Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids
Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids
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DOI：
10.1002/1097-0282(2000/2001)56:3
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发表时间：
2000
期刊：
影响因子：
2.9
通讯作者：
C. C. Hardin-C.;Adam G. Perry;Katie White
中科院分区：
文献类型：
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作者：
C. C. Hardin-C.;Adam G. Perry;Katie White
DNA四链体的解离和组装（和一些四链体RNA）已经在几个严格的水平上进行了表征，从控制每个过程的因素的粗略描述，到这些因素诱导稳定或不稳定的相对能力的半定量比较，再到结合能的定量研究。（热力学），转化率（动力学），并分析其过渡态能量和机制。本调查对这些因素进行了分类，描述了趋势，并侧重于它们之间的相互依存关系。通过添加K+和提高链浓度最有效地诱导四链体组装;然而，Na+、NH 4+、Sr 2+和Pb 2+也是非常有效的稳定剂。四链体解离通常通过热变性、“解链”完成;然而，当四链体和单价阳离子浓度足够低或温度足够高时，几种二价阳离子，例如，Ca ~（2+）、Co ~（2+）、Mn ~（2+）、Zn ~（2+）、Ni ~（2+）、Mg ~（2+）等离子可诱导解离。稳定性还取决于所讨论的链（或多个链）所采用的结构类型。变体包括分子内、双链和四链四链体。其他重要的变量包括链序列，插入环的大小和pH值，特别是当胞嘧啶存在时，碱基甲基化和骨架磷酸盐与硫代磷酸酯的替换。竞争平衡也可以调节四链体DNA的形成。例如，导致沃森-克里克（WC）双链体和发夹DNA、三链体DNA、甚至其他类型的四链体的反应可以与四链体缔合反应竞争链。其他包括非蛋白质催化剂，小分子如芳香族染料，金属卟啉和碳水化合物（渗透剂）。已发现其他核酸链可驱动四链体形成。为了帮助加强每条信息的含义，从每条引用的热力学或动力学数据中得出的每个功能性结论都简要地总结在标准化的表格条目中。John Wiley & Sons，Inc. Biopolymers（Nucleic Acid Sci）56：147-194，2001
The dissociation and assembly of quadruplex DNA structures (and a few quadruplex RNAs) have been characterized at several levels of rigor, ranging from gross descriptions of factors that govern each process, to semiquantitative comparisons of the relative abilities of these factors to induce stabilization or destabilization, to quantitative studies of binding energies (thermodynamics), transformational rates (kinetics), and analysis of their transition‐state energies and mechanisms. This survey classifies these factors, describes the trends and focuses on their interdependencies. Quadruplex assembly is induced most efficiently by added K+ and elevating the strand concentration; however, Na+, NH4+, Sr2+, and Pb2+ are also very effective stabilizers. Quadruplex dissociation is typically accomplished by thermal denaturation, “melting”; however, when the quadruplex and monovalent cation concentrations are low enough, or the temperature is sufficiently high, several divalent cations, e.g., Ca2+, Co2+, Mn2+, Zn2+, Ni2+ and Mg2+ can induce dissociation. Stabilization also depends on the type of structure adopted by the strand (or strands) in question. Variants include intramolecular, two‐ and four‐stranded quadruplexes. Other important variables include strand sequence, the size of intervening loops and pH, especially when cytosines are present, base methylation, and the replacement of backbone phosphates with phosphorothioates. Competitive equilibria can also modulate the formation of quadruplex DNAs. For example, reactions leading to Watson–Crick (WC) duplex and hairpin DNAs, triplex DNAs, and even other types of quadruplexes can compete with quadruplex association reactions for strands. Others include nonprotein catalysts, small molecules such as aromatic dyes, metalloporphyrins, and carbohydrates (osmolytes). Other nucleic acid strands have been found to drive quadruplex formation. To help reinforce the implications of each piece of information, each functional conclusion drawn from each cited piece of thermodynamic or kinetic data has been summarized briefly in a standardized table entry. © 2001 John Wiley & Sons, Inc. Biopolymers (Nucleic Acid Sci) 56: 147–194, 2001