Database construction for the effect of metal ions on nucleic acid folding

核酸（DNA和RNA）的各种折叠模式的信息是非常重要的，因为它是许多研究和广泛领域的研究必不可少的。然而，环境因素如金属离子种类和浓度、共溶质、pH值等对核酸折叠的影响尚不清楚。本研究的目的是建立环境因子对核酸折叠成高阶结构的能量贡献数据库。期望在建立所需的能量数据库后，可以很容易地预测核酸在各种不同条件下的杂交效率。为实现这一目标，计划了一个三步走的战略。具体来说，每个步骤如下：(1)详细分析金属离子对非常感兴趣的功能性核酸的特定结构和功能的影响。(2)参数的建立和数据库的建立，预测了金属离子对核酸折叠的能量贡献，包括双链、三链和四链。(3)利用能量数据库设计最适合检测特定结构的方法，如单核苷酸多态性（SNP）或特殊的三维结构。结果表明，pH值、金属离子和共溶质对平行/反平行双相、平行/反平行三相和g -四重奏/i-基序四相结构稳定性的影响是定量的。此外，还评估了两种结构条件的组合效应。通过参考能量参数数据库，可以按预期设计兼性结构变化。例如，金属离子浓度的改变可以引起核酸构象的剧烈变化，即d（G_4T_4G_4）的反平行g -四重结构向平行取向转变。我们在这项研究中获得的能量参数和由此产生的数据库将成为许多研究核酸的研究人员不可或缺的参考。少

The information about various folding patterns of nucleic acids (DNA and RNA) is very important because it is indispensable for many researches and studies in vast fields. However, little is known about the effect of environmental factors, e.g. kinds and concentration of metal ions, co-solutes, pH and so on, on the nucleic acid folding.The aim of this study is construction of database for the energetic contribution of the environmental factors to the folding of nucleic acids into the higher-order structure. It is expected that one can easily predict the hybridization efficiency of the nucleic acids under various different conditions after the development of the desired energetic database. A three-step strategy was planned for achieving the goal. In concrete, the each step was as follows : (1) Detailed analysis of the effect of metal ions on the specific structures and functions of very interesting functional nucleic acids. (2) Development of parameters and construction of the database … More to predict the energetic contribution of the metal ions to the nucleic acid folding to duplexes, triplexes, and quadruplexes. (3) Design of the most suitable method for detection of specific structures, such as single nucleotide polymorphism (SNP) or special three-dimensional structures, by means of the energetic database.As the result, the pH, metal ion, and co-solute dependency of the stability for many structures of parallel/anti-parallel duplex, parallel/anti-parallel triplex and G-quartet/i-motif quadruplex was quantified. Furthermore, the combinational effect of the conditions was evaluated in either structure. By referring the energetic parameter database, facultative structural changes were able to design as expected. For example, a drastic conformational change of a nucleic acid, i.e. antiparallel G-quadruplex structure of d(G_4T_4G_4) to parallel orientation, could be induced by altered metal ion concentration. Our energy parameters and the resulting database obtained in this study would be the indispensable reference for numerous researchers dealing with nucleic acids. Less