Studies of Binding Mechanism between Nucleic Acids with Silica Surface of Liquid Biopsy and Its Applications in Biomolecular Diagnosis

Nucleic acid detection from liquid biopsy for diagnosis and prognosis has gained intensive attention in the precision medicine paradigm and translation research. To quantitatively collect and qualitatively purified nucleic acids from tissue sample become imperative and inevitable steps before as inlet of any downstream biomolecular detection instruments, such as PCR, qPCR, microarray, NGS and any biosensor instruments for quantitation. Currently, most of the instrumental companies develop their own purification scheme and kits and is the most profitable business model. Arguments on minimum information and quality of sample preparation required for PCR/qPCR nucleic acid molecular detection has moved one step further for data collection for diagnosis and clinical purpose. However, no standard operation procedure (SOP) has reached among users and instruments developers. This is mainly due to that the complexity of the tissue sample and the mechanism of the purification scheme used nowadays is still not well understood. Our previous MOST funded project was to compare current used purification schemes and kits and to develop, possibly, a SOP for the translational clinical data portability among different platforms. We have successfully revealed the key differences among the kits under investigated and we also realized the complicated binding mechanism of using silica based column for nucleic acids purification, which is the mostly adapted scheme for final nucleic purification of the processes.Therefore, in this project, we would like to further study the binding mechanism from thermodynamics perspective of nucleic acids, including DNA and RNA, with silica surface by isothermal titration calorimetry (ITC). The size of the nucleic acids (RNA, mRMA, miRNA, DNA, gDNA, etc...), the type of salts and concentration (salt bridge, hydrogen bonding, hydration, etc…), the pH value (protonation of silica), the binding temperature and the contaminations from the lysis and biofluids are all the parameters under this investigation. The ITC mechanism studies of nucleic acids and silica surface should provide a clear understanding of the nucleic acids qualitative and quantitative purification and can serve as a meaningful translational indicator for molecular discovery, profiling, quantitation, validation and functional analysis.