On the Hydrodynamic Nature of DNA Acoustic Sensing

Anal Chem. 2016 Jun 21;88(12):6472-8. doi: 10.1021/acs.analchem.6b01165. Epub 2016 Jun 7.

Abstract

In this work we provide strong experimental evidence for the hydrodynamic nature of the acoustic wave/biomolecule interaction at a solid/liquid interface. By using a wide range of DNAs of various sizes and by assuming DNA attachment as discrete particles through a neutravidin/biotin link, we prove experimentally that the acoustic ratio (dissipation/frequency) is directly related to the molecules' intrinsic viscosity [η]. The relationship of [η] to the size and shape of biomolecules is described in general and more specifically for linear dsDNA; equations are derived linking the measured acoustic ratio to the number of dsDNA base pairs for two acoustic sensors, the QCM and Love-wave devices operating at a frequency of 35 and 155 MHz, respectively. Single-stranded DNAs were also tested and shown to fit well to the equation derived for the double-stranded molecules while new insight is provided on their conformation on a surface. Other types of DNA are also shown to fit the proposed model. The current work establishes a new way of viewing acoustic sensor data and lays down the groundwork for a surface technique where quantitative information can be obtained at the nanometer scale regarding the shape and size, i.e., conformation of biomolecules at an interface.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acoustics / instrumentation
  • Avidin / chemistry
  • Biosensing Techniques / instrumentation
  • Biosensing Techniques / methods*
  • Biotin / chemistry
  • DNA / analysis*
  • DNA, Single-Stranded / analysis
  • Hydrodynamics
  • Models, Molecular
  • Quartz Crystal Microbalance Techniques / instrumentation
  • Quartz Crystal Microbalance Techniques / methods*
  • Sound
  • Viscosity

Substances

  • DNA, Single-Stranded
  • neutravidin
  • Avidin
  • Biotin
  • DNA