DNA with Artificial Base Pairs

Abstract

The introduction of a single base pair with the electronically complementary base surrogates phenyl- (P) and pentafluorophenyl-deoxyriboside (F5) into DNA oligonucleotides leads to a strong decrease in duplex stability. Longer stretches with alternating P-F5 pairs can lead to duplexes with increased stability as compared to their counterparts with natural A-T base pairs. Optimization of the steric and electronic properties of the P-F5 pair by replacing the phenyl residue with naphthalene, anisole or thioanisole leads to an increase in stability. Complementary charge distribution thus represents a novel design principle for artificial DNA base pairs. These results also highlight the importance of favorable intrastrand stacking interactions in the thermodynamic stabilization of oligonucleotide duplexes. A combination with favorable interstrand stacking could lead to a set of orthogonal, non-hydrogen bonded base pairs. Such artificial pairing systems could be used in many ways. By gradually changing the composition of linearly stacked artificial bases interesting electronic, photophysical and magnetic properties could result. The quasi one-dimensional arrangement of charge transfer complexes might pave the way for applications of the nucleic acid scaffold in material science.