DESIGNED DNA CRYSTALS

设计的 DNA 晶体

• 批准号: 8170586
• 负责人: JENS J BIRKTOFT
• 金额: $ 1.05万
• 依托单位: BROOKHAVEN SCIENCE ASSOC-BROOKHAVEN LAB
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-01 至 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8170586
• 关键词: Binding; Biological; Color; Complex; Computer Retrieval of Information on Scientific Projects Database; Crystallization; DNA; Data Collection; Dyes; Funding; Goals; Grant; Institution; Length; Link; Memory; Molecular; Nature; Optics; Peptides; Proteins; Publishing; Reporting; Research; Research Personnel; Resolution; Resources; Roentgen Rays; Source; Structure; System; Time; United States National Institutes of Health; Vertebral column; base; design; macromolecule; nanoparticle; peptidomimetics; programs; scaffold; synthetic construct

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Our research program is designed to utilize new types of macromolecular building blocks based on branched DNA, as the basis of specifically designed crystalline arrangements 3D structural motifs. The ultimate goals are to provide macromolecular scaffoldings, capable of binding, orienting and juxtaposing a variety of molecules, from biological macromolecules to organic conductors and optical memory components. We proposed and succeeded in determining structures of such a designed 3D system, the tensegrity triangle. This structure is a robust motif with three-fold rotational backbone symmetry, consisting of three helices that are directed in linearly independent directions, i.e., their helix axes do not all share the same plane. The helices are connected pair-wise by three Holliday-like crossover points, so as to produce an alternating over-and-under motif. Recently, we reported [Zheng et al. Nature 461, 74-77 (2009)] the X-ray crystal structure to 4 ¿ of a tensegrity triangle containing a single molecular species, comprised of three helical domains, each containing two double helical turns. Each triangle is centered on a vertex of a rhombohedron, creating a large cavity. Our more recent efforts have been directed in several different directions, all based on the structure of the published two-turn triangle. (A) We have been successful in increasing the numbers of helical turns in the triangle from 2 to 3 and 4 and in determining their crystal structures. While the refined structures all have the structural parameters predicted from their designs, the resolutions of the crystals obtained decrease with the increase in the number of helical turns. We are exploring the effect of changing the length of sticky ends that link the triangles, and also the impact of using natural DNA, rather than synthetic DNA, on the resolution of the crystals. (B) We are attempting to incorporate guest molecules into the internal cavities of the crystal structures; the cavities of the three structures with different length edges (2, 3 and 4 turns) are ~100 nm3, ~375 nm3 and ~1000 nm3. The guest species range from proteins, peptides, and peptidomimetics to dyes, metallic nanoparticles and segments of DNA. Isomorphous crystals have been obtained of such complexes both by co-crystallization and soaking. A report describing the crystal structure of a DNA crystal containing two distinct triangles programmed to crystallize according to the design is ready for submission. In addition, we have also demonstrated that the colors of the crystals can be controlled by the covalent attachment of dye molecules to the different molecules. As a rule our crystals are weakly diffracting, display a high degree of mosaicity and frequently appear in space group P1. Consequently the crystals require long exposure times, small oscillation angles and optimally data collection over 360 degrees.

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 我们的研究计划旨在利用基于分支DNA的新型大分子构建模块，作为专门设计的晶体排列3D结构基序的基础。最终目标是提供大分子支架，能够结合，定向和并列的各种分子，从生物大分子到有机导体和光学存储组件。 我们提出并成功地确定了这样一个设计的三维系统，张拉整体三角形的结构。 该结构是具有三重旋转骨架对称性的稳健基序，由三个螺旋组成，所述螺旋指向线性独立的方向，即，它们的螺旋轴并不都共享同一平面。 螺旋通过三个Holliday样交叉点成对连接，从而产生交替的上下基序。最近，我们报道了[Zheng et al. Nature 461，74-77（2009）]包含单个分子种类的张拉整体三角形的X射线晶体结构，该张拉整体三角形由三个螺旋结构域组成，每个螺旋结构域包含两个双螺旋圈。 每个三角形都以菱形面体的顶点为中心，形成一个大的空腔。 我们最近的努力已经在几个不同的方向，所有的基础上公布的两转三角形的结构。(A)我们已经成功地将三角形中的螺旋圈数从2增加到3和4，并确定了它们的晶体结构。 虽然细化结构都具有从其设计预测的结构参数，但所获得的晶体的分辨率随着螺旋圈数的增加而降低。我们正在探索改变连接三角形的粘性末端的长度的效果，以及使用天然DNA而不是合成DNA对晶体分辨率的影响。(B)我们试图将客体分子引入晶体结构的内部空腔中;具有不同长度边缘（2、3和4匝）的三种结构的空腔为~100 nm 3、~375 nm 3和~1000 nm 3。 客体物种的范围从蛋白质、肽和肽模拟物到染料、金属纳米颗粒和DNA片段。 通过共结晶和浸泡两种方法得到了此类配合物的同晶型晶体。 一份描述DNA晶体结构的报告已经准备好提交，该晶体包含两个不同的三角形，根据设计进行结晶。 此外，我们还证明了晶体的颜色可以通过染料分子与不同分子的共价连接来控制。 一般来说，我们的晶体衍射弱，显示出高度的镶嵌性，经常出现在空间群P1中。 因此，晶体需要长的曝光时间，小的振荡角度和最佳的数据收集超过360度。