Tracking a Molecular Motor with a Nanoscale Optical Encoder

Optical encoders are commonly used in macroscopic machines, such as desktop printers and astronomical telescopes, to make precise measurements of distance and velocity by translating motion into a periodic signal. We have designed and synthesized self-assembling DNA segments incorporating F\"orster resonance energy transfer acceptor dyes at regular intervals. When one of these ``FRET encoders'' is unwound by a donor-labeled helicase molecule, a periodic fluorescence signal is produced, enabling us to monitor translation and rotation of the helicase. I will describe our methods for synthesizing FRET encoders, and show data indicating constant linear motion of a single \emph{E.~coli} DnaB helicase over a distance of hundreds of base pairs.