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So I have been studying an E. coli protein. As the first step I purified it in a pretty standard way - overexpressed it in BL21 DE3 cells and placed it in an ion exchange column, followed by size exclusion chromatography. Interestingly on the size exclusion column the protein fraction from IEX seperated into my protein of interest plus a very defined RNA species (which on a gel ran at ~500kDa). our university has a sequencing service that can accept DNA. Would anyone have suggestions as to how I can identify this I tried RTPCR for this protein using random hexamer primers but to no success.

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    $\begingroup$ Welcome to the Biology Stack Exchange. Please take the tour and visit the help center for more information on how this site works and what we do here. We probably need a few more details on your experiment - How did you identify it as RNA? How do you know the RT-PCR failed? Do you have access to a MinION device? $\endgroup$
    – bob1
    Mar 6 at 19:11

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