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

描述（由申请人提供）：涉及核酸的细胞生化反应发生在盐、co溶质和生物聚合物（如蛋白质）的水溶液中。这些辅溶质，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巨大影响。该项目的长期目标是阐明co溶质调节折叠核酸稳定性的机制，从而更好地了解co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培养一批本科骨干学生，训练他们在现代医学环境中解决生物聚合物折叠问题。本研究将量化甜菜碱、氧化三甲胺（TMAO）和尿素在核酸表面的积累或排除，以关联核酸表面的化学官能团与溶质相互作用。本方案的具体目标是将热展开和蒸汽压渗透（VPO）研究与分子动力学（MD）计算机模拟相结合，以：1.通过量化这些辅质在热变性暴露的双螺旋DNA和RNA表面的化学官能团上的积累或排除，评估甘氨酸甜菜碱、氧化三甲胺和尿素作为核酸二级结构稳定剂/不稳定剂的强度；MD模拟还将用于预测溶剂可及的化学官能团和碱基序列介导的水化作用在双螺旋DNA或RNA表面的溶质积累或排除中所起的作用；2.)利用VPO和MD模拟，量化5'-单磷酸核苷（NMPs）中甘氨酸甜菜碱、氧化三甲胺和尿素的积累或排除，NMPs是DNA和RNA二级和三级结构的单个构建块，并将这些结果与第一个特定目的的结果相结合，以阐明DNA和RNA双螺旋的溶质稳定或不稳定机制；3)利用VPO和MD模拟，量化甘氨酸甜菜碱、氧化三甲胺和尿素在核糖二核苷单磷酸（rDMPs）中的积累或排除，以评估碱基近邻和堆积在与DNA和RNA二级和三级结构的绝对相互作用中的作用。这些实验将为提高对细胞环境中核酸结构稳定性的理解以及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的功能和生物聚合物折叠疾病。

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.