Dr Cherry Fan

PhD Graduate
Department of Chemical & Biological Engineering

The Hong Kong University of Science and Technology

Cherry Tsz-wing Fan is a recipient of the Hong Kong PhD Fellowship (HKPFS) from the Hong Kong Research Grants Council.  She is expected to complete her PhD study in Chemical and Biological Engineering at The Hong Kong University of Science and Technology (HKUST) in August 2018. Driven by her passion for healthcare diagnostics, she has been developing novel biosensing devices by engineering the molecular self-assembly of nucleic acid reactions that are specific and sensitive to the biomarker of interest. In earlier stage of her studies, she leveraged the reaction thermodynamics and kinetics to design nucleic acid probes that rationally improved detection specificity against single nucleotide variants. Later, she integrated these design fundamentals with enzymatic reactions for building a simple DNA variant phasing tool as an alternative to costly sequencing technologies. In her recent exchange at Harvard, she also expanded her expertise to detect single molecular protein biomarkers using small sample volumes. Her enthusiasm in molecular diagnostics has motivated her for exploring these nucleic acid machineries for point-of-care and clinical sensing applications.

Programming Nucleic Acid Based Molecular Machineries for Homogeneous Bioanalyte Detection

Accurate diagnosis can make a life-changing difference to therapeutic options and outcomes, and that is highly dependent on the progress of biomarker discovery as well as the precision of analytical tools available. Nucleic acid has been a popular molecular tool for biosensing applications. This is in particular due to the unique Watson-Crick base pairs that allow single-base programming of the nucleic acid reactions by modulating the sequence information. The biophysics and quantitative characterization, for example the reaction Gibbs free energy - underlying the nucleic acid hybridization reactions, enable rational design of the nucleic acid machineries to finely tune the analytical performance. With rapidly falling synthesis cost and versatile chemical moieties that can be functionalized on synthetic nucleic acids, frontier nucleic acid sensing strategies can be developed to address critical biosensing challenges.

 

In this thesis, we hinge on the thermodynamics, kinetics and functional properties of synthetic nucleic acids to 1) develop a nucleic acid recycling circuit that kinetically discriminates single base mutants through cyclic toehold exchange reactions. This work overcomes the deteriorating specificity amid the signal amplification process in conventional analyte decoupled amplification reactions; 2) create in a first homogeneous single-molecule immunoassay which translates the transient antibody-antigen binding event to amplifiable nucleic acid signals based on multiple nucleic acid extension reactions. The proximity required several times for generating a complete reporter sequence immensely suppresses the background signal suffered in commercialized immunoassays and achieves ultrasensitivity using exceedingly small sample volume; and lastly 3) depict the phase –the exact nucleotide content on a strand by developing a homogeneous polymerase assisted hybridization-based approach where the polymerase is programmed to cause a change in fluorescence signal only if the studied alleles are in cis-conformation. The simplicity of the approach is promising to substitute costly next generation sequencing, indirect statistical computation or assays that require tedious single molecule isolation techniques for phasing at multiple allelic sites.