Structure and Thermodynamics of Aegis Nucleotides P and Z in DNA

Abstract

Artificially expanded genetic information systems (AEGIS) enhance synthetic biology and in vitro primers, probes, and sensors. DNA/RNA design requires the prediction of secondary structures including the expanded alphabet nucleotides. This requires nearest-neighbor thermodynamics analogous to those used for DNA and RNA as well as at least a qualitative understanding of the structure and stability of mismatches. Absorbance melting experiments are presented on oligonucleotides containing P:Z base pairs and P:C, P:T, Z:G, and Z:A mismatches, providing ΔΔH°, ΔΔS°, and ΔΔG°37 values for the modified base pairs. P:Z forms a slightly more stable base pair than G:C, primarily due to entropic stabilization, and the G:Z mismatch is significantly more stable than G:T. Wobble geometries are proposed for the G:Z and P:C mismatches. This work demonstrates that substitution of P for G and Z for T can be a useful tool for the control of the relative thermodynamic stabilities of representative designed secondary structures.