We need help.
We would like to use PCR amplification of rRNA genes to characterize rare bacteria in a sample where there are some very very dominant bacteria.
The problem is that we do not know what those rare bacteria are and would like to use "universal" rRNA PCR primers to amplify the rRNA genes from these organisms. Such universal primers will also amplify the rRNA genes from the dominant organisms.
If the rare organisms are, like, really rare, almost all the PCR products will be from the dominant organisms. We would like to obtain sequence data for the rRNA genes from the rare organisms without sequencing 1000s of the known rRNA genes from the dominant organism. How can we do this?
I know of attempts to block PCR amplification of specific DNAs and also attempts to digest away PCR products or bind ones to a column to get rid of them. But I do not know if any of these methods really work.
Anyone out there know methods that work to do this?
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