Factors stabilizing RNA structures

描述（由申请人提供）：许多RNA的生物学功能取决于具有不规则主链构象和紧密并置的磷酸盐的紧凑三级结构。由此产生的不利静电自由能是折叠的主要障碍，并导致 RNA 三级结构比二级结构对离子和溶剂环境更加敏感。这些研究的长期目标是提供稳定 RNA 三级结构的离子和溶剂相互作用的系统和定量图像，并将该图像与 RNA 的潜在静电特性联系起来。拟议研究的一个主要目的是获得一组 RNA 结构的准确 Mg 2 - RNA 结合等温线，以说明潜在 Mg 2 结合环境的全部范围，包括完全由完全水合 Mg 2 稳定的 RNA、其中 Mg(H20)6[2] 可能与 RNA 结构中的口袋或通道形成氢键的 RNA、在特定位点结合高度脱水离子的 RNA 以及模拟大 RNA 中螺旋紧密堆积的 RNA例如核糖体。还将研究 Mg 2 与部分折叠状态（仅二级结构）捕获的 RNA 的结合，以提供折叠反应期间 Mg 2 结合的净变化图。这些研究将使用新开发的基于荧光的方法来直接测量游离和 RNA 结合的 Mg 2 。其他研究将把“静电塌陷”现象视为大RNA折叠中独立的Mg 2 依赖性转变、RNA对单价离子的选择性（这可能是紧凑RNA的普遍特征并反映靠近RNA表面的单价离子的部分脱水）以及小肽或蛋白质的结合（可作为离子探针和水合水稳定RNA结构）。最后，这些结果将用作与离子 - RNA 相互作用的理论预测进行比较的基准，特别是最近开发的框架，该框架使用非线性泊松-玻尔兹曼方程来描述水合 RNA 结合的 Mg 2 和 Born 模型来计算 RNA 中特定位置处部分脱水离子的能量。预测 RNA 三级构象的 Mg2 依赖性折叠自由能的能力在许多情况下都是有用的。

DESCRIPTION (provided by applicant): The biological functions of many RNAs depend on compact tertiary structures with irregular backbone conformations and close juxtapositions of phosphates. The resulting unfavorable electrostatic free energy is a major barrier to folding, and causes RNA tertiary structure to be much more sensitive to the ion and solvent environment than is secondary structure. The long term goal of these studies is to provide a systematic and quantitative picture of ion and solvent interactions stabilizing RNA tertiary structures, and relate the picture to the underlying electrostatic properties of RNA. A major aim of the proposed studies is to obtain accurate Mg 2+ - RNA binding isotherms for a set of RNA structures that illustrate the full range of potential Mg 2+ binding environments, including RNAs stabilized entirely by fully hydrated Mg 2+, RNAs in which Mg(H20)6[2]+ may be hydrogen bonded to pockets or channels in the RNA structure, RNAs with highly dehydrated ions bound atspecific sites, and RNAs that mimic the close packing of helices in large RNAs such as the ribosome. Mg 2+ binding to RNAs trapped in partially folded states (secondary structure only) will also be studied, to provide a picture of the net change in Mg 2+ binding during the folding reaction. Newly developed fluorescence-based methods for directly measuring free and RNA-bound Mg 2+ will be used in these studies. Other studies will look at the proposed phenomenon of "electrostatic collapse" as a separate, Mg 2+- dependent transition in folding of large RNAs, at the selectivity of RNAs for monovatent ions, which may be a widespread feature of compact RNAs and reflect partial dehydration of monovalent ions bound close to the RNA surface, and at binding of small peptides or proteins that may serve as probes of ions and hydrating water stabilizing an RNA structure. Lastly, these results will be used as benchmarks for comparison with theoretical predictions of ion - RNA interactions, particularly a recently developed framework that uses the non-linear Poisson-Boltzmann equation to describe hydrated RNA-bound Mg 2+ and a Born model to compute the energetics of partially dehydrated ions at specific locations in the RNA. The ability to predict the Mg2+-dependent folding free energies of RNA tertiary conformations would be useful in a number of contexts.