DNA aptamer molecules passivated by alkanethiols can be used for biological detection and screening. Through the use of spectroscopic ellipsometry (SE, optical) and quartz crystal microbalance with dissipation (QCM-D, mechanical) techniques, selective binding of analytes to chemisorbed aptamer probes can be observed in-situ. The system analyzed consists of a gold-coated quartz substrate, a multilayer organic thin film (containing aptamer probe, alkanethiol, and single-stranded DNA analyte), and physiological buffer solution. The attachment and detachment of material, the hybridization efficiency of the aptamer probes, and changes in the porosity of the multilayer organic thin film were all determined by SE/QCM-D.

 

In this contribution, we present the real-time SE/QCM-D characterization of (a) the formation of the aptamer probe layer, (b) the subsequent chemisorption of alkanethiol, and (c) the interrogation of single-stranded DNA that is non-complementary or complementary to the sequence found on the aptamer probe. The aptamer DNA sequence encodes codon 12 of the K-ras gene; mutations of this gene are frequently found among pancreatic cancer patients. We found that introduction of either complementary or non-complementary DNA caused increases of the multilayer organic thin film thickness. However, our SE/QCM-D analysis showed that the porosity of the multilayer organic thin film responded differently depending on the compatibility of the DNA analyte. The SE/QCM-D technique provides evidence for different surface attachment mechanisms and can be useful in characterizing biological interfaces.