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The majority of organic solvent clearing procedures has a simple two step mechanism in common:
The organic solvent clearing leads to very transparent samples and is perfectly suited for dense tissue like tumors, adult tissue, or highly myelinated brain. The majority of immuno-histochemical staining is well conserved.
The most common operating principle of water-based clearing protocols is by depolymerization. By splitting large structures like lipid bilayers into small micelles of different sizes, the opacity is remarkably reduced. Urea can be used as depolimerization agent as with CUBIC clearing. A SDS buffer and an advanced electrophoresis protocol are used for CLARITY clearing.
The clearing protocols differ in complexity and in the degree of translucency that can be achieved. By depolymerization, the entire structure of a sample can be debilitated while the fluorescence of proteins like GFP is well preserved.
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