Remin M
Department of Physics, University of Warsaw, Poland.
J Biomol Struct Dyn. 1997 Oct;15(2):251-64. doi: 10.1080/07391102.1997.10508190.
The effect of a structural change of ribose to deoxyribose, by replacement of 2'-OH by 2'-H, on the conformational equilibrium of the sugar ring is described in terms of one thermodynamic cycle. The method is based on the observation that conformational correlations of the sugar ring--side chain ensemble in DNA and RNA components show one general pattern, reflecting an intrinsic physical property of this ensemble. The pattern determines a choice of model systems to study. The systems consist of pairs of DNA and RNA components, nucleosides and nucleotides in aqueous solution, where all conformational factors are fully controlled. This approach allowed us to describe the thermodynamic cycle and measure its fundamental parameters, equilibrium constants and free energy differences, delta delta G, from a nuclear magnetic resonance study. The delta delta G values as determined for pairs of ribo- and deoxyribo-nucleosides in classes of syn-constrained and anti-preferred models, are comparable and lie in a narrow range, delta delta G = 1.7 +/- 0.1 [kJ/mol]. For pairs of ribo- and deoxyribo-nucleotides, the delta delta G values also lie in narrow ranges, delta delta G = 1.7 +/- 0.1 [kJ/mol] for 5'-phosphate nucleotides and delta delta G = 1.9 +/- 0.1 [kJ/mol] for 3'-phosphate nucleotides, i.e. similar to those observed for nucleosides. The measured quantity, delta delta G, is generally observed in a relatively narrow range, delta delta G = 1.75 +/- 0.15 [kJ/mol], irrespective of the class of the model system. This quantity represents a "pure" constant contribution, pe one sugar moiety, as a "driving force" for the N-->S shift in the sugar ring conformational equilibrium, when one compares RNA and DNA. This important thermodynamic quantity, delta delta G, has not hitherto been determined for nucleic acids. Ultimately the delta delta G quantity is revealed in the tendency to adopt S(C2'endo) sugar puckering domain by the majority of DNA structures, whereas RNA generally adopt an N(C3'endo) puckering domain. A possible biological significance of the delta delta G quantity may include evolutionary aspects of nucleic acids.
通过将核糖的2'-OH替换为2'-H从而转变为脱氧核糖，这种结构变化对糖环构象平衡的影响是根据一个热力学循环来描述的。该方法基于这样的观察结果：DNA和RNA组分中糖环-侧链整体的构象相关性呈现出一种普遍模式，反映了该整体的内在物理性质。这种模式决定了用于研究的模型系统的选择。这些系统由DNA和RNA组分、核苷和核苷酸在水溶液中的对组成，其中所有构象因素都得到了充分控制。这种方法使我们能够描述热力学循环，并通过核磁共振研究测量其基本参数、平衡常数和自由能差ΔΔG。在顺式受限和反式偏好模型类别中，核糖核苷和脱氧核糖核苷对的ΔΔG值具有可比性，且处于较窄范围，ΔΔG = 1.7±0.1 [kJ/mol]。对于核糖核苷酸和脱氧核糖核苷酸对，ΔΔG值也处于较窄范围，5'-磷酸核苷酸的ΔΔG = 1.7±0.1 [kJ/mol]，3'-磷酸核苷酸的ΔΔG = 1.9±0.1 [kJ/mol]，即与核苷观察到的值相似。测量的量ΔΔG通常在相对较窄的范围内观察到，ΔΔG = 1.75±0.15 [kJ/mol]，与模型系统的类别无关。当比较RNA和DNA时，这个量代表了一个糖部分的“纯”恒定贡献，作为糖环构象平衡中N→S转变的“驱动力”。这个重要的热力学量ΔΔG迄今尚未针对核酸确定。最终，ΔΔG量体现在大多数DNA结构倾向于采用S(C2'内型)糖折叠域，而RNA通常采用N(C3'内型)折叠域。ΔΔG量的一个可能的生物学意义可能包括核酸的进化方面。
