title: On the Hydrodynamic Nature of DNA Acoustic Sensing.
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.
authors.affiliation: Institute of Molecular Biology & Biotechnology, FO.R.T.H , Vassilika Vouton, 70013, Heraklion, Greece.
authors.forename: Achilleas
authors.initials: A
authors.lastname: Tsortos
authors.affiliation: Institute of Molecular Biology & Biotechnology, FO.R.T.H , Vassilika Vouton, 70013, Heraklion, Greece.
authors.forename: George
authors.initials: G
authors.lastname: Papadakis
authors.affiliation: Institute of Molecular Biology & Biotechnology, FO.R.T.H , Vassilika Vouton, 70013, Heraklion, Greece.|Department of Biology, University of Crete , Vassilika Vouton, 71409, Heraklion, Greece.
authors.forename: Electra
authors.initials: E
authors.lastname: Gizeli
mesh_terms: D000162:Acoustics / Q000295:instrumentation; D001360:Avidin / Q000737:chemistry; D015374:Biosensing Techniques / Q000295:instrumentation / Q000379:methods*; D001710:Biotin / Q000737:chemistry; D004247:DNA / Q000032:analysis*; D004277:DNA, Single-Stranded / Q000032:analysis; D057446:Hydrodynamics; D008958:Models, Molecular; D058525:Quartz Crystal Microbalance Techniques / Q000295:instrumentation / Q000379:methods*; D013016:Sound; D014783:Viscosity
chemical_list: D004277:DNA, Single-Stranded; C093483:neutravidin; D001360:Avidin; D001710:Biotin; D004247:DNA