polony gel-enabled spatial multiomics

In the history of DNA arrays, polymerase colonies (polonies; also known as clonal DNA clusters in Illumina next-generation sequencing flowcells) represent the finest feature to construct a DNA array. They have one of the smallest feature sizes, a mean diameter of ~0.5 micrometer at a high density (≥ 1.2 × 10⁶ polonies/mm²) or possibly smaller by amplification in a constraint space, such as microwells fabricated by nanolithography. They are cheap to make—instead of being chemically synthesized in columns or on a chip, they are in situ enzymatically amplified from single-molecule DNA templates deposited on an array. In a single polony, we can generate > 10⁴ copies of the original template serving as probes or templates for different applications.

Polonies can be efficiently amplified inside or atop crosslinked polyacrylamide gels (like those widely used for protein electrophoresis) to form polony gels. Our lab pioneers in two polony gel-based technologies, SMI-seq and Pixel-seq. SMI-seq amplifies DNA tags of proteins embedded in a gel, where the tags of proteins forming a complex result in polyclonal polonies, allowing the determination of molecular interactions by imaging-based sequencing. Pixel-seq uses “continuous” polony gels comprising densely packed features on a gel surface, each bearing a unique spatial barcode, for spatial capture and sequencing of single-cell transcriptomes and proteomes in tissues.

We are exploring new applications of polony gels by improving the fabrication and integration with other technologies. We aim to utilize their spatial resolution and enormous multiplexing capacity for mapping biomolecules, modifications, and interactions in cells and tissues.