Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan.
Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan.
Bioorg Med Chem. 2020 Apr 1;28(7):115350. doi: 10.1016/j.bmc.2020.115350. Epub 2020 Feb 6.
A triplex-forming oligonucleotide (TFO) can recognize the homopurine-homopyrimidine sequence in DNA duplexes and inhibit the transcription of targeted mRNAs. Recently, we reported that N-acetyl-2,7-diamino-1,8-naphthyridine (N), incorporated into a TFO, has high binding ability and base recognition selectivity for the pyrimidine bases in the purine-rich chain of the DNA duplex at pH 7.4. However, it was found in this study that the difference in the T values between the pyrimidine bases and purine bases decreased by more than 4 °C at pH 6.0-7.0. To improve the low base recognition selectivity of the TFO, we designed a new artificial base, Q, with a quinoline skeleton. The T values of the triplexes containing Q:T-A or Q:C-G were more than 13 °C higher than those of the triplexes containing Q:A-T or Q:G-C at pH 7.4. We also observed that under more acidic conditions (pH 6.0-7.0), the base recognition selectivity of Q in a triplex was higher than that of N, although the binding ability of Q in a triplex was similar to that of N. Additionally, we found that Q, incorporated into the TFO, could accurately recognize the C-G base pair in the hairpin DNA, similar to the C-G base pair.
三链形成寡核苷酸（TFO）可以识别 DNA 双链中的同嘌呤-同嘧啶序列，并抑制靶向 mRNA 的转录。最近，我们报道了 N-乙酰-2,7-二氨基-1,8-萘啶（N），整合到 TFO 中，在 pH 7.4 时对 DNA 双链中富含嘌呤链的嘧啶碱基具有高结合能力和碱基识别选择性。然而，在这项研究中发现，在 pH 6.0-7.0 时，嘧啶碱基和嘌呤碱基之间 T 值的差异降低了超过 4°C。为了提高 TFO 的低碱基识别选择性，我们设计了一种具有喹啉骨架的新型人工碱基 Q。在 pH 7.4 时，含有 Q:T-A 或 Q:C-G 的三聚体的 T 值比含有 Q:A-T 或 Q:G-C 的三聚体的 T 值高 13°C 以上。我们还观察到，在更酸性的条件下（pH 6.0-7.0），Q 在三聚体中的碱基识别选择性高于 N，尽管 Q 在三聚体中的结合能力与 N 相似。此外，我们发现整合到 TFO 中的 Q 可以准确识别发夹 DNA 中的 C-G 碱基对，类似于 C-G 碱基对。
