Structure and Function of Nucleic Acid Therapeutics

描述(申请人提供)：我们的研究有三个主要的长期目标：(I)详细分析核酸类似物的结构/功能，用于设计下一代反义寡核苷酸(Aon)和具有潜在抗癌、抗病毒和抗炎适应症的RNAi疗法；(Ii)确定在病因学背景下研究的核酸类似物的晶体结构(核酸结构的起源)；(Iii)DNA精细结构的结构研究，以评估序列和阳离子对构象的相对影响。我们将用来确定三维结构的主要工具是X射线结晶学。在第一个项目中，将特别关注反义化合物的两个关键特征：RNA亲和力和反义RNA底物的来源，并被E.coliRNaseH结合和识别。将确定选定的第二代和第三代AON和第一代siRNA修饰的晶体结构。这些结构数据将与它们的热力学稳定性、核酸酶抗性、对大肠杆菌RNase H降解的敏感性(AONS)以及与Isis制药公司(AONS)和Alnylam制药公司(SiRNAs)合作的总体疗效相关联。此外，我们将通过求解DNA的晶体结构来回答为什么RNase H结合双链RNA(DsRNA)，但不切割与RNA配对的RNA链(不同于与DNA配对的那些)：RNA-RNaseH和dsRNA-RNaseH复合体。在第二个项目中，我们将使用部分或全部修饰的寡核苷酸来分析骨架较短的天然核酸的替代品，即三氟呋喃糖核酸和吡喃葡萄糖核酸(TNA和LPNA)的晶体结构。第三个项目是我们先前努力的延伸，目的是最大限度地提高DNA晶体结构的分辨率，了解序列和金属离子对DNA双链构象的相对影响。我们将使用中子散射，分析具有代表性的寡核苷酸的结构，并显示全部和部分占据的碱金属离子结合部位。这项研究的具体目标是：(1)第二代和第三代Aon修饰的晶体分析，以及结构与现有的体外和体内功能数据的相关性；(2)RNAi途径所允许的siRNA修饰的晶体分析，以提高RNA亲和力和对siRNA的核酸酶抗性；(3)与RNA形成的复合体中作为RNaseH底物的AON(阿拉伯核酸)的结构研究；(4)DNA的晶体结构：RNARNase H和dsRNA-RNase H复合体；(5)人工核酸配对系统的晶体分析；以及(6)DNA双链的中子衍射研究和携带甲基膦的DNA的高分辨X射线结构。

DESCRIPTION (provided by applicant): Our research has three main long-term objectives: (i) Detailed analyses of the structure/function of nucleic acid analogs, for the design of the next generation of antisense oligonucleotide (AON) and RNAi therapeutics with potential anticancer, antiviral and anti-inflammatory indications; (ii) Determination of crystal structures of nucleic acid analogs studied in the context of etiology (origin of nucleic acid structure); (iii) Structural investigation of DNA fine structure, for assessing the relative influence of sequence and cations on conformation. The main tool we will use for determining the three dimensional structures is X-ray crystallography. In the first project, two key features of antisense compounds will be given particular attention: RNA affinity and the origins of antisense-RNA substrate binding and recognition by E.coli RNase H. The crystal structures of selected 2nd and 3rd generation AON and 1st generation siRNA modifications will be determined. The structural data will be correlated with their thermodynamic stabilities, nuclease resistances, susceptility to E. coli RNase H degradation (AONs) and overall efficacy, in collaboration with Isis Pharmaceuticals Inc. (AONs) and Alnylam Pharmaceuticals (siRNAs). In addition, we will seek to answer the question why RNase H binds double-stranded RNA (dsRNA), but does not cleave RNA strands paired to RNA (unlike those paired to DNA), by solving the crystal structures of DNA:RNA-RNase H and dsRNA-RNase H complexes. In the second project, we will analyze the crystal structures of alternatives to the natural nucleic acids with shorter backbones; i.e., threofuranosyl and lyxopyranosyl nucleic acid (TNA and LPNA, resp.), using either partially or all-modified oligonucleotides. The third project is an extension of our previous efforts to maximize the resolution of DNA crystal structures, to gain insight into the relative influence of sequence and metal cations on DNA duplex conformation. We will use neutron scattering, to analyze the structure of a representive oligodeoxynucleotide, and to visualize fully and partially occupied alkali metal ion binding sites. The specific aims of this research are: (1) Crystallographic analyses of 2nd and 3rd generation AON modifications, and correlation of the structures with existing in vitro and in vivo functional data; (2) Crystallographic analyses of siRNA modifications that are tolerated by the RNAi pathway, to improve RNA affinity and nuclease resistance of siRNA; (3) Structural studies of AONs (arabino nucleic acids) that, in complex with RNA, are substrates of RNase H; (4) Crystal structures of DNA:RNARNase H and dsRNA-RNase H complexes; (5) Crystallographic analyses of artificial nucleic acid pairing systems; and (6) Neutron diffraction studies of a DNA duplex and high-resolution X-ray structures of DNAs carrying methylphosphonates.