Surface Dynamics Study of DNA Loop Formation Using Surface Plasmon Resonance

Abstract

Electrochemical proximity assay (ECPA), was recently developed for direct protein quantitation as low as 158 fM. In this assay, the loop-like DNA structure holds methylene blue (MB-DNA) in close proximity with the gold surface when target is present, ensuring efficient electron transfer. However, for studying DNA binding dynamics on gold surfaces, investigations were carried by immobilizing SH-DNA onto SPR sensor surface to form self-assembled monolayer. DNA loop and MB-DNA oligonucleotides were alternately hybridized to the SH-DNA complementarily forming loop-like structure. Sensogram results showed increase in refractive angle (RA) when DNA alternately hybridized with complementary strands, however upon elimination of DNA loop or SH-DNA showed no discernible RA signal, suggesting loss in loop structure. We found that the SH-DNA binding on the gold surface was affected by free thiols moieties. Purification of SH-ssDNA led to signal enhancement in target binding in comparison to non-purified. We anticipate the feasibility of this study in improving the speed and sensitivity of ECPA-based biomarker recognition.