Effect of loop sequence and size on DNA aptamer stability
Effect of loop sequence and size on DNA aptamer stability
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DOI：
10.1021/bi9919044
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发表时间：
2000-02-15
期刊：
影响因子：
2.9
通讯作者：
Shafer, RH
中科院分区：
文献类型：
--
作者：
Smirnov, I;Shafer, RH
凝血酶适体是一种15聚体寡脱氧核糖核苷酸，其折叠成单分子四链体，由通过两个外部环和一个中心环连接的两个鸟嘌呤四联体的堆叠组成，并对凝血酶具有高亲和力。我们已经进行了系统的检查，在KCl中，凝血酶适体类似物的热力学稳定性含有序列修饰的一个或多个循环中，以及在四联体的数量。已经进行了UV熔解研究，以获得这些适体的相关热力学参数。用单分子变性的双态模型对这些数据进行van 't霍夫分析，给出了与实验观察的极好拟合。热力学分析表明，母体适体中的中心环序列对于稳定性是最佳的。在这个或其他循环中的修改可以影响Delta H度、Delta S度或两者。在S-末端添加单个G降低稳定性，而在3 '-末端添加G增加稳定性。凝血酶适体的差示扫描量热法实验表明，热容量的变化，而不是：通过UV测量检测，伴随着适体的展开。
The thrombin aptamer is a 15-mer oligodeoxyribonucleotide that: folds into a unimolecular quadruplex consisting of a stack of two guanine quartets connected by two external loops and one central loop and possesses a high affinity for thrombin. We have undertaken a systematic examination, in KCI, of the thermodynamic stability of thrombin aptamer analogues containing sequence modifications in one or more of the loops, as well as in the number of quartets. UV melting studies have been carried out to obtain the relevant thermodynamic parameters for these aptamers. van't Hoff analysis of these data, with a two-state model for unimolecular denaturation, gave excellent fits to the experimental observations, Thermodynamic analysis indicates that the central loop sequence in the parent aptamer is optimal for stability. Modifications in this or other loops can effect either Delta H degrees, Delta S degrees, or both. Addition of a single G at the S-end decreases stability while addition of a G at the 3'-end increases stability. Differential scanning calorimetry experiments on the thrombin aptamer reveal that a heat capacity change, not: detected by UV measurements, accompanies the unfolding of the aptamer.