Tunable and Stable Triplex DNA Structure for Surface Plasmon Resonance Detection of UV-Induced DNA Damage

Ultraviolet (UV) irradiation can destroy hydrogen bonds, leading to DNA deformation or destruction. Triplex DNA is produced by combining Watson-Crick and Hoogsteen base pairing under certain conditions. The UV-induced damage of target DNA may influence the triplex DNA formation; thus, a simple and sensitive surface plasmon resonance (SPR) assay of the DNA damage process was proposed. The experimental conditions for forming the triplex DNA were explored, and the stability comparison between duplex and triplex DNA was performed. The triplex DNA possessed higher stability under acidic pH and sufficient Mg²⁺, and the sequence length could remarkably influence its stability. By derivatization of the triplex structure with two biotin tags, the incorporation of streptavidin resulted in amplified SPR signals. However, UV-induced damage of biotinylated target DNA attenuated the triplex DNA formation, and smaller SPR signals were attained. The SPR signals were inversely and linearly dependent on the UV irradiation doses that represented the photodamage levels in the range of 0.117-1.75 kJ/m², and the detection limit was estimated to be 0.039 kJ/m². Through the competitive assay, UV-induced damage of unbiotinylated target DNA can also be detected. The proposed method serves as a viable means for the detection of UV-induced DNA damage based on the triplex DNA structure.