are, overall, similar to dsDNA, we have discovered a striking difference in the energy landscape at the buckling torque under positive twist. These measurements of the fundamental properties of dsRNA can inform quantitative models of RNA function in vivo, for example of the packing of viral RNA genomes or of the mechanical function of double-stranded regions in functional RNAs.[1] Lipfert, Kerssemakers, Jager & Dekker, Nature Methods (2010).[2] Lipfert, Wiggin, Kerssemakers, Pedaci & Dekker, Nature Communications (2011).