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. Author manuscript; available in PMC: 2022 Feb 4.
Published in final edited form as: Nat Rev Methods Primers. 2021 Dec 16;1(1):84. doi: 10.1038/s43586-021-00080-9

Figure 2: Concept of hydrogel embedding.

Figure 2:

(a) Tissue biomolecules are fixed chemically or physically to a hydrogel mesh generated in situ, and then cell membranes are removed during delipidation to enable chemical transport and optical transparency. (b) In CLARITY hydrogel embedding, paraformaldehyde (PFA), bis-acrylamide (Bis) and acrylic acid (AA) are used to covalently link the primary amines of proteins and nucleic acids to a polyacrylamide (pAAm) hydrogel mesh generated through free radical polymerization. Free radical generation and subsequent polymerization is initiated by the chemical VA044 when it is warmed to a temperature of 37°C. (c) A tissue-hydrogel’s pore size, expandability, transparency, and biomechanical stability can be modulated based on the delipidation temperature and the concentrations of the sodium dodecyl sulfate (SDS) delipidation detergent, the PFA fixative and the Bis crosslinker.