Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada.
J Am Chem Soc. 2011 Mar 30;133(12):4518-26. doi: 10.1021/ja110495c. Epub 2011 Mar 3.
Oligodeoxyribonucleotides (ODN) with repeats of the human telomeric sequence can adopt different tetrahelical conformations that exhibit similar energetic parameters. We studied the volumetric properties of the folded and unfolded states of an ODN with four repeats of the human telomeric sequence, d[A(GGGTTA)(3)GGG], by combining pressure-perturbation calorimetry (PPC), vibrating tube densimetry, ultrasonic velocimetry, and UV melting under high pressure. We carried out our volumetric measurements in aqueous buffers at pH 7 containing 20, 50, and 100 mM NaCl. All of the methods employed yielded volumetric parameters that were in excellent agreement. The molar volume changes, ΔV, of the conformational transition leading to formation of the folded state are large and positive. At 50 mM NaCl, the average transition volume, ΔV(tr), obtained from all the methods is 56.4 ± 3.5 cm(3) mol(-1) at the transition temperature of 47 °C, with ΔV(tr) decreasing with an increase in temperature. We carried out a molecular dynamics simulation of the change in the intrinsic geometric parameters of the ODN accompanying quadruplex formation. On the basis of the experimental and computational results, the folding transition of the ODN is accompanied by a release of 103 ± 44 water molecules from its hydration shell to the bulk. This number corresponds to ~18% of the net hydration of the coil conformation.
寡脱氧核苷酸（ODN）具有人类端粒序列的重复，可以采用不同的四螺旋构象，这些构象表现出相似的能量参数。我们通过结合压力微扰量热法（PPC）、振动管密度计、超声速度计和高压下的 UV 熔融，研究了具有四个人类端粒序列重复的 ODN（d[A（GGGTTA）（3）GGG]）折叠和展开状态的体积性质。我们在 pH 7 的含有 20、50 和 100 mM NaCl 的水性缓冲液中进行了体积测量。所有采用的方法都产生了体积参数，这些参数非常吻合。导致折叠状态形成的构象转变的摩尔体积变化，ΔV，很大且为正值。在 50 mM NaCl 下，从所有方法获得的平均转变体积ΔV（tr）在 47°C 的转变温度下为 56.4±3.5 cm(3)mol(-1)，随着温度的升高而减小。我们对 ODN 伴随四链体形成的固有几何参数变化进行了分子动力学模拟。根据实验和计算结果，ODN 的折叠转变伴随着从其水合壳释放 103±44 个水分子到主体。这个数字对应于螺旋构象的净水合作用的约 18%。
