Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. In geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T–A and U–A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.

通过三螺旋形成肽核酸 (PNA) 对双链 DNA 和非编码 RNA 的序列特异性靶向在治疗、诊断和纳米技术领域引起了相当大的关注。E-碱基（3-oxo-2,3-dihydropyridazine）通过侧链连接分子连接到 PNA Hoogsteen 链的聚酰胺主链上，通常用于胸腺嘧啶 4-oxo 基团的氢键识别和大沟中的尿嘧啶核酸碱基。我们报告了量子化学计算方法的应用，结合源自同型嘧啶 PNA·DNA-PNA 异源三链体实验结构的空间限制，研究接头灵活性对 E 碱基与胸腺嘧啶结合相互作用的影响和几何优化模型系统中的尿嘧啶碱基。在包含 β-丙氨酸接头的模型系统 (J Am Chem Soc 119:11116, 1997) 中，N2 E-碱基原子和目标嘧啶碱基 4-氧代基团之间的氢键形成被发现会导致显着的内部应变能和潜在的破坏低聚环境中站内芳香碱基堆积相互作用的研究。在包含 3-反式烯烃接头 (Bioorg Med Chem Lett 14:1551, 2004) 中，E-碱从目标嘧啶碱中脱离出来进入溶剂中。这些发现与 T-A 和 U-A 反转位点杂交实验中的量热测量结果一致。相比之下，对新型 2-顺式烯烃接头设计的计算表明，它可以允许与胸腺嘧啶 4-氧代基团同时进行 E-碱基氢键合，对胸腺嘧啶 5-甲基基团进行规避和溶剂筛选，并维持三链体内站立基础堆叠交互。