DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters

We show that in silico design of DNA
secondary
structures is improved by extending the base pairing alphabet beyond
A–T and G–C to include the pair between 2-amino-8-(1′-β-d-2′-deoxyribofuranosyl)-imidazo-[1,2-a]-1,3,5-triazin-(8H)-4-one and 6-amino-3-(1′-β-d-2′-deoxyribofuranosyl)-5-nitro-(1H)-pyridin-2-one, abbreviated as P and Z. To obtain the thermodynamic parameters needed to include P–Z
pairs in the designs, we performed 47 optical melting experiments
and combined the results with previous work to fit free energy and
enthalpy nearest neighbor folding parameters for P–Z pairs
and G–Z wobble pairs. We find 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. Additionally,
we extrapolated the set of loop, terminal mismatch, and dangling end
parameters to include the P and Z nucleotides. These parameters were
incorporated into the RNAstructure software package for secondary
structure prediction and analysis. Using the RNAstructure Design program,
we solved 99 of the 100 design problems posed by Eterna using the
ACGT alphabet or supplementing it with P–Z pairs. Extending
the alphabet reduced the propensity of sequences to fold into off-target
structures, as evaluated by the normalized ensemble defect (NED).
The NED values were improved relative to those from the Eterna example
solutions in 91 of 99 cases in which Eterna-player solutions were
provided. P–Z-containing designs had average NED values of
0.040, significantly below the 0.074 of standard-DNA-only designs,
and inclusion of the P–Z pairs decreased the time needed to
converge on a design. This work provides a sample pipeline for inclusion
of any expanded alphabet nucleotides into prediction and design workflows.