What instrument can enable our eye to see an allele?

electron microscope would work

An allele is a sequence of DNA and since DNA is only 2nm wide an electron microcope would be needed to give the necessary magnification.

The closest technique to this is called FISH (Fluorescent in-situ hybridization).

This uses a DNA probe, which is fluorescently-labelled, so it will glow under fluorescent light. This probe can be designed to it will specifically recognise a certain gene or allele (by making its base-sequence complementary to that of the target sequence).
It is added to cells, and if there allele is present, it will bind, and will be visible under fluorescence microscopy.

This is therefore a highly-technically modified version of light microscopy. I am unaware of any electron microscopy version.