Effect of Target Structure on Cross-Linking by Psoralen-Derivatized Oligonucleoside Methylphosphonates

A series of psoralen-derivatized oligodeoxyribonucleoside methylphosphonates were examined for their abilities to cross-link to DNA and RNA oligonucleotide targets. These targets were designed to have either a random coil or a hairpin structure in solution. The methylphosphonate oligomers cross-linked with approximately the same rates to the random coil DNA and RNA targets, although the extent of cross-linking to the DNA target was higher than that to the RNA target. For a given methylphosphonate sequence, cross-linking decreased as the temperature increased, and this behavior paralleled the interaction of the oligomer with the target as determined by ultraviolet melting experiments. The oligomers also cross-linked efficiently with the DNA hairpin target, but little or no cross-linking was observed with the RNA hairpin. In the case of these hairpin targets, the extent of cross-linking was dependent upon the location of the oligomer binding site relative to the stem and loop regions of the hairpin. The lack of reactivity with the RNA hairpin may be due to the high stability of the stem of this target versus that in the DNA target and the relatively lower efficiency of binding of the methylphosphonates to RNA versus DNA targets. The sequences of the oligomers are complementary to vesicular stomatitis virus M-protein mRNA. One of the oligomers was tested, and was found to cross-link at 20 °C to VSV N-mRNA to approximately the same extent as observed for cross-linking with the random coil RNA target, suggesting that the mRNA binding site for the oligomer most likely is in a somewhat open conformation. The results of our experiments suggest that target structure and sequence can have a significant influence on binding/ cross-linking reactions of psoralen-derivatized oligonucleoside methylphosphonates and that these parameters will most likely influence binding/cross-linking of these oligomers to cellular RNA targets such as mRNA.