Sequence-specific DNA strand cleavage by 111In-labeled peptide nucleic acids

Peptide nucleic acids (PNAs) bind tightly and sequence-specifically to single- and double-stranded nucleic acids, and are hence of interest in the design of gene-targeted radiotherapeutics that could deliver the radiodamage to designated DNA and/or RNA sites. As a first step towards this goal, we developed a procedure for incorporation of Auger electron-emitting radionuclide (indium-111) into PNA oligomers and studied the efficiency of PNA-directed cleavage of single-stranded DNA targets. Accordingly, diethylene triamine penta-acetic acid (DTPA) was conjugated to the lysine-appended mixed-base PNAs and sequence-homologous DNA oligomer with a proper linker for comparative studies. By chelation of PNA-DTPA and DNA-DTPA conjugates with ¹¹¹In³⁺ in acidic aqueous solutions, ¹¹¹In-labeled PNA and DNA oligomers were obtained. Targeting of single-stranded DNA with PNA-DTPA-[¹¹¹In] conjugates yielded highly localized DNA strand cleavage; the distribution of breaks along the target DNA strand has two maxima corresponding to both termini of PNA oligomer. After 10–14 days, the overall yield of breaks thus generated within the PNA-targeted DNA by ¹¹¹In decay was 5–7% versus 2% in the case of control oligonucleotide DNA-DTPA-[¹¹¹In]. The estimated yield of DNA strand breaks per nuclear decay is ~0.1 for the PNA-directed delivery of ¹¹¹In, which is three times more than for the DNA-directed delivery of this radionuclide. This in vitro study shows that ¹¹¹In-labeled PNAs are much more effective than radiolabeled DNA oligonucleotides for site-specific damaging of DNA targets. Accordingly, we believe that PNA oligomers are promising radionuclide delivery tools for future antisense/antigene radiotherapy trials.