Rational engineering of dynamic DNA systems
Rational engineering of dynamic DNA systems
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DOI：
10.1002/anie.200800675
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发表时间：
2008-01-01
影响因子：
16.6
通讯作者：
Niemeyer, Christof M.
中科院分区：
文献类型：
--
作者：
Feldkamp, Udo;Niemeyer, Christof M.
在过去的四分之一个世纪中，DNA分子作为纳米范围内结构的支架材料的应用已经从简单的设计发展，但突破性的四臂双螺旋连接基序[1]到复杂结构基序的自组装，作为构建块形成大的超分子结构。[2]DNA的关键特性使其对自下而上的纳米技术如此有吸引力，这是单链核酸与沃森-克里克互补序列杂交形成稳定双螺旋的非凡特异性。因此，一组精心设计的寡核苷酸可以被编程以自组装成各种各样的超结构。此外，各种稳定或亚稳态之间的可逆转变机制，如二级结构构象，可以被工程化到DNA超结构中，使得静态支架成为动态纳米器件。[3]这样的装置可以执行例如机械工作，[4]翻译信息，[5]聚集和解离纳米颗粒，[6]或结合和释放蛋白质。[7]虽然现在静态DNA阵列的设计越来越多地遵循系统规则，这些规则允许对所需超结构进行逆合成分析以获得将形成这些结构的合适的寡核苷酸组，[8，9]动态DNA装置通常通过单独的方法制备，这些方法利用各种构象状态，过渡反应和各自的触发刺激，例如寡核苷酸置换，缓冲液的离子强度或pH值的变化，或小分子的结合。[3，10]在最近的出版物中，Pierce和合作者介绍了一种用于动态DNA系统的系统开发的方法，该方法基于包括单链序列、双链体和发夹环的基本构建块，并且涉及允许各种结构构象相互连接的杂交/解离途径。[11]在他们的概念的初步演示中，他们描述了杂交反应的级联，这些级联被编程以促进复杂静态超结构的逐步自组装，以及实现动态DNA设备的不同构象状态之间的转变。
During the past quarter of a century the application of DNA molecules as a scaffold material for constructions in the nanometer range has developed from the design of simple, yet ground-breaking four-armed double-helical junction motifs [1] to the self-assembly of complex structural motifs which serve as building blocks to form large supramolecular constructs.[2] The key property of DNA that makes it so attractive for bottom-up nanotechnology is the extraordinary specificity of the hybridization of single-stranded nucleic acids with their Watson–Crick complements to form stable double helices. Thus, a set of carefully designed oligonucleotides can be programmed to self-assemble into a broad range of diverse superstructures. In addition, reversible transition mechanisms between various stable or metastable states, such as secondary structure conformations, can be engineered into DNA superstructures such that static scaffolds become dynamic nanodevices.[3] Such devices may perform, for example, mechanical work,[4] translate information,[5] aggregate and dissociate nanoparticles,[6] or bind and release proteins.[7] While the design of static DNA arrays nowadays increasingly follows systematic rules which allow the retrosynthetic analysis of desired superstructures to obtain suitable sets of oligonucleotides that will form these structures,[8, 9] dynamic DNA devices are usually prepared by individual approaches, which take advantage of various conformational states, transition reactions, and respective triggering stimuli, such as oligonucleotide displacement, changes in ionic strengths or pH values of buffers, or binding of small molecules.[3, 10] In a recent publication, Pierce and co-workes introduced a methodology for the systematic development of dynamic DNA systems which is based on elementary building blocks comprising single-stranded sequences, duplexes, and hairpin loops, and involves hybridization/dissociation pathways that allow various structural conformations to be interconnected.[11] In an initial demonstration of their concept, they describe cascades of hybridization reactions that are programmed to facilitate the step-wise self-assembly of complex static superstructures as well as to accomplish transition between different conformational states of a dynamic DNA device.