Solution structure of a truncated anti-MUC1 DNA aptamer determined by mesoscale modeling and NMR
Solution structure of a truncated anti-MUC1 DNA aptamer determined by mesoscale modeling and NMR
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DOI：
10.1111/j.1742-4658.2011.08440.x
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发表时间：
2012-02-01
期刊：
影响因子：
5.4
通讯作者：
du Penhoat, Catherine Herve
中科院分区：
文献类型：
--
作者：
Baouendi, Meriem;Cognet, Jean A. H.;du Penhoat, Catherine Herve
粘蛋白1是上皮性癌症早期诊断的公认靶点。利用足迹实验鉴定了与可变数目串联重复粘蛋白1肽结合的S1.3/S2.2 DNA适体的核苷酸。这些结合核苷酸大多数位于总适体的25个核苷酸可变区。截断的和总适配体在过冷水中的质子和二维核磁共振光谱显示了共同的氢键网络，并指出了该25-mer序列单独或嵌入在总适配体中的类似二级结构。核磁共振滴定实验证实TTT三环结构是主要的结合位点，并表明截断的适体在与可变数目串联重复肽相互作用时，其初始结构是保守的。核磁共振化学位移数据的热依赖性表明，碱基配对的核苷酸在47 +/- 4℃时协同熔融。采用新的中尺度分子模型、分子动力学和核磁共振波谱研究相结合的方法确定了25-mer寡核苷酸的结构。它包含三个沃森-克里克对，三个连续的错偶和四个沃森-克里克对，由TTT三环motif覆盖。三维模型结构（PDB）和生物聚合物链弹性分子模型分别符合核磁共振和长无约束分子动力学（10 ns）。
Mucin 1 is a well-established target for the early diagnosis of epithelial cancers. The nucleotides of the S1.3/S2.2 DNA aptamer involved in binding to variable number tandem repeat mucin 1 peptides have been identified using footprinting experiments. The majority of these binding nucleotides are located in the 25-nucleotide variable region of the total aptamer. Imino proton and 2D NMR spectra of truncated and total aptamers in supercooled water reveal common hydrogen-bonding networks and point to a similar secondary structure for this 25-mer sequence alone or embedded within the total aptamer. NMR titration experiments confirm that the TTT triloop structure is the primary binding site and show that the initial structure of the truncated aptamers is conserved upon interaction with variable number tandem repeat peptides. The thermal dependence of the NMR chemical shift data shows that the base-paired nucleotides melt cooperatively at 47 +/- 4 degrees C. The structure of the 25-mer oligonucleotide was determined using a new combined mesoscale molecular modeling, molecular dynamics and NMR spectroscopy investigation. It contains three WatsonCrick pairs, three consecutive mispairs and four WatsonCrick pairs capped by a TTT triloop motif. The 3D model structures (PDB ) and biopolymer chain elasticity molecular models are consistent with both NMR and long unconstrained molecular dynamics (10 ns) in explicit water, respectively.