By modifying oligos with methacrylate (Acrydite), they can be copolymerized with additional acrylamide monomers to form polyacrylamide. In this way, oligos can be embedded into the polymer to perform a wide variety of functions.

Oligos embedded in gels in this manner can still interact with their environment, for example, to bind complementary DNA. By using methacrylate-labeled aptamers, it is possible to construct hydrogels that enable the specific detection of even the smallest amounts of a target molecule.

In other applications, the copolymerized oligos are designed to form cross-links with one another, which make the hydrogel stiffer and less permeable. When the oligos bind to their target molecule, the cross-links dissolve and the gel becomes more permeable again, for example, to other embedded active compounds.

In the context of smiFISH (single-molecule inexpensive FISH), the reporter probe can be labeled with a methacrylate molecule in addition to a fluorescent dye, which enables the use of expansion microscopy. In this technique, structures labeled with such reporters are physically enlarged by embedding them in a hydrogel. The hydrogel can then be uniformly swollen to increase the distance between the cellular structures. This, in turn, allows for more precise differentiation between spatially overlapping fluorescence signals.

Literatur:

1. Immobilization of acrylamide-modified oligonucleotides by co-polymerization. Rehman FN, Audeh M, Abrams ES, Hammond PW, Kenney M, Boles TC; Nucl. Acids Res. (1999), 22(2) 649-655. doi: 10.1093/nar/27.2.649.

2. Biomedical Applications of DNA-Based Hydrogels. Gačanin J, Synatschke CV, Weil T; Adv. Funct. Mater. (2020), 30 1906253. doi: 10.1002/adfm.201906253.

3. smiFISH and FISH-quant – a flexible single RNA detection approach with super-resolution capability. Tsanov N, Samacoits A, Chouaib R, Traboulsi A-M et al.; Nucl. Acids Res. (2016), 44(22) e165. doi: 10.1093/nar/gkw784.