fluorescent primers

Daniel Mcgoldrick ez005139 at chip.ucdavis.edu
Fri Apr 21 11:26:12 EST 1995


	I have been sequencing a large number of microsatellite clones, and 
the time has come to design primer sets from the sequence data. I am 
using a Hitachi FM Bio fluorescent scanner that excites at around 539 nm 
and we have filters to read 585 and 605 nm emissions. Currently, I am 
researching methods for generating fluorescently labeled primers, and 
have found a number of companies that offer post labeling kits. In addition, 
there are a few products out there that allow a tagged amidite to be used 
during synthesis of the oligo. 
	I need 40 microsatellite primer pairs to complete my thesis work, 
and that means I need to have at least 20 primers labeled and working. 
Ideally, I would like to multiplex my PCR reactions and do dual color 
analysis. Should I go with a post synthesis labeling, get an amidite for 
our pharmacia oligosynthesizer? Does anyone know about the stability and 
best emission properties of the various choices for the fluor in my case? 
	I know there are a lot of patent and $$$ games being played right
now..but compounds like XRITC etc have been around and are relatively
cheap compared to the [...] dyes.  If anyone has had experience with this
kind of chemistry and can offer a naive graduate student some advice for
the quickest and cheapest way to go, I would be very grateful (I don't mind
if I have to brush the dust off of my old text books and get into some
organic chemistry...). 

						Any Words from the Wise?
						Daniel J McGoldrick
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UC Davis - Genetics Graduate Group
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