Optimization and functionalization of red-shifted rhodamine dyes
- Zwitterion form is fluorescent and colored; lactone form is not and colorless.
- Lactone form is lipophyllic; some mix seems more bioavailable and also results in fluorogenic dyes.
- Good many experiments with either putting fluorine on the azetidines or on the benzyl ring.
- Fluorine on the azetidine pushes the toward lactone form; fluorine on the benzyl ring pushes it toward the zwitterion.
- Si-rhodamine and P-rhodamine adopt the lactone form, and adding appropriate fluorines can make them fluorescent again. Which makes for good red-shifted dyes, ala JF669
- N-CH3 can be substituted in the oxygen position too, resulting in blue-shifted dye which is a good stand-in for EGFP.
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