DNA and RNA Stability in Glycine Betaine, TMAO, and Urea Solutions: Correlating S

甘氨酸甜菜碱、TMAO 和尿素溶液中 DNA 和 RNA 的稳定性：关联 S

• 批准号: 7882805
• 负责人: GREGORY W MUTH
• 金额: $ 19.56万
• 依托单位: ST. OLAF COLLEGE
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-06-01 至 2014-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7882805
• 关键词: Address; Adenine; Amino Acids; Area; Base Composition; Base Pairing; Base Sequence; Bathing; Betaine; Biochemical Reaction; Biological Process; Biopolymers; Chemicals; Computer Simulation; Cytosine; DNA; DNA Maintenance; Disease; Double-Stranded RNA; Elements; Environment; Exclusion; Foundations; Guanine; Guanine + Cytosine Composition; Human; Hydration status; Individual; Investigation; Ionic Strengths; Lipids; Mediating; Medical; Modeling; Molecular Conformation; Molecular Structure; Nucleic Acid Folding; Nucleic Acid Precursors; Nucleic Acids; Nucleosides; Nucleotides; Physiological; Play; Process; Proteins; RNA; RNA Stability; Ribonucleosides; Role; Salts; Site; Solutions; Solvents; Structure; Students; Study Section; Surface; Telomerase RNA Component; Thymine; Training; Transition Temperature; United States National Institutes of Health; Uracil; Urea; Water; Work; aqueous; base; college; design; functional group; improved; in vivo; insight; molecular dynamics; nucleic acid stability; nucleic acid structure; nucleoside monophosphate; pressure; protein structure; public health relevance; research study; solute; stem; sugar; trimethyloxamine; vapor

DESCRIPTION (provided by applicant): Cellular biochemical reactions involving nucleic acids occur in aqueous solutions of salts, cosolutes, and biopolymers, such as proteins. These cosolutes, small organic solutes such as amino acids, nucleic acid precursors, simple sugars, and metabolites, can have dramatic influences on the structure and stability of nucleic acids. The long-term objective of this project is to elucidate the mechanism of cosolute-modulated folded nucleic acid stability, so as to better understand cosolute interactions with biopolymers and how these interactions influence biopolymer structural change and biochemical reactions. Additionally, these experiments will generate a cadre of undergraduate students at St. Olaf College that are trained to address biopolymer folding problems in a modern medical setting. The investigations detailed in this proposal will quantify accumulation or exclusion of glycine betaine, trimethylamine oxide (TMAO), and urea at nucleic acid surfaces to correlate cosolute interactions with chemical functional groups on the nucleic acid surfaces. The specific aims of this proposal will combine thermal unfolding and vapor pressure osmometry (VPO) studies with molecular dynamics (MD) computer simulations to: 1.) assess the strength of glycine betaine, TMAO, and urea as nucleic acid secondary structure stabilizers/destabilizers by quantifying the accumulation or exclusion of these cosolutes from chemical functional groups on double-helical DNA and RNA surfaces exposed during thermal denaturation; MD simulations will also be used to predict the roles solvent accessible chemical functional groups and base sequence-mediated hydration play in cosolute accumulation or exclusion at the double-helical DNA or RNA surface; 2.) quantify the accumulation or exclusion of glycine betaine, TMAO, and urea from nucleoside 5'-monophosphates (NMPs), the individual building blocks of DNA and RNA secondary and tertiary structures, using VPO and MD simulations and couple these results with those from the first specific aim to elucidate the mechanism of cosolute stabilization or destabilization of DNA and RNA double-helices; 3.) quantify the accumulation or exclusion of glycine betaine, TMAO, and urea from ribodinucleoside monophosphates (rDMPs) using VPO and MD simulations to assess the roles of base nearest-neighbor and stacking in cosolute interactions with DNA and RNA secondary and tertiary structures. These experiments will provide a foundation for an improved understanding of nucleic acid structural stability in cellular environments and a broader understanding of biopolymer folding and unfolding processes, leading to insights into biopolymer function and biopolymer folding diseases. PUBLIC HEALTH RELEVANCE: Secondary and tertiary structures of nucleic acids (DNA and RNA) are essential for proper biological function. This project seeks to understand how cellular solutes such as metabolites, amino acids, and sugars facilitate the gain or loss of nucleic acid structure. The experiments detailed in this proposal will improve our understanding of nucleic acid folding and unfolding processes and provide insights into nucleic acid function and biopolymer folding diseases.

描述（由申请人提供）：涉及核酸的细胞生物化学反应发生在盐、共溶质和生物聚合物（如蛋白质）的水溶液中。这些共溶质，小的有机溶质，如氨基酸，核酸前体，单糖和代谢物，可以对核酸的结构和稳定性产生显着的影响。该项目的长期目标是阐明共溶质调节折叠核酸稳定性的机制，以便更好地理解共溶质与生物聚合物的相互作用以及这些相互作用如何影响生物聚合物的结构变化和生化反应。此外，这些实验将在圣奥拉夫学院产生一批本科生，他们将接受培训，以解决现代医学环境中的生物聚合物折叠问题。在这个建议中详细的调查将量化积累或排除甘氨酸甜菜碱，氧化三甲胺（TMAO），和尿素在核酸表面相关的共溶质与核酸表面上的化学官能团的相互作用。该提案的具体目标将结合联合收割机热展开和蒸汽压渗透压（VPO）的研究与分子动力学（MD）计算机模拟：1。）通过量化这些共溶质在热变性期间暴露的双螺旋DNA和RNA表面上的化学官能团的累积或排除，评估甘氨酸甜菜碱、TMAO和尿素作为核酸二级结构稳定剂/去稳定剂的强度;分子动力学模拟也将用于预测溶剂可及的化学官能团和碱基序列的作用-介导的水合作用在双螺旋DNA或RNA表面的共溶质积累或排斥中起作用; 2.）使用VPO和MD模拟定量甘氨酸甜菜碱、TMAO和尿素从核苷5 '-单磷酸（NMP）（DNA和RNA二级和三级结构的单独构建块）的积累或排除，并将这些结果与来自第一个具体目的的结果相结合，以阐明DNA和RNA双螺旋的共溶质稳定化或不稳定化的机制; 3.）使用VPO和MD模拟量化核糖核苷单磷酸（rDMP）中甜菜碱、TMAO和尿素的积累或排除，以评估碱基最近邻和堆积在与DNA和RNA二级和三级结构的共溶质相互作用中的作用。这些实验将为更好地理解细胞环境中的核酸结构稳定性和更广泛地理解生物聚合物折叠和展开过程提供基础，从而深入了解生物聚合物功能和生物聚合物折叠疾病。 核酸（DNA和RNA）的二级和三级结构对正常的生物功能至关重要。该项目旨在了解细胞溶质如代谢物，氨基酸和糖如何促进核酸结构的获得或丧失。本提案中详细介绍的实验将提高我们对核酸折叠和解折叠过程的理解，并提供对核酸功能和生物聚合物折叠疾病的见解。