Target Alkylation of Single and Double Strand DNA by Peptide Nucleic Acids

Abstract

Quinone methides (QMs) generated in vivo can alkylate DNA and function as anti-cancer drugs. Delivery of QMs to target DNA is necessary to reduce the side effects caused by indiscriminate reaction. Previous, DNA was conjugated with a QM and was successfully used to deliver this QM to complementary DNA sequences. Peptide nucleic acids (PNAs) conjugates of QM are now being developed for in vivo application since PNA binds to its complementary DNA or RNA and PNA resists degradation by nucleases and proteases.

The PNA1-QMP1 conjugate is capable of alkylating more than 60% of a complementary ssDNA when added at nearly stoichiometric quantities. No alkylation was observed if non-complementary DNA was treated with the conjugate. PNA1-QMP1 can alkylate a non-complementary DNA only when both the PNA and DNA target bind to a template strand. When no target sequences were present in solution, QM can react with nucleophiles from PNA1 and generate PNA1-QM1 self adduct. ssDNA can be alkylated by PNA1-QM1 self adduct with a 40% yield. The self adduct can survive after an incubation for 7 days in aqueous solution and preserve half of its original ability to alkylate complementary DNA. The reversibility and stability of the self adduct suggest that it can be used in cells. ssRNA can also be recognized and modified by PNA conjugates with a similar yield as earlier demonstrated with ssDNA. A PNA1-QM1 self adduct may also function as a telomerase inhibitor by alkylating RNA within telomerase.

Polypyrimidine PNAs were prepared to bind to the major groove of duplex DNA selectively and expand the potential targets from single to double strand DNA. A cytosine-rich PNA recognized dsDNA and delivered an electron-rich QMP2 to its target sequences. The polypurine strand within a target dsDNA was alkylated at 37°C with a yield of 26%. PAN-QMP2 also showed strong selectivity toward its fully matched dsDNA over one base mismatch in the triplex recognition site. Successful delivery of a QMP to target single and double strand DNA by PNAs confirms that the use of PNA in vivo to target pre-selected sequences is feasible.