Localizomics: spatial omics using DNA-based super-resolution microscopy

Super-resolution fluorescence microscopy is a powerful tool for biophysical and biological research. We use the transient binding of short fluorescently labeled oligonucleotides (DNA-PAINT) for easy-to-implement multiplexed super-resolution imaging that achieves molecular-scale resolution.
In this talk, I will discuss our group’s vision of enabling standard off-the-shelf fluorescence microscopy hardware to become a tool for spatial omics. This will allow researchers to visualize most biomolecules and probe their network-wide interactions in single cells, tissues, and beyond with single-molecule localization microscopy: Localizomics.
To enable this, I will first introduce major technical advancements in DNA-PAINT including approaches that achieve sub-10-nm spatial resolution and spectrally unlimited multiplexing in whole cells. I will then discuss novel protein labeling probes such as Slow Off-rate Modified Aptamers (SOMAmers) that are poised to allow DNA-barcoded labeling of much of the proteome in an intact cellular environment.
Next, I will discuss efforts to substantially increase DNA-PAINT’s traditionally relatively slow image acquisition speeds to achieve experimental throughputs necessary for network-wide molecular interrogation. To this end, we employed rationale, de novo DNA sequence design and repetitive sequence motifs and demonstrate in vitro and in situ imaging achieving 100-times faster imaging speeds without compromising image quality or spatial resolution. This improvement now makes DNA-PAINT applicable to high-throughput studies with biomedical relevance.
Finally, I will present first applications of these new capabilities to cell surface receptor imaging and quantification at thus far elusive spatial resolutions and levels of multiplexing. This is poised to yield fundamental insights into the molecular architecture of surface receptor interactions and potentially enable the future development of more refined “pattern”-based therapeutics.