Sarma M H, Gupta G, Sarma R H
Institute of Biomolecular Stereodynamics, State University of New York, Albany 12222.
J Biomol Struct Dyn. 1984 Jun;1(6):1423-55. doi: 10.1080/07391102.1984.10507529.
CD spectra of poly(dA-dT).poly(dA-dT) in low salt (10-100 mM NaCl) and high salt (4-6 M CsF) are different i.e. 275 nm band gets inverted in going from low to high salt (Vorhickova et. al., J. Mol. Biol. 166, 85, 1983). However, from CD spectra alone it is not possible to decipher any structural differences that might exist between the low and high salt forms of poly(dA-dT).poly(dA-dT). Hence, we took recourse to high resolution NMR spectroscopy to understand the structural properties of poly(dA-dT).poly(dA-dT) in low and high salt. A detailed analysis of shielding constants and extensive use of NOE studies under minimum spin diffusion conditions using C(8)-deuterated poly(dA-dT).poly(dA-dT) enabled us to come up with the following conclusions (i) base-pairing is Watson-Crick under low and high salt conditions. (ii) under both the conditions of salt the experimental data can be explained in terms of an equilibrium blend of right and left-handed B-DNA duplexes with the left-handed form 70% and the right-handed 30%. In a 400 base pairs long poly(dA-dT).poly(dA-dT) (as used in this study), equilibrium between right and left-handed helices can also mean the existence of both helical domains in the same molecule with fast interchange between these domains or/and unhindered motion/propagation of these domains along the helix axis. (iii) However, there are other structural differences between the low and high salt forms of poly(dA-dT).poly(dA-dT); under the low salt condition, right- and left-handed B-DNA duplexes have mononucleotide as a structural repeat while under the high salt conditions, right- and left-handed B-DNA duplexes have dinucleotide as a structural repeat. In the text we provide the listing of torsion angles for the low and high salt structural forms. (iv) Salt (CsF) induced structural transition in poly(dA-dT).poly(dA-dT) occurs without any breakage of Watson-Crick pairing. (v) The high salt form of poly(dA-dT).poly(dA-dT) is not the left-handed Z-helix. Although the results above from NMR data are quite unambiguous, a question still remains i.e. what does the salt (CsF) induced change in the CD spectra of poly(dA-dT).poly(dA-dT) really indicate? Interestingly, we could show that the salt (CsF) induced change in poly(dA-dT).poly(dA-dT) is quite similar to that caused by a basic polypeptide viz. poly-L(Lys2-Ala)n i.e. both the agents induced a psi-structure in DNA.
聚（dA-dT）·聚（dA-dT）在低盐（10 - 100 mM NaCl）和高盐（4 - 6 M CsF）条件下的圆二色光谱不同，即从低盐到高盐时，275 nm波段发生反转（Vorhickova等人，《分子生物学杂志》166, 85, 1983）。然而，仅从圆二色光谱无法解读聚（dA-dT）·聚（dA-dT）在低盐和高盐形式之间可能存在的任何结构差异。因此，我们借助高分辨率核磁共振光谱来了解聚（dA-dT）·聚（dA-dT）在低盐和高盐条件下的结构特性。对屏蔽常数的详细分析以及在最小自旋扩散条件下使用C(8)-氘代聚（dA-dT）·聚（dA-dT）进行的广泛核Overhauser效应（NOE）研究，使我们得出以下结论：（i）在低盐和高盐条件下，碱基配对均为沃森-克里克配对。（ii）在两种盐条件下，实验数据都可以用右手和左手B-DNA双链体的平衡混合物来解释，其中左手形式占70%，右手形式占30%。在一个400个碱基对长的聚（dA-dT）·聚（dA-dT）（如本研究中所用）中，右手和左手螺旋之间的平衡也可能意味着同一分子中同时存在这两种螺旋结构域，且这些结构域之间能够快速互换和/或沿螺旋轴自由移动/传播。（iii）然而，聚（dA-dT）·聚（dA-dT）的低盐和高盐形式之间还存在其他结构差异；在低盐条件下，右手和左手B-DNA双链体以单核苷酸作为结构重复单元，而在高盐条件下，右手和左手B-DNA双链体以二核苷酸作为结构重复单元。在文中我们提供了低盐和高盐结构形式的扭转角列表。（iv）盐（CsF）诱导聚（dA-dT）·聚（dA-dT）发生结构转变时，沃森-克里克配对没有任何断裂。（v）聚（dA-dT）·聚（dA-dT）的高盐形式不是左手Z-螺旋。尽管上述来自核磁共振数据的结果相当明确，但仍有一个问题存在，即盐（CsF）诱导的聚（dA-dT）·聚（dA-dT）圆二色光谱变化究竟意味着什么？有趣的是，我们可以证明盐（CsF）诱导的聚（dA-dT）·聚（dA-dT）变化与一种碱性多肽即聚-L（Lys2-Ala）n引起的变化非常相似，即这两种试剂都能在DNA中诱导出ψ-结构。
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