No ssDNA-reporter cleavage in Cas12a collateral cleavage assay- what are possible causes
I am performing Cas12a collateral‑cleavage experiments using a 39 bp unmodified DNA reporter probe (no fluorophore labels). After incubating Cas12a with crRNA, reactions were separated by PAGE gel and stained with CelRed. I notice that the probe band in my experimental lane is even slightly darker than that of the negative‑control lane. Does this indicate no cleavage has occurred? Could anyone help interpret my PAGE gel results? PS:my crRNAs were synthesized by in-vitro T7 transcription and purified using column-based RNA purification kits.
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