Birac Jeffrey J, Sherman William B, Kopatsch Jens, Constantinou Pamela E, Seeman Nadrian C
Department of Chemistry, New York University, New York, NY 10003, USA.
J Mol Graph Model. 2006 Dec;25(4):470-80. doi: 10.1016/j.jmgm.2006.03.005. Epub 2006 Apr 19.
We present geometry based design strategies for DNA nanostructures. The strategies have been implemented with GIDEON-a graphical integrated development environment for oligonucleotides. GIDEON has a highly flexible graphical user interface that facilitates the development of simple yet precise models, and the evaluation of strains therein. Models are built on a simple model of undistorted B-DNA double-helical domains. Simple point and click manipulations of the model allow the minimization of strain in the phosphate-backbone linkages between these domains and the identification of any steric clashes that might occur as a result. Detailed analysis of 3D triangles yields clear predictions of the strains associated with triangles of different sizes. We have carried out experiments that confirm that 3D triangles form well only when their geometrical strain is less than 4% deviation from the estimated relaxed structure. Thus geometry-based techniques alone, without detailed energetic considerations, can be used to explain certain general trends in DNA structure formation. We have used GIDEON to build detailed models of double crossover and triple crossover molecules, evaluating the non-planarity associated with base tilt and junction misalignments. Computer modeling using a graphical user interface overcomes the limited precision of physical models for larger systems, and the limited interaction rate associated with earlier, command-line driven software.
我们展示了基于几何结构的DNA纳米结构设计策略。这些策略已通过GIDEON（一种用于寡核苷酸的图形化集成开发环境）得以实施。GIDEON拥有高度灵活的图形用户界面，便于开发简单而精确的模型，并对其中的应变进行评估。模型基于未扭曲的B-DNA双螺旋结构域的简单模型构建。通过对模型进行简单的点击操作，可以使这些结构域之间磷酸主链连接中的应变最小化，并识别可能由此产生的任何空间冲突。对三维三角形的详细分析能够清晰预测与不同大小三角形相关的应变。我们进行的实验证实，只有当三维三角形的几何应变与估计的松弛结构偏差小于4%时，它们才能良好形成。因此，仅基于几何结构的技术，无需详细的能量考量，就可用于解释DNA结构形成中的某些一般趋势。我们已使用GIDEON构建了双交叉和三交叉分子的详细模型，评估了与碱基倾斜和连接点错位相关的非平面性。使用图形用户界面进行计算机建模克服了大型系统物理模型精度有限以及早期命令行驱动软件交互速率有限的问题。
