Krishnan Rajagopal, Oh Dennis H
Department of Dermatology, University of California at San Francisco, San Francisco, CA 94121, USA.
J Nucleic Acids. 2010 Jul 25;2010:523498. doi: 10.4061/2010/523498.
Triplex-forming oligonucleotides (TFOs) with both DNA and 2'-O-methyl RNA backbones can direct psoralen photoadducts to specific DNA sequences. However, the functional consequences of these differing structures on psoralen photoreactivity are unknown. We designed TFO sequences with DNA and 2'-O-methyl RNA backbones conjugated to psoralen by 2-carbon linkers and examined their ability to bind and target damage to model DNA duplexes corresponding to sequences within the human HPRT gene. While TFO binding affinity was not dramatically affected by the type of backbone, psoralen photoreactivity was completely abrogated by the 2'-O-methyl RNA backbone. Photoreactivity was restored when the psoralen was conjugated to the RNA TFO via a 6-carbon linker. In contrast to the B-form DNA of triplexes formed by DNA TFOs, the CD spectra of triplexes formed with 2'-O-methyl RNA TFOs exhibited features of A-form DNA. These results indicate that 2'-O-methyl RNA TFOs induce a partial B-to-A transition in their target DNA sequences which may impair the photoreactivity of a conjugated psoralen and suggest that optimal design of TFOs to target DNA damage may require a balance between binding ability and drug reactivity.
具有DNA和2'-O-甲基RNA骨架的三链形成寡核苷酸（TFO）可将补骨脂素光加合物导向特定的DNA序列。然而，这些不同结构对补骨脂素光反应性的功能影响尚不清楚。我们设计了通过2-碳连接子与补骨脂素共轭的具有DNA和2'-O-甲基RNA骨架的TFO序列，并检测了它们结合和靶向损伤对应于人类HPRT基因内序列的模型DNA双链体的能力。虽然TFO的结合亲和力不受骨架类型的显著影响，但2'-O-甲基RNA骨架完全消除了补骨脂素的光反应性。当补骨脂素通过6-碳连接子与RNA TFO共轭时，光反应性得以恢复。与由DNA TFO形成的三链体的B型DNA不同，由2'-O-甲基RNA TFO形成的三链体的圆二色光谱呈现出A型DNA的特征。这些结果表明，2'-O-甲基RNA TFO在其靶DNA序列中诱导了部分B到A的转变，这可能会损害共轭补骨脂素的光反应性，并表明靶向DNA损伤的TFO的优化设计可能需要在结合能力和药物反应性之间取得平衡。
