title: Fluidic switching in nanochannels for the control of Inchworm: a synthetic biomolecular motor with a power stroke.
abstract: Synthetic molecular motors typically take nanometer-scale steps through rectification of thermal motion. Here we propose Inchworm, a DNA-based motor that employs a pronounced power stroke to take micrometer-scale steps on a time scale of seconds, and we design, fabricate, and analyze the nanofluidic device needed to operate the motor. Inchworm is a kbp-long, double-stranded DNA confined inside a nanochannel in a stretched configuration. Motor stepping is achieved through externally controlled changes in salt concentration (changing the DNA's extension), coordinated with ligand-gated binding of the DNA's ends to the functionalized nanochannel surface. Brownian dynamics simulations predict that Inchworm's stall force is determined by its entropic spring constant and is ∼ 0.1 pN. Operation of the motor requires periodic cycling of four different buffers surrounding the DNA inside a nanochannel, while keeping constant the hydrodynamic load force on the DNA. We present a two-layer fluidic device incorporating 100 nm-radius nanochannels that are connected through a few-nm-wide slit to a microfluidic system used for in situ buffer exchanges, either diffusionally (zero flow) or with controlled hydrodynamic flow. Combining experiment with finite-element modeling, we demonstrate the device's key performance features and experimentally establish achievable Inchworm stepping times of the order of seconds or faster.
authors.affiliation: Division of Solid State Physics, Lund University, Box 118, 22100 Lund, Sweden. heiner.linke@ftf.lth.se.
authors.forename: Cassandra S
authors.initials: CS
authors.lastname: Niman
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Zuckermann
authors.forename: Martina
authors.initials: M
authors.lastname: Balaz
authors.forename: Jonas O
authors.initials: JO
authors.lastname: Tegenfeldt
authors.forename: Paul M G
authors.initials: PM
authors.lastname: Curmi
authors.forename: Nancy R
authors.initials: NR
authors.lastname: Forde
authors.forename: Heiner
authors.initials: H
authors.lastname: Linke
mesh_terms: D000818:Animals; D000845:Annelida / Q000502:physiology; D032701:Biomimetics / Q000295:instrumentation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D004058:Diffusion; D004735:Energy Transfer; D004867:Equipment Design; D019544:Equipment Failure Analysis; D044085:Microfluidics / Q000295:instrumentation*; D020409:Molecular Motor Proteins / Q000737:chemistry / Q000648:ultrastructure; D009038:Motion; D036103:Nanotechnology / Q000295:instrumentation*; D009690:Nucleic Acid Conformation; D013314:Stress, Mechanical; D014159:Transducers
chemical_list: D020409:Molecular Motor Proteins; D004247:DNA