Proteins are the fundamental functional blocks in our cells. Sensitive detection and accurate characterization of unknown protein species, or complex samples, underlie all areas of modern biomedical research, and is key to understanding complex gene regulatory network, cell signaling and differentiation, as well as to diagnosis and treatment of diseases. However, in contrast to the rapid advancement in DNA sequencing technologies, a general-purpose protein sequencing method that is both sensitive and accurate is still lacking.
Studying proteins on single molecules allows the ultimate sensitivity and profiling accuracy. Super-resolution microscopy (e.g. DNA-PAINT) combined with amino acid signature labelling and biophysical protein stretching provides a unique approach for full-protein analysis that cannot be achieved by mass spectrometry or peptide-based profiling. Combined with specific chemistries for post-translational modifications (PTM), our method further allows PTM profiling in single, intact protein molecules.
We develop new approaches for DNA sequencing, that enables highly scalable (100,000 or higher) single-cell analysis or clinical sample testing. Our novel non-linear amplification principle allows effective compression of mRNA dynamic range, greatly increases effective sequencing depth, and leads to deeper and highly scalable single-cell profiling. During the covid pandemic, we developed a method (One-Seq) for scalable SARS-CoV-2 viral diagnostics using a one-step reaction that accomplishes viral lysis, reverse transcription and sample barcoding. Our method employed DNA bioengineering techniques to ensure faithful and specific viral RNA detection even in the presence of high background (106 : 1 dynamic range).
Super-resolution microscopy methods have revealed intricate sub-diffraction organization inside the cell and shed light on new biological principles governing cellular architecture and behavior. We develop super-resolution microscopy methods that push the limit of imaging, and probe into the nanometer-scale organisation and complexity of cells and tissues. In particular, we developed the DNA-PAINT method, which exploits transient binding between short DNA oligonucleotide to generate single-molecule localizations, that achieved higher sensitivity, molecular-resolution (<5 nm) imaging on single molecules, even in the presence of crowded molecular surroundings. Harnessing the programmable binding between DNA strands, DNA-PAINT allows high-accuracy molecular quantitation and highly multiplexed imaging, useful for interrogation of complex organisation and interplay of many molecular targets (e.g. proteins, RNA and DNA). By exploiting the stochastic binding for real-time control, we further developed a first method for optically targeted molecular delivery that achieved super-resolution precision and single-molecule sensitivity (Action-PAINT), which opens a new window for correlated and functional molecular analysis, isolation, and even live activation.
We employ DNA nanotechnology to build nano-mechanical machines with nanometer-level geometric precision and custom-designed properties, such as hydrodynamic behavior. As an example, we developed a minuscule DNA rotor that is ~160 nm in diameter and amplifies the rotational movement of a single dsDNA molecule for faithful microscopy readout. Our collaborators used this nano-rotor to study the activity of DNA processing enzymes with single-base accuracy and real-time kinetics measurement.
