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Hi everyone,
this is the main discussion space for BOMB protocol #4.4 BOMB Nucleotide removal using silica-coated MNPs
Here you can post all your questions and feedback!To whom is interested in RNA clean-ups: We also tried to purify small RNAs (gRNAs and tRNAs) with this protocol. Even though the respective molecules are about 70-100 nts, the yield for these was below 40% with the conditions used in #4.4. However, we’re confident that with a little optimization that issue could be resolved.
Hi,
have you ever tried to use the nucleotide removal protocol to cleanup sequencing reactions? There some commercial kits utilizing magnetic beads for this purpose and I was wondering if we could be able to deal with as well in the BOMB system
Best – Gosia
Just so you know that someone has seen your question. No, unfortunately I have never tried this. But, obviously the 4.4 Protocol has been tried and tested by the team before we released it.
I have to admit that I do not fully understand your question.
Maybe I am just missing the point (likely) but what you want to achieve is to remove unused NTPs after Sanger sequencing? This should work perfectly well with this protocol.
You could also just try the #4.2_BOMB_clean-up_size_exclusion_carboxyl protocol.
This I have used extensively as we currently perform PBAT on a near daily basis, which inevitably produces a lot of very short fragments as well as surplus dNTPS during the subsequent PCR. All of which have to be removed for the Low Coverage Whole Genome Sequencing we perform as the final step.
Combined with a ladder and some adjustment this PEG cleanup (#4.2) allows for incredibly easy exclusion of too short fragments.
Cheers
Tim M
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