DNA - DNA interactions with atomic detail

DNA - DNA 与原子细节的相互作用

• 批准号: 8372141
• 负责人: Nathan A. Baker
• 金额: $ 35.67万
• 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/8372141
• 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. PUBLIC HEALTH RELEVANCE: The project will advance fundamental understanding of the mechanisms of DNA and RNA packaging in living cells, which is vital to understanding of the molecular basis of human disease and development of novel powerful therapies.

描述（由申请人提供）：DNA和RNA冷凝在生物学和生物技术方面都具有广泛的兴趣。这些核酸（NAS）的体内包装可以有效地存储遗传信息。体外包装的策略对于开发治疗剂至关重要，例如非病毒基因递送。 DNA双链体之间的同样充电吸引力是DNA冷凝的必不可少的先驱，可以通过具有明显不同的物理特性的多价离子诱导，范围从球形三）无机离子，钴六角性胺，通过在活细胞中发现的较小的杆状，较少的电荷浓度多胺。例如，精子和精子。尽管RNA对生物学具有相同的重要性，但关于双链RNA冷凝的几乎一无所知。 RNA干扰（RNAI）过程的最新发现是确定是否可以将短RNA双链体包装以进行治疗应用的强大动机。该建议的广泛目标是开发一种定量机制，以直接导致离子诱导的DNA或RNA吸引力直接导致多价离子-NA双链相互作用。该机制将在其基础上具有基本物理学，但将足够详细地解决许多实际问题，例如核酸凝结的序列依赖性以及RNA与DNA冷凝行为的显着差异。现有的理论模型强调了产生这些吸引力的离子相关性的必要性，但是没有共识存在描述原子水平吸引力的机制。仅当前的实验方法就没有解决各种核酸凝结现象的原子详细图片的分辨率。为了了解DNA或RNA双链体之间的相反诱导的吸引力的机制，我们将开发并通过实验测试一种新方法来建模核酸的离子环境，从而提供必要的分辨率。该方法将基于新型的隐式溶剂/显式离子模型（用于速度和采样效率）与传统的显式溶剂分子动力学模拟（用于微秒时间尺度（最高详细信息）上的传统显式溶剂分子动力学模拟，将大规范的蒙特卡洛模拟（用于速度和采样效率）集成。我们方法的独特特征是，将与实验紧密整合开发计算模型。多价离子-NA相互作用的预测将通过对离子与核酸周围的空间分布的实验测量进行验证。数据将用于细化模型的参数。小角度X射线散射技术将探测Na双链离子大气的结构，而使用紫外线光谱法的冷凝实验将提供与该理论的特定预测的其他比较程度。一旦达到了简单系统的理论和实验之间的一致性，我们将探讨核酸序列和拓扑结构在凝结中的作用，并对生物学上重要的多元素精子和精子如何促进核酸片段之间的吸引力有一种原子理解。 公共卫生相关性：该项目将提高对活细胞中DNA和RNA包装机制的基本理解，这对于了解人类疾病的分子基础和新型强大疗法的发展至关重要。