DNA-Based Formation of a Supported, Three-Dimensional Lipid Vesicle Matrix Probed by QCM-D and SPR

Although water-soluble biomolecules can now be efficiently handled in surface-based biosensor formats, generic protocols for immobilizing membrane proteins are still, to a large extent, lacking. Herein, we extend the application areas of single stranded (ss) DNA-modified small unilamellar vesicles (ss-DNASUVs) by demonstrating a strategy whereby a three-dimensional matrix of SUVs can be created by utilizing sequential DNA hybridization between ss-DNA-SUVs carrying complementary DNA sequences. Although in a parallel work we have explored the use of such three-dimensional templates for the improved analysis of membrane proteins, herein the primary focus is on the applicability of the quartz crystal with dissipation monitoring (QCM-D) technique for analyzing these types of soft and relatively thick films. Using this approach it was, for the first time, experimentally verified that a soft film probed in an aqueous environment reaches a thickness region where film-resonance behavior is observed. Although this complicates the straightforward transformation of changes in frequency to coupled mass, it demonstrates that operating the QCM-D technique at multiple harmonics, combined with theoretical modeling using a Voigt-based viscoelastic model, can be used to translate the response into appropriate mass uptake (and thickness) quantification-including the determination and separation of the effective viscoelastic components of the film. These data are further compared with surface plasmon resonance (SPR) data on the same system, where the exponentially decaying sensing depth is only weakly dependent.