Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures.
Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures.
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DOI：
10.1093/nar/gkr1173
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发表时间：
2012-04
影响因子：
14.9
通讯作者：
Bathe M
中科院分区：
文献类型：
--
作者：
Kim DN;Kilchherr F;Dietz H;Bathe M
DNA纳米技术使复杂的纳米级结构的程序化合成在材料和生物科学的各种应用成为可能。精确控制三维解决方案的形状和目标设计的机械灵活性是实现所需功能的重要因素。由于设计的纳米结构的实验验证耗时且成本高，因此纳米结构形状和灵活性的预测物理模型具有显着提高设计过程的能力。在这里，我们显著扩展和实验验证了DNA折纸的计算建模框架之前提出的CanDo [Castro，C.E.]Kilchherr F。、金D.-N。、Shiao E.L.瓦乌,T。Wortmann, P。,洗澡,M。迪茨,H。（2011）支架DNA折纸的引物。Nat,冰毒。[j].农业学报，8,221-229。3D解决方案的形状和灵活性是根据碱基对连接图预测的，现在考虑DNA双螺旋的缺口，单链DNA的熵弹性，以及建模线框结构所需的远距离交叉，除了以前的建模(Castro，C.E.等)，只考虑双螺旋DNA结构域的典型扭曲、弯曲和拉伸刚度。利用32螺旋DNA束对内部交叉密度介导的纳米结构柔韧性进行了系统的实验验证，首次证明我们的模型不仅可以预测复杂DNA纳米结构的三维溶液形状，还可以预测其机械柔韧性。因此，我们的模型代表了对基于dna的纳米结构形状和灵活性定量理解的重要进展，我们预计该模型将显著增加使用核酸设计的合成纳米结构的数量和种类。
DNA nanotechnology enables the programmed synthesis of intricate nanometer-scale structures for diverse applications in materials and biological science. Precise control over the 3D solution shape and mechanical flexibility of target designs is important to achieve desired functionality. Because experimental validation of designed nanostructures is time-consuming and cost-intensive, predictive physical models of nanostructure shape and flexibility have the capacity to enhance dramatically the design process. Here, we significantly extend and experimentally validate a computational modeling framework for DNA origami previously presented as CanDo [Castro,C.E., Kilchherr,F., Kim,D.-N., Shiao,E.L., Wauer,T., Wortmann,P., Bathe,M., Dietz,H. (2011) A primer to scaffolded DNA origami. Nat. Meth., 8, 221–229.]. 3D solution shape and flexibility are predicted from basepair connectivity maps now accounting for nicks in the DNA double helix, entropic elasticity of single-stranded DNA, and distant crossovers required to model wireframe structures, in addition to previous modeling (Castro,C.E., et al.) that accounted only for the canonical twist, bend and stretch stiffness of double-helical DNA domains. Systematic experimental validation of nanostructure flexibility mediated by internal crossover density probed using a 32-helix DNA bundle demonstrates for the first time that our model not only predicts the 3D solution shape of complex DNA nanostructures but also their mechanical flexibility. Thus, our model represents an important advance in the quantitative understanding of DNA-based nanostructure shape and flexibility, and we anticipate that this model will increase significantly the number and variety of synthetic nanostructures designed using nucleic acids.
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影响因子：
15
作者：
Ke, Yonggang;Douglas, Shawn M.;Liu, Minghui;Sharma, Jaswinder;Cheng, Anchi;Leung, Albert;Liu, Yan;Shih, William M.;Yan, Hao
通讯作者：
Yan, Hao
影响因子：
3
作者：
Tang, Guang;Peng, Liwei;Ludtke, Steven J.
通讯作者：
Ludtke, Steven J.
影响因子：
14.9
作者：
Douglas SM;Marblestone AH;Teerapittayanon S;Vazquez A;Church GM;Shih WM
通讯作者：
Shih WM
影响因子：
38.3
作者：
通讯作者：
--
影响因子：
64.8
作者：
Douglas, Shawn M.;Dietz, Hendrik;Liedl, Tim;Hoegberg, Bjoern;Graf, Franziska;Shih, William M.
通讯作者：
Shih, William M.