DNA - DNA interactions with atomic detail

DNA - DNA 与原子细节的相互作用

• 批准号: 8543745
• 负责人: Nathan A. Baker
• 金额: $ 31.34万
• 依托单位: VIRGINIA POLYTECHNIC INST AND ST UNIV
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-28 至 2016-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8543745
• 关键词: Address; Agreement; Algorithms; Amines; Area; Base Sequence; Behavior; Biology; Biotechnology; Cells; Charge; Chemicals; Cobalt; Computer Simulation; Consensus; DNA; Data; Dependence; Double-Stranded RNA; Electrostatics; Employee Strikes; Environment; Epigenetic Process; Foundations; Gene Delivery; Generations; Genetic; Goals; Human Development; In Vitro; Ions; Lead; Life; Measurement; Mediating; Methods; Modeling; Molecular; Morphologic artifacts; Motivation; Nature; Nucleic Acids; Nucleic acid sequencing; Physical condensation; Physics; Plague; Polyamines; Precipitation; Process; RNA; RNA Interference; Reporting; Resistance; Resolution; Roentgen Rays; Role; Sampling; Simulate; Solutions; Solvents; Spatial Distribution; Spectrum Analysis; Speed; Spermidine; Stress; Structure; System; Techniques; Testing; Theoretical model; Therapeutic; Time; Viral; Water; Work; base; driving force; hexaamminecobalt(II); human disease; in vivo; interest; model development; molecular dynamics; non-viral gene delivery; novel; novel strategies; nucleic acid structure; physical property; planetary Atmosphere; polyion; research study; retinal rods; simulation; sound; theories; therapeutic development

DESCRIPTION (provided by applicant): DNA and RNA condensation is of broad interest in both biology and biotechnology. The in vivo packaging of these nucleic acids (NAs) enables the efficient storage of genetic information; strategies for in vitro packaging are crucial for development of therapeutics, e.g., for non-viral gene delivery. Like-charge attraction between DNA duplexes is an essential precursor of DNA condensation and can be induced by multivalent ions with distinctly different physical properties, ranging from the spherical trivalen inorganic ion, cobalt hexa-amine, through the more rod-like, less charge-dense polyamines found in living cell; e.g., spermine and spermidine. Despite an equal importance of RNA to biology, almost nothing is known about double-stranded RNA condensation. The recent discovery of the RNA interference (RNAi) process is strong motivation for determining whether short RNA duplexes can be packaged for therapeutic applications. The broad goal of this proposal is to develop a quantitative mechanism for multivalent ion-NA duplex interactions that leads directly to ion-induced DNA or RNA attraction. This mechanism will have basic physics at its foundation, yet will be detailed enough to address many practical questions such as sequence dependence of nucleic acid condensation and the striking differences in RNA vs. DNA condensation behavior observed experimentally. Existing theoretical models stress the necessity of ion correlations for generation of these attractive forces, yet no consensus exists describing the mechanism for the attraction at atomic level. Current experimental methods alone do not have the resolution to deliver the atomically detailed picture of the diverse nucleic acid condensation phenomena. To understand the mechanism of counterion-induced attraction between DNA or RNA duplexes, we will develop and experimentally test a new approach to modeling ionic environments of nucleic acids that provides the necessary resolution. The approach will integrate grand canonical Monte Carlo simulations based on novel implicit solvent/explicit ion models (for speed and sampling efficiency) with the traditional explicit solvet molecular dynamics simulations on microsecond time scales (for the highest level of detail). The distinctive feature of our approach is that the computational models will be developed in tight integration with the experiment. Predictions of multivalent ion-NA interactions will be validated by experimental measurement of ion association to and spatial distribution around nucleic acids; the data will be used to fine- tune parameters of the model. Small angle X-ray scattering techniques will probe the structure of NA duplex ionic atmospheres, while condensation experiments using UV spectroscopy will provide additional degrees of comparison with specific predictions of the theory. Once agreement between theory and experiment on simpler systems is reached, we will explore the role of nucleic acid sequence and topology in condensation, and develop an atomistic understanding of how the biologically important polyions spermine and spermidine facilitate attraction between nucleic acid fragments.

描述（由申请人提供）：DNA 和 RNA 浓缩在生物学和生物技术中引起了广泛的兴趣。这些核酸（NA）的体内包装能够有效存储遗传信息；体外包装策略对于治疗药物的开发至关重要，例如非病毒基因传递。 DNA双链体之间的同电荷吸引力是DNA缩合的重要前体，可以由具有明显不同物理性质的多价离子诱导，范围从球形三价无机离子、六胺钴，到活细胞中发现的更棒状、电荷密度较低的多胺；例如，精胺和亚精胺。尽管 RNA 对生物学同样重要，但人们对双链 RNA 缩合几乎一无所知。最近发现的 RNA 干扰 (RNAi) 过程是确定短 RNA 双链体是否可以包装用于治疗应用的强大动力。该提案的总体目标是开发一种多价离子-NA 双链体相互作用的定量机制，直接导致离子诱导的 DNA 或 RNA 吸引力。该机制将以基础物理学为基础，但也足够详细，足以解决许多实际问题，例如核酸缩合的序列依赖性以及实验观察到的 RNA 与 DNA 缩合行为的显着差异。现有的理论模型强调离子相关性对于产生这些吸引力的必要性，但在描述原子水平上的吸引力机制方面尚未达成共识。目前的实验方法本身不具备提供各种核酸缩合现象的原子详细图像的分辨率。为了了解 DNA 或 RNA 双链体之间抗衡离子诱导的吸引力的机制，我们将开发并实验测试一种新方法来模拟核酸的离子环境，以提供必要的分辨率。该方法将基于新型隐式溶剂/显式离子模型（用于速度和采样效率）的大正则蒙特卡罗模拟与微秒时间尺度上的传统显式溶剂分子动力学模拟（用于最高级别的细节）相结合。我们方法的显着特点是计算模型将与实验紧密结合开发。多价离子-NA相互作用的预测将通过实验测量核酸的离子关联和周围的空间分布来验证；该数据将用于微调模型的参数。小角度 X 射线散射技术将探测 NA 双链离子大气的结构，而使用紫外光谱的凝聚实验将提供与理论具体预测的额外程度的比较。一旦理论与实验在更简单的系统上达成一致，我们将探索核酸序列和拓扑在缩合中的作用，并对生物学上重要的聚离子精胺和亚精胺如何促进核酸片段之间的吸引形成原子理解。