Improved DNA Primer/Probe/Aptamer Structure Design Pipeline

In September 2023, the ACS Synthetic Biology journal published a research article by T.M. Pham, T. Miffin, H.Y. Sun, K.K. Sharp, X. Wang, M.Y. Zhu, S. Hoshika, R.J. Peterson, S.A. Benner, J.D. Kahn, and D.H. Mathews showing that DNA secondary structure simulations are improved by extending the base pairing alphabet beyond A?T and G?C to include so-called "P" and "Z" nucleotides. Prior work established that P and Z prefer pairing with each other above all single mismatches, except that G?Z pairs are roughly as stable as A?T pairs. In this work, 47 optical melting experiments were used and the team found that G?Z pairs have stability comparable to that of A?T pairs and should, therefore, be included as base pairs in structure prediction and design algorithms.

In addition, the research team imputed the set of loop, terminal mismatch, and dangling end parameters to include the P and Z nucleotides. Using this new, improved pipeline to solve the Eterna design challenge, the team solved 99 of the 100 design problems. This work provides a new pipeline for including expanded alphabet nucleotides in prediction and design workflows.

Raymond J. Peterson, PhD

CEO, DNA Analytics