Psoralens plus ultraviolet A (UVA) therapy are widely used in the treatment of psoriasis and other inflammatory skin diseases. Psoralens intercalate at 5′ TA 3′ sites and react with thymines upon exposure to UVA. With absorption of the first UVA photon, psoralens form monoadducts (MA), and subsequent exposures may convert furan-sided MA to interstrand crosslinks (XL). This ability to manipulate lesion formation makes psoralens attractive agents for studying DNA damage and repair and for potentially controlling the therapeutic response. Triplex-forming oligonucleotides (TFOs) offer a promising approach to target drugs such as psoralens to specific genes of interest in living cells. However the metabolic activities and electrostatic forces of the cell introduce a major obstacle to this interesting drug delivery system.
In order to overcome barriers to intracellular binding to DNA, TFOs have been extensively engineered. One strategy has been to utilize 2′-O
-methyl RNA which has been reported to significantly enhance the binding affinity relative to DNA-based TFOs [1
]. It has been suggested that the C3′-endo conformation of the ribose sugar is appropriate for triplex formation [6
] and that 2′-O
-methyl RNA enhances the TFO association rate without hindering the activity of a psoralen conjugated at the 5′ terminus [1
]. However, the C3′-endo conformation of an RNA TFO also introduces major structural changes in the major groove and in the helical periodicity of the target sequence [6
]. For example, in an intramolecular triplex formed by a 2′-O
-methyl RNA pyrimidine-motif TFO, the helical twist increased, and the helical axis was displaced in the purine-Hoogsteen pair, introducing a dominant A-like structure, when compared with the corresponding DNA TFO, where the dominant structure is B-form [6
]. In addition, an RNA third strand has also been reported to induce conformational changes in the sugars of the purine strand of duplex DNA, which resulted in a local B-to A-DNA transition [11
]. Partial B- to A-DNA transitions have also been observed in triplexes formed by 2′-O
-methyl RNA strands [13
]. These induced transitions may potentially alter the activity of TFO-conjugated drugs that interact with the DNA. In this work, we studied the effects of the 2′-O
-methyl RNA TFO modification on the photoreactivity of psoralens conjugated to them. We observed that relative to the corresponding DNA TFOs, 2′-O
-methyl TFOs can dramatically restrict psoralen reactivity in association with a B- to A-DNA transition in the target sequence.