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

基本信息

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
项目类别：
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

项目摘要

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）：涉及核酸的细胞生化反应发生在盐，宇宙和生物聚合物的水溶液中，例如蛋白质。这些杂质，小的有机溶质，例如氨基酸，核酸前体，简单的糖和代谢物，对核酸的结构和稳定性产生巨大影响。该项目的长期目标是阐明颜色调节折叠核酸稳定性的机制，以便更好地理解与生物聚合物的宇宙相互作用，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（St. Olaf College）创建一群本科生，并接受了培训，可以解决现代医疗环境中的生物聚合物折叠问题。该提案中详细介绍的研究将量化核酸表面上的甘氨酸甜菜碱，三甲胺（TMAO）和尿素的积累或排除，以将颜色相互作用与核酸表面上的化学官能团相关。 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在热变性期间暴露； MD模拟还将用于预测溶剂可访问的化学官能团和基础序列介导的水合在颜色的积累中或在双螺旋DNA或RNA表面排除的作用； 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.）使用VPO和MD模拟评估基本邻居邻居和综合相互作用在与DNA和RNA二级和tertiary结构的综合相互作用中，使用核核苷单磷酸盐（RDMP）量化甘氨酸，tmao和尿素的积累或排除。这些实验将为改善细胞环境中核酸结构稳定性的理解和对生物聚合物折叠和展开过程的更广泛理解提供基础，从而深入了解生物聚合物功能和生物聚合物折叠疾病。公共卫生相关性：核酸（DNA和RNA）的二级和三级结构对于适当的生物学功能至关重要。该项目试图了解细胞溶液如何促进核酸结构的增益或损失等细胞溶液。该提案中详述的实验将提高我们对核酸折叠和展开过程的理解，并提供对核酸功能和生物聚合物折叠疾病的见解。