Factors stabilizing RNA structures

描述（由申请人提供）：许多rna的生物学功能依赖于具有不规则骨干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，并将图像与RNA的潜在静电特性联系起来。提出研究的主要目的是获得准确的Mg 2 +——核糖核酸绑定等温线的RNA结构说明潜在的全套Mg 2 +绑定环境,包括RNA稳定完全由完全水化Mg 2 +, RNA的毫克(h2o) 6[2] +氢连着口袋或渠道的RNA结构,RNA与高度脱水离子绑定atspecific网站,和RNA,模仿的密切包装在核糖体等大型RNA螺旋。还将研究部分折叠状态（仅二级结构）的rna与Mg 2+的结合，以提供折叠反应期间Mg 2+结合的净变化图。新开发的基于荧光的直接测量游离和rna结合的Mg +的方法将用于这些研究。其他研究将把提出的“静电塌陷”现象视为一个单独的、依赖于mg2 +的转变，在大RNA折叠中，在RNA对单价离子的选择性上，这可能是致密RNA的一个普遍特征，反映了靠近RNA表面的单价离子的部分脱水，以及在小肽或蛋白质的结合上，可以作为离子探针和水合水稳定RNA结构。最后，这些结果将用作离子- RNA相互作用理论预测的比较基准，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中特定位置部分脱水离子的能量学。预测依赖于Mg2+的RNA三级构象的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.