Creating mismatched DNA duplex using NAB

This can be done using NAB which comes as a part of Ambertools. The strategy would be to create two Watson Crick duplexes such that one of them contains our desired 5'-3' strand and the other contains our 3'-5' strand. The next step would be to simply merge the two pdb files such that the new pdb file contains information about only two strands which we are interested in.

As an example let's try to make a DNA duplex containing one TG mismatched base pair i.e. two strands with the following sequence- 5'-GCTCATGACAGA-3' 3'-CGAGTGCTGTCT-5'

STEPS

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1. Load the following modules using