Lipfert Jan, Doniach Sebastian, Das Rhiju, Herschlag Daniel
Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands; email:
Annu Rev Biochem. 2014;83:813-41. doi: 10.1146/annurev-biochem-060409-092720. Epub 2014 Mar 5.
Ions surround nucleic acids in what is referred to as an ion atmosphere. As a result, the folding and dynamics of RNA and DNA and their complexes with proteins and with each other cannot be understood without a reasonably sophisticated appreciation of these ions' electrostatic interactions. However, the underlying behavior of the ion atmosphere follows physical rules that are distinct from the rules of site binding that biochemists are most familiar and comfortable with. The main goal of this review is to familiarize nucleic acid experimentalists with the physical concepts that underlie nucleic acid-ion interactions. Throughout, we provide practical strategies for interpreting and analyzing nucleic acid experiments that avoid pitfalls from oversimplified or incorrect models. We briefly review the status of theories that predict or simulate nucleic acid-ion interactions and experiments that test these theories. Finally, we describe opportunities for going beyond phenomenological fits to a next-generation, truly predictive understanding of nucleic acid-ion interactions.
离子环绕在核酸周围，形成所谓的离子氛围。因此，如果不能合理深入地理解这些离子的静电相互作用，就无法理解RNA和DNA的折叠与动力学，以及它们与蛋白质之间和彼此之间的复合物。然而，离子氛围的潜在行为遵循的物理规则与生物化学家最为熟悉和习惯的位点结合规则不同。本综述的主要目的是让核酸实验人员熟悉核酸 - 离子相互作用背后的物理概念。在整个过程中，我们提供了用于解释和分析核酸实验的实用策略，以避免因过于简化或错误的模型而产生的陷阱。我们简要回顾了预测或模拟核酸 - 离子相互作用的理论现状以及检验这些理论的实验。最后，我们描述了超越现象学拟合，对核酸 - 离子相互作用进行下一代真正预测性理解的机会。
