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骨架构象和磷酸盐紧密并列的紧凑三级结构。由此产生的不利的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敏感。这些研究的长期目标是提供一个系统的和定量的图片离子和溶剂相互作用稳定RNA的三级结构，并与图片的基本静电性质的RNA。本研究的主要目的是获得一组RNA结构的准确的Mg 2+ - RNA结合等温线，这些RNA结构说明了潜在的Mg 2+结合环境的全部范围，包括完全由完全水合的Mg 2+稳定的RNA，其中Mg（H2O）6[2]+可能与RNA结构中的口袋或通道氢键合的RNA，具有结合在特定位点的高度脱水离子的RNA，以及模仿大RNA（如核糖体）中螺旋紧密堆积的RNA。Mg 2+与部分折叠状态（仅二级结构）的RNA结合也将进行研究，以提供折叠反应期间Mg 2+结合的净变化。新开发的基于荧光直接测量游离和RNA结合的Mg 2+的方法将用于这些研究。其他研究将着眼于所提出的“静电塌陷”现象，作为大RNA折叠中的一种单独的Mg 2+依赖性转变，以及RNA对一价离子的选择性，这可能是紧凑RNA的一个普遍特征，反映了结合在RNA表面附近的一价离子的部分脱水，以及可以作为离子探针的小肽或蛋白质与稳定RNA结构的水合水的结合。最后，这些结果将被用作基准比较与离子- RNA相互作用的理论预测，特别是最近开发的框架，使用非线性泊松-玻尔兹曼方程来描述水合RNA结合Mg 2+和玻恩模型计算能量的部分脱水离子在特定位置的RNA。预测RNA三级构象的Mg 2+依赖性折叠自由能的能力在许多情况下是有用的。

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.