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.

该副本是使用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这是调查员的机构。 我们的研究计划旨在利用基于分支DNA的新型大分子构建块，这是专门设计的晶体布置3D结构基序的基础。最终目标是提供大分子支架，能够结合，定向和并置从生物大分子到有机导体和光学记忆成分的各种分子。我们提出并成功地确定了这种设计的3D系统的结构，即紧张的三角形。该结构是一个可靠的基序，具有三个折叠骨干对称性，由三个螺旋组成，该螺旋是针对线性独立方向的三个螺旋，即它们的螺旋轴并非全部共享同一平面。这些螺旋通过三个类似霍利迪的跨界点将螺旋连接起来，以产生替代性的过头和下图案。最近，我们报道了[Zheng等。 Nature 461，74-77（2009）] X射线晶体结构到4`to tensegrity三角形，其中包含一个分子物种，该物种由三个螺旋结构域组成，每个结构域都包含两个双螺旋转弯。每个三角形都以菱形的顶点为中心，形成一个大腔。我们最近的努力是针对多个不同方向的，所有这些都基于已发表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旋转数量从2到3和4增加，并确定其晶体结构。虽然精制结构都具有根据其设计预测的结构参数，但晶体的分辨率随着螺旋旋转数量的增加而降低。我们正在探索改变三角形的粘性末端的长度，以及使用天然DNA而不是合成DNA对晶体分辨率的影响。 （b）我们试图将客座分子纳入晶体结构的内部空腔；具有不同长度边缘（2、3和4转）的三个结构的空腔为〜100 nm3，〜375 nm3和〜1000 nm3。客人物种范围从蛋白质，胡椒粉和胡椒质到染料，金属纳米颗粒和DNA片段。通过共结晶和浸泡，已经获得了此类复合物的异态晶体。一份报告描述了DNA晶体的晶体结构，该晶体包含两个不同的三角形以根据设计进行结晶的三角形。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附着来控制。通常，我们的晶体是弱衍射的，表现出高度的镶嵌性，并且经常出现在太空群P1中。因此，晶体需要长时间的曝光时间，较小的振荡角和360度以上的最佳数据收集。