Optimizing Stem Length To Improve Ligand Selectivity in a Structure-Switching Cocaine-Binding Aptamer,ACS Sensors

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Optimizing Stem Length To Improve Ligand Selectivity in a Structure-Switching Cocaine-Binding Aptamer
ACS Sensors ( IF 8.2 ) Pub Date : 2017-10-02 00:00:00 , DOI: 10.1021/acssensors.7b00619
Miguel A. D. Neves ₁ , Aron A. Shoara ₁ , Oren Reinstein ₁ , Okty Abbasi Borhani ₁ , Taylor R. Martin ₁ , Philip E. Johnson ₁

Affiliation

Understanding how aptamer structure and function are related is crucial in the design and development of aptamer-based biosensors. We have analyzed a series of cocaine-binding aptamers with different lengths of their stem 1 in order to understand the role that this stem plays in the ligand-induced structure-switching binding mechanism utilized in many of the sensor applications of this aptamer. In the cocaine-binding aptamer, the length of stem 1 controls whether the structure-switching binding mechanism for this aptamer occurs or not. We varied the length of stem 1 from being one to seven base pairs long and found that the structural transition from unfolded to folded in the unbound aptamer is when the aptamer elongates from 3 to 4 base pairs in stem 1. We then used this knowledge to achieve new binding selectivity of this aptamer for quinine over cocaine by using an aptamer with a stem 1 two base pairs long. This selectivity is achieved by means of the greater affinity quinine has for the aptamer compared with cocaine. Quinine provides enough free energy to both fold and bind the 2-base pair-long aptamer while cocaine does not. This tuning of binding selectivity of an aptamer by reducing its stability is likely a general mechanism that could be used to tune aptamer specificity for tighter binding ligands.

中文翻译：

优化茎长以提高结构转换可卡因结合适体中的配体选择性

在基于适体的生物传感器的设计和开发中，了解适体的结构和功能之间的关系至关重要。我们分析了一系列具有不同长度茎1的可卡因结合适体，以了解该茎在该适体的许多传感器应用中利用的配体诱导的结构转换结合机制中所起的作用。在可卡因结合适体中，茎1的长度控制是否发生针对该适体的结构转换结合机制。我们将茎1的长度从1个碱基对改变为7个碱基对，发现在未结合的适体中，结构从未折叠到折叠的转变是当适体在茎1中从3个碱基对延长到4个碱基对时。然后，我们通过使用具有两个碱基对长的茎1的适体，利用该知识来实现该适体对奎宁对可卡因的新结合选择性。通过与可卡因相比，奎宁对适体具有更高的亲和力，可以实现这种选择性。奎宁提供足够的自由能来折叠并结合2个碱基对的适体，而可卡因则不能。通过降低适体的稳定性来调节适体的结合选择性可能是可用于调节对更紧密结合配体的适体特异性的一般机制。

更新日期：2017-10-02

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