Effect of target structure on cross-linking by psoralen-derivatized oligonucleoside methylphosphonates

Melting experiments on psoralen-derivatized oligonucleoside methylphosphonates with a random coil or a hairpin in solution reveal that the binding and cross-linking reactions are affected by target structure and sequence. The oligomer binding site position in the target RNA and the nature of the oligomer backbone enhance the binding of oligonucleotides containing phosphodiester or phosphorothiate internucleotide linkages to RNA-hairpins.