Universal next-generation biomolecule enrichment technique for molecular diagnostics

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2020Cataloged from PDF of thesis.Includes bibliographical references (pages 182-200).Rapid and reliable detection of ultralow-abundance nucleic acids and proteins in complex biological media may greatly advance clinical diagnostics and biotechnology development. Because of the slow mass transport and weak binding kinetics at ultralow concentration of target biomolecules, enrichment of target biomolecules plays an essential role in the detection of ultralow-abundance biomolecules. Currently, nucleic acid tests rely on enzymatic processes for target amplification (e.g. polymerase chain reaction), which have many inherent issues restricting their implementation in diagnostics. On the other hand, there exist no protein amplification techniques, greatly limiting the development of protein-based diagnosis.By learning from the desired and undesired features of existing techniques, we designed the blueprint of the next-generation biomolecule enrichment technique, which should ideally be universally applicable to all kinds of biomolecules and be capable of specifically enriching only the target biomolecules among the background biomolecules by billion-fold rapidly. Electrokinetic concentration is a promising candidate for the next-generation biomolecule enrichment technique, because of its simple architecture and ease of operation, high concentration speed, universal applicability, and the rich physics of the system that may enable the development of new functionalities. We defined a technical roadmap of engineering the primitive electrokinetic concentration technique toward the next-generation biomolecule enrichment technique. We start by deciphering the mechanism of electrokinetic concentration (Chapter 2), which is instrumental in the rational design and innovation of the system.We next developed specific enrichment of target biomolecules in the electrokinetic concentrator based on electrophoretic mobility-based separation and mobility engineering of affinity binders (Chapter 3). We went on to realize the billion-fold enrichment capability of electrokinetic concentrator by massive parallelization and hierarchical cascading of unit electrokinetic concentrators (Chapter 4). After that, we demonstrated the engineered electrokinetic concentrator as an integrated, self-contained platform for universal amplification-free molecular diagnostics (Chapter 5). Finally, we interfaced the engineered electrokinetic concentrator with standard analytics to enhance their analysis sensitivity and greatly simplify their workflows (Chapter 6). At the end of the thesis, we conclude this thesis and present our outlooks on the future directions (Chapter 7).by Wei Ouyang.Ph. D.Ph.D. Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Scienc