Tracking the Motion of a Biomolecular Machine with a Nanoscale Optical Encoder

Speaker(s): Everett Lipman

Molecular motors are essential components of the machinery of life, enabling processes such as DNA replication, transcription, and repair, protein synthesis, and muscle movement. In order to understand the details of how they function, it is necessary to track one at a time, a task that is complicated by the disparity between their sizes (about 5 nm) and the resolution of optical microscopes (about 200 nm). In macroscopic machines, such as inkjet printers or astronomical telescopes, precise measurements of distance and velocity are frequently made with optical encoders, which translate motion into a periodic signal. We have created a nanometer-scale optical encoder by incorporating a series of fluorescent dye molecules into a strand of DNA. Near-field energy transfer from a dye on a molecular motor to those in the encoder produces a periodic signal we can use to monitor translational and rotational motion. I will describe the physics underlying this technique, self-assembly of the nanoscale encoder, and what we have been able to learn about a helicase protein, which separates double-stranded DNA prior to replication.