troubles with PCR

[Ari Kahn]

I am studying genetic diversity in wild rice by looking at intronic 
regions between tandemly repeated nrDNA.  Using PCR, one species 
(Zizania aquaticus) amplifies readily, another species (Zizania 
pelustris) amplifies sometimes, and the last species (texana) I can 
not get to amplify.
	I figure since all my reaction conditions are the same between each 
species that my problem with amplification lies in my DNA samples.  
So, assuming this, I ran out my stock and dilution samples on a gel 
to visualize them.  I noticed two things:  One is that the molecular 
weight of the samples differed; i.e. pelustris had the highest 
molecular weight DNA (a tight band on top), followed by aquaticus 
(it was a continuous streak), and then texana had the lowest (with 
most of the streak towards the bottom).  Two is that aquaticus had 
very little tRNA visible, while in pelustris and aquaticus the tRNA 
was obvious.
	I think the reason I¹m not able to amplify texana is that either 
the RNA is interfering with my reactions or that my DNA for texana 
is too low molecular weight.  Does this seem logical or are there 
other considerations I¹m not taking into account?

Ari Kahn
ak01706 at swt.edu