Effect of terminal amino acids on the stability and specificity of PNA-DNA hybridisation

The effect of various charged or hydrophobic amino acids on the hybridisation of fully complementary and mismatch PNA-DNA duplexes was investigated via UV melting curve analysis. The results described here show that the thermal stability and binding specificity of PNA probes can be modified by conjugation to amino acids and these effects should be considered in experimental design when conjugating PNA sequences to solubility enhancing groups or cell transport peptides. Where stabilisation of a duplex is important, without there being a corresponding need for specific binding to fully complementary targets, the conjugation of multiple lysine residues to the C-terminus of PNA may be the best probe design. If, however, the key is to obtain maximum discrimination between fully complementary and mismatch targets, a replacement of glutamic acid for lysine as the routine solubility enhancing group is recommended.