Jaclynn
Have you considered glycerin?
This has the advantage over many of the clearing agents already mentioned of
being completely miscible with water. The refractive index of glycerin is
between 1.44 to 1.47. This does not therefore give a completely transparent view
of objects but often this is an advantage in localizing areas and being able to
see landmarks within whole mounts.
Also glycerin is compatible with various antioxidants that can be used to
decrease fading of  fluorescent labels due to the excitation illumination.
Glycerin retains lipids but I suspect that this would  not be a problem with
your specimens.
I would recommend that you infiltrate the glycerin into the specimen slowly
using graded glycerin solutions or with the specimen in water, adding glycerin
dropwise. This is the most gentle.
The RI of glycerin can be changed.
65 ml glycerin, 35 ml water ...  RI of 1.42.
50 ml. glycerin, 50 ml. water...RI of 1.397-1.401
The RI can be increased by the addition of one of the following, zinc
sulphocarbonate, cadmium chloride, chloral hydrate or zinc iodate. However most
of those containing heavy metals would tend to suppress the fluorescence.
Barry


Jaclynn Lett wrote:

> We're looking for clearing agents for viewing whole mounts of mouse cochleas
> under the dissecting scope.  They'll be labeled with fluorescent tags such
> as Cy-3, Texas Red and ethidium homodimers, so the clearing agent must not
> dissolve the tag.  Also, since we'll be looking at the tissue under a scope,
> the agent should not be toxic nor have obnoxious fumes.
>
> I'm aware of the citrus-based clearing agents, and oils such as wintergreen
> (methyl salicylate), but have no idea as to they're suitability for our
> purpose (or whether the cochleas should be decalcified as well).
>
> If anyone has any insight, I would much appreciated the assistance.
>
> Thank you,
>
> Jaclynn M. Lett, Research Technician
>
> Fay and Carl Simons Center for Biology of Hearing and Deafness
> Central Institute for the Deaf
> 4560 Cla