TY - JOUR
T1 - Architecture with GIDEON, a program for design in structural DNA nanotechnology
AU - Birac, Jeffrey J.
AU - Sherman, William B.
AU - Kopatsch, Jens
AU - Constantinou, Pamela E.
AU - Seeman, Nadrian C.
N1 - Funding Information:
This research has been supported by grants GM-29554 from NIGMS, N00014-98-1-0093 from ONR, grants DMI-0210844, EIA-0086015, CCF-0432009, CCF-0523290, and CTS-0103002 from the NSF, 48681-EL from ARO and NTI-001 from Nanoscience Technologies, Inc. to N.C.S.
PY - 2006/12
Y1 - 2006/12
N2 - 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.
AB - 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.
KW - DNA
KW - DNA double crossover
KW - DNA models
KW - DNA tensegrity triangle
KW - DNA triple crossover
KW - GIDEON
KW - Geometrical molecular modeling
KW - Graphical user interface
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U2 - 10.1016/j.jmgm.2006.03.005
DO - 10.1016/j.jmgm.2006.03.005
M3 - Article
C2 - 16630733
AN - SCOPUS:33746587908
SN - 1093-3263
VL - 25
SP - 470
EP - 480
JO - Journal of Molecular Graphics and Modelling
JF - Journal of Molecular Graphics and Modelling
IS - 4
ER -