Derivatives of dPMTO, dMTMO, and dTPT3 as efficient genetic alphabets for artificial DNA

The stability of natural DNA relies mainly on the hydrogen-bonding interactions between its nucleobases. However, recently, several hydrophobic nucleobases, such as dPTMO, dMTMO, and dTPT3, were synthesized to expand the genetic codes that do not make hydrogen-bonding base pair interactions in DNA. Although such bases were recognized by DNA polymerases during replication, the artificial DNA was found to be unstable and to contain intercalated bases. To make stable artificial DNA that can be recognized by DNA polymerases, dPTMO, dMTMO, and dTPT3 were modified to contain hydrophilic groups at their Watson-Crick faces. In doing so, 25 derivatives of dPTMO, 33 derivatives of dMTMO, and 31 derivatives of dTPT3 were generated that can form hydrogen-bonding interactions in DNA. Subsequently, base pair interactions between different derivatives of dPTMO and dTPT3 and between different derivatives of dMTMO and dTPT3 were studied to identify the most stable purine:pyrimidine base pairs. Interestingly, 16 base pairs are identified to be more stable than the three hydrogen-bonded canonical G:C pair, among which dPTMO-20:dTPT3-19, dPTMO-21:dTPT3-19, dMTMO-28:dTPT3-19, and dMTMO-29:dTPT3-19 were found to be highly stable, with binding energy lying between -22 and -23 kcal/mol. It is thus proposed that hybrid bases, such as dPTMO-20, dPTMO-21, dMTMO-28, dMTMO-29, and dTPT3-19, would serve as effective artificial bases to expand the genetic alphabet.

The ωB97X-D/6-31 + G* level of dispersion-corrected Density Functional Theory was employed to generate derivatives of dPTMO, dMTMO, and dTPT3 by modifying their Watson-Crick faces with various hydrogen-bond donors and acceptors, enabling them to form hydrogen-bonding interactions. Subsequently, 174 base pair structures were optimized at the same level of theory to identify the canonical G:C-like base pairs. All structures were optimized in the aqueous medium by employing the Integral Equation Formalism of the Polarized Continuum Model (IEFPCM) of the Self-Consistent Reaction Field (SCRF) theory. To get more accurate binding energies, the ωB97X-D/AUG-cc-pVDZ level of theory was used to compute the single-point energy values in the aqueous medium.