The crystal microbalance DNA hybridization biosensor: The effect of target position relative to the sensor surface and the role of gravity

Richard Derek Craven


The quartz crystal microbalance (QCM) senses changes in the inertia of matter bound to its surface. Theorists predicted that the QCM's response to non-rigid matter would decrease with distance from the QCM's surface. This is experimentally verified using DNA attached to a polymer coated QCM oscillated in contact with buffer solution. Sandwich hybridization is used to increase, step-wise, the length of the end-tethered DNA. QCM frequency is found to decrease as the reciprocal square-root of DNA mass when the QCM sensor surface faces Earth. It is proposed that, in this orientation, the DNA's mass is proportional to distance from the QCM's sensor surface. The QCM itself does not respond to gravity, but molecules bound to it can. By extending DNA, step-wise, on QCM sensors facing alternately up and down, it is found that a longer DNA molecule can be sensed in the up orientation. While the effect of gravity on buffer solutions is shown to be negligible, gravity is shown to have a pronounced effect on the tethered DNA. The experimental evidence obtained is consistent with DNA being elongated toward Earth when the sensor surface faces down, and folded-over, or partially collapsed, toward Earth when the sensor faces up. It is proposed that the orientation effect is caused by the heterogeneous nature of the solution in the liquid cell used. Because the DNA is tethered, the solution volume near the sensor occupied by DNA is more dense than the solution further away. This density difference accounts for gravity's effect. Also demonstrated is that the QCM's response decreases linearly with an increase in tethered DNA mass, so long as the solution layer thickness occupied by DNA is constant. It is further shown that the QCM's response slope as a function of DNA mass decreases when the DNA layer is moved further from the QCM by an intervening polymer layer, but the response retains linearity so long as the DNA's layer thickness is constant. These are the first experimental verifications of the relationship between distance from the sensor surface and response, and the first report of an effect of gravity on QCM measurements.