Facile synthesis of advanced photodynamic molecular beacon architectures

Nucleic acid photodynamic molecular beacons (PMBs) are a class of activatable photosensitizers that increase singlet oxygen generation upon binding a specific target sequence. Normally, PMBs are functionalized with multiple solution-phase labeling and purification steps. Here, we make use of a flexible solid-phase approach for completely automated synthesis of PMBs. This enabled the creation of a new type of molecular beacon that uses a linear superquencher architecture. The 3′ terminus was labeled with a photosensitizer by generating pyropheophorbide-labeled solid-phase support. The 5′ terminus was labeled with up to three consecutive additions of a dark quencher phosphoramidite. These photosensitizing and quenching moieties were stable in the harsh DNA synthesis environment and their hydrophobicity facilitated PMB purification by HPLC. Linear superquenchers exhibited highly efficient quenching. This fully automated synthesis method simplifies not only the synthesis and purification of PMBs, but also the creation of new activatable photosensitizer designs.