KINETICS FOR HYBRIDIZATION OF PEPTIDE NUCLEIC-ACIDS (PNA) WITH DNA AND RNA STUDIED WITH THE BIACORE TECHNIQUE

The binding of a mixed-sequence pentadecamer PNA (peptide nucleic acid ) containing all four nucleobases to the fully complementary as well a s various singly mismatched RNA and DNA oligonucleotides has been syst ematically investigated using thermal denaturation and BIAcore surface -interaction techniques. The rate constants for association (k(a)) and dissociation (k(d)) of the duplex formation as well as the thermal st ability (melting temperature, T-m) of the duplexes have been determine d. Upon binding to PNA tethered via a biotin-linker to streptavidin at the dextran/gold surface, DNA and RNA sequences containing single mis matches at various positions in the center resulted in increased disso ciation and decreased association rate constants. T-m values for PNA.R NA duplexes are on average 4 degrees C higher than for PNA.DNA duplexe s and follow quantitatively the same variation with mismatches as do t he PNA.RNA duplexes. Also a faster k(a) and a slower k(d) are found fo r PNA.RNA duplexes compared to the PNA.DNA duplexes. An overall fair c orrelation between T-m, k(a), and k(d) is found for a series of PNA.DN A and PNA.RNA duplexes although the determination of k(a) seemed to be prone to artifacts of the method and was not considered capable of pr oviding absolute values representing the association rate constant in bulk solution.