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首页> 外文期刊>The journal of physical chemistry, B. Condensed matter, materials, surfaces, interfaces & biophysical >Conformational Dynamics of an ATP-Binding DNA Aptamer: A Single-Molecule Study
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Conformational Dynamics of an ATP-Binding DNA Aptamer: A Single-Molecule Study

机译：ATP结合DNA适体的构象动力学：单分子研究。

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摘要

Nucleic acid aptamers are single-stranded RNA or DNA molecules that bind to their targets with high specificity and affinity. Although their biomedical applications have been booming, it is still debatable whether an aptamer recognizes its target through "induced fit" or "conformational selection", a central question in molecular recognition. To address this question, an ATP-binding DNA aptamer was selected as a model system and the conformational properties of this aptamer with and without the presence of ATP were investigated by single-pair Forster resonance energy transfer (spFRET) spectroscopy. The single-molecule results indicate that the aptamer can fold into a double-stranded-like structure, similar to the ligand-bound conformation, even without the presence of ATP. The folded structure is thermally stable at high salt concentrations and becomes rather dynamic at low salt concentrations. Although in the latter condition, the aptamer prefers unfolded structures, it can occasionally migrate to the folded conformation for a short time before being unfolded again. The binding of ATP to the aptamer stabilizes the folded structure, which populates the ligand-bound state of the aptamer, thus shifting the conformational equilibrium. Collectively, our data support that the ATP-binding DNA aptamer recognizes ATP ligand through "conformational selection".
机译：核酸适体是单链RNA或DNA分子，它们以高特异性和亲和力结合其靶标。尽管它们的生物医学应用正在蓬勃发展，但适体是否通过“诱导的契合”或“构象选择”识别其靶标仍是有争议的，这是分子识别的核心问题。为了解决这个问题，选择了一个ATP结合DNA适体作为模型系统，并通过单对Forster共振能量转移（spFRET）光谱研究了有和没有ATP时该适体的构象性质。单分子结果表明，即使不存在ATP，适体也可以折叠成双链样结构，类似于配体结合的构象。折叠的结构在高盐浓度下是热稳定的，而在低盐浓度下变得相当动态。尽管在后一种情况下，适体更喜欢未折叠的结构，但它有时偶尔会迁移到折叠的构象，然后再再次展开。 ATP与适体的结合稳定了折叠结构，该结构构成了适体的配体结合状态，从而改变了构象平衡。总体而言，我们的数据支持ATP结合DNA适体通过“构象选择”识别ATP配体。

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