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Dear Scott,
I agree with Simon; CFP/YFP would be the best option for ratiometric FRET measurements
or for methods based on measuring sensitized emission of the acceptor (e.g. filter FRET).
I would certainly use optimized FPs: cerulean/SCFP3A and citrine/venus/SYFP2 (all with
A206K mutations to prevent dimerization).
For donor based methods (FLIM, acceptor photobleaching) we found that yellow/red pairs
are a substantial improvement over CFP/YFP:
http://dx.doi.org/10.1371/journal.pone.0001011
If you like you can obtain constructs that have directly linked donor-acceptor proteins as
positive controls for FRET:
http://wwwmc.bio.uva.nl/~joachim/Resources-DNA.html
Regards,
Joachim.
Dr. Joachim Goedhart
Section Molecular Cytology
Swammerdam Institute for Life Sciences
University of Amsterdam
Kruislaan 316
NL-1098 SM Amsterdam
The Netherlands
Tel: +31(0)20 525 7774
Fax: +31(0)20 525 6271
http://wwwmc.bio.uva.nl/~joachim