Identification of unknown bacteria isolate using molecular techniques - (Dec/09/2007 )
I have an unknown isolate and I wish to identify it using molecular biological techinques. After extracting the plasmid, I don't know which restriction enzyme to use since REs are specific for certain bacteria only.
Say, if I'm able to ligate the fragment of plasmid I want and then run PCR, what's next? Extracting the bands from the gel? Even doing the PCR needs a specific primers.
See here: http://openwetware.org/wiki/Bacterial_species_identification
for a reference list. Your bacteria may not even have a plasmid; you want to extract the genomic DNA and examine a highly conserved gene. Normally the 16S rDNA gene is chosen, and essentially every species has had its 16S region sequenced, so finding a close match is quite straightforward.