The tRNALeu (UAA) group I intron is found at a very specific insertion site and its presence at this location is apparently conserved across the Cyanobacteria (including plastids). For the amplification of tRNALeu (UAA) group I introns in Cyanobacteria, we have followed the instructions provided by Paulsrud and Lindblad (1998), partially reproduced below:
"Two primer pairs (outer and inner, respectively) were designed for specific amplification of cyanobacterial tRNALeu (UAA) introns by nested PCR. Both the specificity and the increased sensitivity obtained with nested PCR were necessary for good amplification from the biologically complex lichen samples containing only small amounts of cyanobiont cells. All primers contained a restriction site (lowercase letters) to facilitate cloning.
The outer primers were:
The inner primers were:
The primers were designed by Jeff Elhai, Department of Biology, University of Richmond, Richmond, Va."
O’Brien, H., Miadlikowska, J., and Lutzoni, F. 2005. Assessing host specialization in symbiotic Cyanobacteria associated with four closely related species of the lichen fungus Peltigera. European Journal of Phycology 40:363-378.
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Paulsrud, P., and Lindblad, P. 1998. Sequence variation of the tRNA(Leu) intron as a marker for genetic diversity and specificity of symbiotic cyanobacteria in some lichens. Applied & Environmental Microbiology 64: 310–315.