Team:UChile Biotec/Results
1. Sequences Obtention
To validate the utility of JAWS for generating aptazymes sequences from the DNAzyme HRP mimicking and an aptamer for any other molecule, the sequence of an aptamer for AMP was introduced into the program, with the purpose of contrasting the catalytic activity of this aptazyme to the catalytic activity of an aptazyme that has already been characterized and tested in the literature and also by our team last year (APTZ_AMP_P) [1].
The sequence which its free energy difference had the highest value among all of the sequences given by the software was chosen (first sequence of Annex 1, notebook), because this difference consists in the difference of energies between the inactive and active state, so it is the sequence that has the least probability to move from an inactive state to an active state arbitrarily, avoiding false positives.
In addition, since the software delivers sequences with two DNAzymes, one on each flank of the sequence and adjacent to the generated linkers (because the software was designed this way, see Heidelberg 2015 project for more information), the sequences chosen to synthesize and subsequently carry out the enzymatic tests were chosen as delivered by the program (raw) and truncated, with the DNAzyme of the 3 'flank excised based on the configuration of the aptazyme APTZ_AMP_P.
The same procedure was done for DNAzyme HRP mimicking and aptamers specific for saxitoxin (APT_STX) and oxadaic acid (APT_OX) described in the literature [2][3]. All the sequences extracted from the literature and the ones obtained with JAWS are described in Annex 1 (notebook)