Effect of mismatches on hybridization of PNAs containing universal bases

CHED 824

Andrika Cooper, Mahesh K Yarlagadda, and Stephen A. Woski, swoski@bama.ua.edu. Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, AL 35487
Universal bases pair equally well with each of the four canonical DNA bases on the complementary strand. Dimethylaminonaphthalimide (DANI) has shown promise as a fluorescent promiscuous residue in peptide nucleic acids (PNAs). One question regarding the utility of such bases in PNA probes is the effect they may have on mismatch discrimination. The stabilities of PNA-DNA duplexes containing both a DANI residue and a mismatch will be presented. The role of location of the mismatch will also be discussed.