Kinetics for Hybridization of Peptide Nucleic Acids (PNA) with DNA and RNA Studied with the BIAcore Technique

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Abstract
The binding of a mixed-sequence pentadecamer PNA (peptide nucleic acid) containing all four nucleobases to the fully complementary as well as various singly mismatched RNA and DNA oligonucleotides has been systematically investigated using thermal denaturation and BIAcore surface-interaction techniques. The rate constants for association (ka) and dissociation (kd) of the duplex formation as well as the thermal stability (melting temperature, Tm) of the duplexes have been determined. Upon binding to PNA tethered via a biotin-linker to streptavidin at the dextran/gold surface, DNA and RNA sequences containing single mismatches at various positions in the center resulted in increased dissociation and decreased association rate constants. Tm values for PNA•RNA duplexes are on average 4 °C higher than for PNA•DNA duplexes and follow quantitatively the same variation with mismatches as do the PNA•DNA duplexes. Also a faster ka and a slower kd are found for PNA•RNA duplexes compared to the PNA•DNA duplexes. An overall fair correlation between Tm, ka, and kd is found for a series of PNA•DNA and PNA•RNA duplexes although the determination of ka seemed to be prone to artifacts of the method and was not considered capable of providing absolute values representing the association rate constant in bulk solution.