Do you have to use a restriction enzyme to relieve ITR secondary structures and increase target accessibility?

It is highly recommended and an important step in the protocol. ITR secondary structures reduce target accessibility and negatively affect quantification of ITR targets and non-ITR targets.
We recommend using the following HpaII restriction enzymes: Thermo Scientific™ HpaII (10 U/µL, cat. nos. ER0511, ER0512) or Invitrogen™ Anza™ 93 HpaII (cat. no. IVGN0936).

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