Preferential interactions of glycine betaine and of urea with DNA: Implications for DNA hydration and for effects of these solutes on DNA stability
Preferential interactions of glycine betaine and of urea with DNA: Implications for DNA hydration and for effects of these solutes on DNA stability
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DOI：
10.1021/bi049096q
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发表时间：
2004-11-23
期刊：
影响因子：
2.9
通讯作者：
Record, MT
中科院分区：
文献类型：
--
作者：
Hong, J;Capp, MW;Record, MT
用蒸汽压渗透法研究了甘氨酸甜菜碱（GB）和尿素在盐水溶液中与小牛胸腺DNA的相互作用。渗透压摩尔浓度作为溶质和DNA浓度的函数的分析产生溶质对DNA的化学势μ（2）的影响。虽然GB和尿素通常都是核酸变性剂，因此必须与解链时暴露的核酸表面有利地相互作用，但VPO证明两者都不与双链体DNA有利地相互作用。GB的加入大大增加了DNA的mu（2），表明GB在双螺旋附近的平均局部浓度远低于其整体浓度。相比之下，尿素的加入对双链体DNA的μ（2）几乎没有影响，这表明双链体DNA附近的尿素平均局部浓度几乎与本体溶液中的相同。定性地，我们得出结论，GB的不均匀分布的发生主要是因为双链体DNA和GB更喜欢与水相互作用，而不是彼此。与GB与各种蛋白质表面相互作用的热力学数据的比较（Felitsky等人，Biochemistry，43，14732-14743）表明GB主要被排除在阴离子DNA表面之外，并且阴离子DNA磷酸盐氧表面的水合（大于或类似于17 H2O/核苷酸或大于或类似于0.22 H2O埃（-2））涉及至少两层水。通过对尿素和GB对DNA解链影响的文献数据分析，我们认为尿素是一种有效的非特异性核酸变性剂，因为它与变性过程中暴露的G、C、特别是T或U碱基的极性酰胺样表面有良好的相互作用，而GB是一种特异性GC变性剂，因为它与单链状态下的G和/或C表面有良好的相互作用。
Interactions of the solutes glycine betaine (GB) and urea with mononucleosomal calf thymus DNA in aqueous salt solutions are characterized by vapor pressure osmometry (VPO). Analysis of osmolality as a function of solute and DNA concentration yields the effect of the solute on the chemical potential, mu(2), of the DNA. Although both GB and urea generally are nucleic acid denaturants and therefore must interact favorably with the nucleic acid surface exposed upon melting, VPO demonstrates that neither interacts favorably with duplex DNA. Addition of GB greatly increases mu(2) of DNA, indicating that the average local concentration of GB in the vicinity of the double helix is much less than its bulk concentration. By contrast, addition of urea has almost no effect on mu(2) of duplex DNA, indicating that the average local concentration of urea in the vicinity of duplex DNA is almost the same as in bulk solution. Qualitatively, we conclude that the nonuniform distribution of GB occurs primarily because duplex DNA and GB prefer to interact with water rather than with each other. Comparison with thermodynamic data for the interaction of GB with various protein surfaces (Felitsky et al., Biochemistry, 43, 14732-14743) shows that GB is excluded primarily from anionic DNA surface and that the hydration of anionic DNA phosphate oxygen surface (greater than or similar to 17 H2O per nucleotide or greater than or similar to 0.22 H2O Angstrom(-2)) involves at least two layers of water. From analysis of literature data for effects of urea and of GB on DNA melting, we propose that urea is an effective nonspecific nucleic acid denaturant because of its favorable interactions with the polar amide-like surface of G, C, and especially T or U bases exposed in denaturation, whereas GB is a specific GC denaturant because of its favorable interaction with G and/or C surface in the single-stranded state.