Folding of the thrombin aptamer into a G-quadruplex with Sr2+:: Stability, heat, and hydration
Folding of the thrombin aptamer into a G-quadruplex with Sr2+:: Stability, heat, and hydration
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DOI：
10.1021/ja010008o
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发表时间：
2001-11-07
影响因子：
15
通讯作者：
Marky, LA
中科院分区：
文献类型：
--
作者：
Kankia, BI;Marky, LA
DNA适体d（G（2）T（2）G（2）TGTG（2）T（2）G（2））在K+存在下呈分子内G-四链体结构。它对凝血酶的亲和力与抑制凝血酶催化的纤维蛋白凝块形成有关。在这项工作中，我们使用了光谱学，量热法，密度和超声技术的组合，以确定的光谱特性，热力学和水合作用的G-四链体与各种单价和二价金属离子的形成。阳离子-适体复合物的形成相对快速且高度可重复。它们的CD光谱和熔融曲线作为链浓度的函数的比较表明，K+，Rb+，NH 4+，Sr 2+，和Ba 2 +-形成分子内阳离子适配体复合物，其转变温度高于25 ℃。然而，阳离子Li+、Na+、Cs+、Mg 2+和Ca 2+在非常低的温度下形成较弱的络合物。这与离子半径在1.3-1.5埃范围内的金属离子很好地配合在络合物的两个G-四重态内，而其他阳离子不能的观察结果一致。Sr（2+）适体和K+-适体复合物的热力学解折叠曲线的比较表明，Sr（2+）-适体复合物更稳定，接近18 ℃，并且以8.3 kcal/mol的较低吸热热解折叠。这与Sr 2+和K+与适体结合的放热分别为-16.8 kcal/mol和-25.7 kcal/mol非常一致。此外，阳离子结合的体积和可压缩性参数显示主要由两个贡献引起的水合作用：阳离子和鸟嘌呤原子团的脱水和单链折叠成G-四链体结构后的水吸收。
It has been shown that the DNA aptamer d(G(2)T(2)G(2)TGTG(2)T(2)G(2)) adopts an intraniolecular G-quadruplex structure in the presence of K+. Its affinity for trombin has been associated with the inhibition of thrombin-catalyzed fibrin clot fort-nation. In this work, we used a combination of spectroscopy, calorimetry, density, and ultrasound techniques to determine the spectral characteristics, thermodynamics, and hydration effects for the formation of G-quadruplexes with a variety of monovalent and divalent metal ions. The formation of cation-aptamer complexes is relatively fast and highly reproducible. The comparison of their CD spectra and melting profiles as a function of strand concentration shows that K+, Rb+, NH4+, Sr2+, and Ba2+-form intramolecular cation-aptanter complexes with transition temperatures above 25 degreesC. However, the cations Li+, Na+, Cs+, Mg2+, and Ca2+ form weaker complexes at very low temperatures. This is consistent with the observation that metal ions with ionic radii in the range 1.3-1.5 Angstrom fit well within ' the two G-quartets of the complex, while the other cations cannot. The comparison of thermodynamic unfolding profiles of the Sr(2+)aptamer and K+-aptamer complexes shows that the Sr2+-aptamer complex is more stable, by similar to 18 degreesC, and unfolds with a lower endothermic heat of 8.3 kcal/mol. This is in excellent agreement with the exothermic heats of -16.8 kcal/mol and -25.7 kcal/mol for the binding of Sr2+ and K+ to the aptamer, respectively. Furthermore, volume and compressibility parameters of cation binding show hydration effects resulting mainly from two contributions: the dehydration of both cation and guanine atomic groups and water uptake upon the folding of a single-strand into a G- quadruplex structure.