药物结合对DNA水合作用的影响：25℃下纺锤菌素与聚（dAdT）·聚（dAdT）、聚（dA）·聚（dT）双链体以及聚（dT）·聚（dA）·聚（dT）三链体结合的声学和密度测定表征

Influence of drug binding on DNA hydration: acoustic and densimetric characterizations of netropsin binding to the poly(dAdT).poly(dAdT) and poly(dA).poly(dT) duplexes and the poly(dT).poly(dA).poly(dT) triplex at 25 degrees C.

作者信息

Chalikian T V, Plum G E, Sarvazyan A P, Breslauer K J

机构信息

Department of Chemistry, Rutgers, State University of New Jersey, Piscataway 08855.

出版信息

Biochemistry. 1994 Jul 26;33(29):8629-40. doi: 10.1021/bi00195a003.

DOI:10.1021/bi00195a003

PMID:8038152

Abstract

We use high-precision acoustic and densimetric techniques to determine, at 25 degrees C, the changes in volume, delta V, and adiabatic compressibility, delta Ks, that accompany the binding of netropsin to the poly(dAdT).poly(dAdT) and poly(dA).poly(dT) duplexes, as well as to the poly(dT).poly(dA).poly(dT) triplex. We find that netropsin binding to the heteropolymeric poly(dAdT).poly(dAdT) duplex is accompanied by negative changes in volume, delta V, and small positive changes in compressibility, delta Ks. By contrast, netropsin binding to the homopolymeric poly(dA).poly(dT) duplex is accompanied by large positive changes in both volume, delta V, and compressibility, delta Ks. Furthermore, netropsin binding to the poly(dT).poly(dA).poly(dT) triplex causes changes in both volume and compressibility that are nearly twice as large as those observed when netropsin binds to the poly(dA).poly(dT) duplex. We interpret these macroscopic data in terms of binding-induced microscopic changes in the hydration of the DNA structures and the drug. Specifically, we find that netropsin binding induces the release of approximately 22 waters from the hydration shell of the poly(dAdT).poly(dAdT) heteropolymeric duplex, approximately 40 waters from the hydration shell of the poly(dA).poly(dT) homopolymeric duplex, and about 53 waters from the hydration shell of the poly(dA).poly(dT), induces the release of 18 more water molecules than netropsin binding to the heteropolymeric duplex, poly(dAdT).poly(dAdT). On the basis of apparent molar volume, phi V, and apparent molar adiabatic compressibility, phi Ks, values for the initial drug-free and final drug-bound states of the two all-AT duplexes, we propose that the larger dehydration of the poly(dA).poly(dT) duplex reflects, in part, the formation of a less hydrated poly(dA).poly(dT)-netropsin complex compared with the corresponding poly(dAdT).poly(dAdT)-netropsin complex. In conjunction with our previously published entropy data [Marky, L. A., & Breslauer, K. J. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 4359-4363], we calculate that each water of hydration released to the bulk solvent by ligand binding contributes 1.6 cal K-1 mol-1 to the entropy of binding. This value corresponds to the average difference between the partial molar entropy of water in the bulk state and water in the hydration shells of the two all-AT duplexes. When netropsin binds to the poly(dT).poly(dA).poly(dT) triplex, the changes in both volume and compressibility suggest that the binding event induces more dehydration of the triplex than of the duplex state. Specifically, we calculate that netropsin binding to the poly(dT).poly(dA).poly(dT) triplex causes the release of 13 more waters than netropsin binding to the poly(dA).poly(dT) duplex.(ABSTRACT TRUNCATED AT 400 WORDS)

摘要

我们使用高精度声学和密度测定技术，在25摄氏度下测定了纺锤菌素与聚（dAdT）·聚（dAdT）、聚（dA）·聚（dT）双链体以及聚（dT）·聚（dA）·聚（dT）三链体结合时伴随的体积变化（ΔV）和绝热压缩率变化（ΔKs）。我们发现，纺锤菌素与异聚体聚（dAdT）·聚（dAdT）双链体结合时，体积出现负变化（ΔV），压缩率有小的正变化（ΔKs）。相比之下，纺锤菌素与同聚体聚（dA）·聚（dT）双链体结合时，体积（ΔV）和压缩率（ΔKs）均出现大的正变化。此外，纺锤菌素与聚（dT）·聚（dA）·聚（dT）三链体结合导致的体积和压缩率变化几乎是其与聚（dA）·聚（dT）双链体结合时观察到的变化的两倍。我们根据结合诱导的DNA结构和药物水合作用的微观变化来解释这些宏观数据。具体而言，我们发现纺锤菌素与聚（dAdT）·聚（dAdT）异聚体双链体结合会使其水合壳层释放约22个水分子，与聚（dA）·聚（dT）同聚体双链体结合会使其水合壳层释放约40个水分子，与聚（dT）·聚（dA）·聚（dT）三链体结合会使其水合壳层释放约53个水分子，比与异聚体双链体聚（dAdT）·聚（dAdT）结合多释放18个水分子。根据两种全AT双链体初始无药物状态和最终药物结合状态的表观摩尔体积（φV）和表观摩尔绝热压缩率（φKs）值，我们认为聚（dA）·聚（dT）双链体更大程度的脱水部分反映了与相应的聚（dAdT）·聚（dAdT） - 纺锤菌素复合物相比，形成的聚（dA）·聚（dT） - 纺锤菌素复合物水合程度更低。结合我们之前发表的熵数据[Marky, L. A., & Breslauer, K. J. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 4359 - 4363]，我们计算得出，配体结合释放到本体溶剂中的每个水合水分子对结合熵的贡献为1.6 cal K⁻¹ mol⁻¹。该值对应于本体状态下水的偏摩尔熵与两种全AT双链体水合壳层中水的偏摩尔熵的平均差值。当纺锤菌素与聚（dT）·聚（dA）·聚（dT）三链体结合时，体积和压缩率的变化表明结合事件诱导三链体的脱水程度大于双链体状态。具体而言，我们计算得出，纺锤菌素与聚（dT）·聚（dA）·聚（dT）三链体结合比与聚（dA）·聚（dT）双链体结合多释放13个水分子。（摘要截于400字）