Molecular Basis for Viscoelastic Response of Nano-Mechanical Biosensors

John Sieber, Kai Huang, and Izabela Szlufarska

The use of micro-and nano-electromechanical systems for the detection of molecules has been explored in the scientific community.  Recent advances in the functionalization of surfaces have created opportunities for biosensing capabilities.  Experimental techniques have been developed to create stable biofunctionalized structures using amorphous carbon and diamond films [1].

Fig1. Functionalization of amorphous carbon to produce bonded DNA adduct of carbon surface [1]

These biofunctionalized films attached to quartz crystal microbalance (QCM) have been used in the detection of selected DNA oligonucleotides.  Detection is accomplished by measuring the changes in resonance frequency when the complimentary DNA strand is attached to the surface.  While this method qualitatively provides evidence of attachment, a lack of understanding in the change of frequency due to specific molecular attachment hinders further progress in this area.  The complexity of molecular interactions and rheological effects in solution provide obstacles in the study of these systems.

In order to determine the relationship between resonance frequency and type of biomolecule in natural and physiological environments, large scale molecular dynamics simulations will be employed.  Simulations of organic alkene functionalized carbon film surfaces and DNA functionalized carbon film surfaces will be analyzed for energy dissipation and molecular mechanism for these dissipations.  In addition, the effect of temperature and solution ionic strength on the energy dissipation in oscillations will be studied to determine the effect of environmental conditions on resonance frequency.

Fig2. The mechanical model for MD simulations

Understanding of the specific relations of resonance frequency and system characteristics will allow application of these systems in the detection of specific targeted biomolecules.  These biosensors can be used for monitoring and detection of pathogens in the environment or in the body.  Finally, understanding of this system will allow further research into DNA functionalized surfaces and applications in the biotechnology field.

References:
[1]  Bin Sun, Paula E. Colavita, Heesuk Kim, Matthew Lockett, Matthew S. Marcus, Lloyd M. Smith,Robert J Hamers. Covalent Photochemical Functionalization of Amorphous Carbon Thin Films for Integrated Real-Time Biosensing.  Langmuir 2006, 22, 9598.