Are they any methods of purifying sub 100 base pair ssDNA sequences directly from gel electrophoresis?

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Rajesh Dev Sarkar

Better to use Acrylamide gels.

You can have a look at this earlier discussion-

https://www.researchgate.net/post/good_protocol_for_purifying_single_strand_DNA_through_gel_electrophoresis/amp

António Maximiano Fernandes

Yes is possible. But 100bp is to small and special care should be taken. Long and forced centrifugation may lost your dna thorough filter