Gene targeting by triplex-forming oligonucleotides (TFOs) 1 has proven useful for gene modulation in vivo. Photoreactive molecules have been conjugated to TFOs to direct sequence-specific damage in double-stranded DNA. However, the photoproducts are often repaired efficiently in cells. This limitation has led to the search for sequence-specific photoreactive reagents that can produce more genotoxic lesions. Here we demonstrate that photoactivated pyrene-conjugated TFOs (pyr-TFOs) induce DNA strand breaks near the pyrene moiety with remarkably high efficiency, and also produce covalent pyrene-DNA adducts. Free radical scavenging experiments demonstrated a role for singlet oxygen activated by the singlet-excited state of pyrene in the mechanism of pyr-TFO-induced DNA damage. In cultured mammalian cells, the effect of photoactivated pyr-TFO-directed DNA damage was to induce mutations, in the form of deletions, ~7-fold over background levels, at the targeted site. Thus, pyr-TFOs represent a potentially powerful new tool for directing DNA strand breaks to specific chromosomal locations for biotechnological and potential clinical applications.Triplex-forming oligonucleotides (TFOs) ‡ have been employed to modulate gene structure and function, both in vitro and in vivo. When conjugated to DNA damaging agents, TFOs can induce site-directed DNA damage resulting in enhanced mutagenesis and recombination [reviewed in (1-8)]. Reactive molecules that have been conjugated to TFOs include, but are not limited to, 2-amino-6-vinylpurine, haloacetyl amide, aryl nitrogen mustard, N 4 ,N 4 -etheno-5-methyldeoxycytidine, and various psoralen derivatives. All of these induce sitespecific cross-linking and/or alkylation in double-stranded DNA (dsDNA) (9-15). Psoralenlinked TFOs (pso-TFOs), which can induce covalent monoadducts on one strand or cross-links with both strands of duplex DNA with high efficiency and sequence specificity, are the most studied of the photoreactive TFOs. Pso-TFOs can yield site-specific DNA damage with high efficiency and have been used to introduce mutations and inactivate target genes. However, the existence of cellular mechanisms for repairing the pso-TFO photoproducts without introduction of sequence errors has limited their utility. † Funding was provided in part from National Institutes of Health (CA93729 to K.M.V.) and National Institute of Environmental Health Sciences (ES007784). 1 Abbreviations: Aprt, adenine phosphoribosyl transferase; DMF, dimethylformamide; DSB, double-strand break; dsDNA, doublestranded DNA; EMSA, electrophoretic mobility shift assay; HMWC, high molecular weight complex; PAH, polycyclic aromatic hydrocarbon; pso-, psoralen; pyr-, pyrene; strand breaks, SBs; TFO, triplex-forming oligonucleotide.
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NIH-PA Author ManuscriptRecent efforts by several groups have improved the binding affinity and sequence specificity of TFOs in vivo. For example, Puri and colleagues found that 2'-O-aminoethyl (2'-AE) ribose substitutions within p...