Fluidic switching in nanochannels for the control of Inchworm: a synthetic biomolecular motor with a power stroke

Nanoscale. 2014 Dec 21;6(24):15008-19. doi: 10.1039/c4nr04701j. Epub 2014 Nov 4.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Annelida / physiology
  • Biomimetics / instrumentation
  • DNA / chemistry*
  • DNA / ultrastructure*
  • Diffusion
  • Energy Transfer
  • Equipment Design
  • Equipment Failure Analysis
  • Microfluidics / instrumentation*
  • Molecular Motor Proteins / chemistry
  • Molecular Motor Proteins / ultrastructure
  • Motion
  • Nanotechnology / instrumentation*
  • Nucleic Acid Conformation
  • Stress, Mechanical
  • Transducers*

Substances

  • Molecular Motor Proteins
  • DNA