ABSTRACT The aptamer-target binding affinity can be influenced by some environmental parameters, e.g. temperature and molecular crowding agents. Molecular dynamics (MD) simulation is a potent approach to highlight the effect of such parameters. In this study, we represent an MD simulation investigation to clarify the influence of temperature and molecular crowding on the sensitivity of T30695 aptamer toward Pb2+. The binding Gibbs energies (ΔGbind) are calculated for the aptamer-Pb2+ complex at the different temperatures, clarifying that its greatest value is at 37°C. Hence, the aptamer possesses the highest specificity toward Pb2+ at this temperature. The MD simulation results of the crowding effect, imitated by ethanol, proves that the most aptamer sensitivity toward Pb2+ is in the solution with 5% v/v concentration of ethanol. The aptamer specificity is studied under the MD-introduced optimal conditions by a colorimetric approach. The detection limits of 192 and 83.61 pM are obtained at 27°C and 37°C, respectively. They are computed 192 and 148 pM in the aqueous and ethanol solutions, respectively. The experimental results are in agreement with the MD ones, proving success of MD simulation to specify the environmental conditions in which the sensitivity of the aptamer is the greatest toward its target.

中文翻译：

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温度和分子拥挤对 T30695 适体对 Pb2+ 离子敏感性的影响：联合分子动力学模拟和实验研究

摘要适体-靶标结合亲和力会受到一些环境参数的影响，例如温度和分子拥挤因子。分子动力学 (MD) 模拟是突出此类参数影响的有效方法。在这项研究中，我们代表了一项 MD 模拟研究，以阐明温度和分子拥挤对 T30695 适体对 Pb2+ 的敏感性的影响。计算适体-Pb2+ 复合物在不同温度下的结合吉布斯能 (ΔGbind)，表明其最大值是在 37°C。因此，适体在该温度下对 Pb2+ 具有最高的特异性。由乙醇模拟的拥挤效应的 MD 模拟结果证明，适配体对 Pb2+ 的敏感性最高的是在乙醇浓度为 5% v/v 的溶液中。通过比色法在 MD 引入的最佳条件下研究适体特异性。在 27°C 和 37°C 下分别获得 192 和 83.61 pM 的检测限。它们在水溶液和乙醇溶液中分别计算为 192 和 148 pM。实验结果与 MD 一致，证明 MD 模拟成功指定了适体对其目标灵敏度最大的环境条件。