期刊
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
卷 25, 期 4, 页码 470-480出版社
ELSEVIER SCIENCE INC
DOI: 10.1016/j.jmgm.2006.03.005
关键词
GIDEON; geometrical molecular modeling; graphical user interface; DNA; DNA models; DNA tensegrity triangle; DNA double crossover; DNA triple crossover
类别
资金
- NIGMS NIH HHS [GM-29554, R37 GM029554, R01 GM029554] Funding Source: Medline
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. (c) 2006 Elsevier Inc. All rights reserved.
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