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Doxorubicin (Dox) is widely used for breast cancer treatment but causes serious side- effects including cardiotoxicity that may adversely impact patient lifespan even if treatment is successful. The present invention relates to selective conjugation of Dox to a single site in a DNA hairpin resulting in a highly stable complex that enables Dos to be used more effectively. Selective conjugation of Dox to G15 in the hairpin loop was verified using site-specific labeling with [2- 15N3-2'-deoxyguanosme in conjunction with [1 H-15NJ 2D NM R while 1:1 stoichiometry for the conjugate was validated by ESI-QTOF mass spectrometry and UV spectroscopy. Molecular modeling indicated covalently bound Dox also intercalated into the stem of the hairpin and stability studies demonstrated the resulting Dox-conjugated hairpin (DCH) complex had a half-life > 30 h, considerably longer than alternative covalent and non- covalent complexes. Secondary conjugation of DCH with folic acid (FA) resulted in increased internalization into breast cancer cells. The dual conjugate, DCH-FA, can be used tor safer and more effective chemotherapy with Dox and this conjugation strategy can be expanded to include additional anti-cancer drugs.

DNA decoys have been developed for the inhibition of transcriptional regulation of gene expression. However, the present methodology lacks the spatial and temporal control of gene expression that is commonly found in nature. Here, we report the application of photoremovable protecting groups on nucleobases of nuclear factor κB (NF-κB) DNA decoys to regulate NF-κB-driven transcription of secreted alkaline phosphatase using light as an external control element. The NF-κB family of proteins is comprised of important eukaryotic transcription factors that regulate a wide range of cellular processes and are involved in immune response, development, cellular growth, and cell death. Several diseases, including cancer, arthritis, chronic inflammation, asthma, neurodegenerative diseases, and heart disease, have been linked to constitutively active NF-κB. Through the direct incorporation of caging groups into an NF-κB decoy, we were able to disrupt DNA:DNA hybridization and inhibit the binding of the transcription factor to the DNA decoy until UV irradiation removed the caging groups and restored the activity of the oligonucleotide. Excellent light-switching behavior of transcriptional regulation was observed. This is the first example of a caged DNA decoy for the photochemical regulation of gene expression in mammalian cells and represents an important addition to the toolbox of light-controlled gene regulatory agents.

The naturally occurring nitroalkenes, including nitrolinoleic (NO2-LA) and nitrooleic (NO2-OA)1 acids, are implicated in the modulation of multiple signaling pathways resulting in several important bioactivities including vasodilation, inhibition of inflammation, and inhibition of platelet activation and function (1-4). In addition, these nitrated unsaturated fatty acids are among the most potent endogenous ligand activators of PPARγ—a nuclear receptor involved in the transcription of genes associated with carbohydrate and lipid homeostasis, cellular differentiation, and inflammation (5-8). The physiological importance of these nitroalkenes is indicated by their relative abundance in vivo with aggregate levels reported to be around 1-2 μM in normal human plasma and erythrocytes (9)—levels in excess of those necessary to significantly activate PPARγ-dependent transcription in vitro (10, 11). In order to understand how nitroalkene activities are regulated at the cellular level, we previously demonstrated that NO2-LA forms conjugates with glutathione, rapidly and non-enzymatically, under physiological conditions (12). These conjugates are efficiently effluxed by MRP1, a ubiquitous ATP-dependent glutathione conjugate transporter, and combined conjugation plus MRP1-mediated efflux profoundly attenuates PPARγ-dependent transcription activation in response to NO2-LA (12). Here we demonstrate that activation of PPARγ by NO2-OA is similarly affected by non-enzymatic conjugation and efflux. Moreover, we investigated whether expression of representative isozymes of the soluble forms of glutathione S-transferase (GST) would influence NO2-LA and NO2-OA bioactivities either by catalyzing their conjugation with glutathione or by an alternative mechanism. Indeed, we show that while expression of GSTA1-1, GSTM1a-1a, or GSTP1a-1a significantly attenuates the activation of PPARγ-dependent transcription by NO2-LA and NO2-OA, none of these isozymes, or GSTA4-4, is able to catalyze glutathione conjugation of the nitroalkenes. Rather, these GSTs appear to influence transcription via avid covalent and non-covalent interactions with the nitroalkenes and their glutathione conjugates thereby sequestering them from their nuclear target, PPARγ.