The Graphical Integrated Development Environment for OligoNucleotides

We are proud to annouce the release of GIDEON, the first software package which specifically addresses the needs of the SDN (Structural DNA Nanotechnology) research community and industry.  GIDEON is a 3-D modeling and simulation tool for creating and testing SDN models within a virtual environment.  Computer modeling using a graphical user interface (GUI) overcomes the limited precision and practicality of physical models for larger systems, and the limited interaction rate associated with earlier, command-line driven software.

GIDEON provides a user-friendly GUI that allows straightforward construction and viewing of complex SDN models with ideal precision.  Click the pictures in the table below to get a closer look at GIDEON's features and applications.

If you would like more information about GIDEON (especially getting a copy), then please send email to

Click the following pictures for a larger view.

GIDEON has a highly flexible graphical user interface that facilitates the development of simple yet precise models, and the evaluation of strains therein.

Simple point and click manipulations of the model allow the minimization of strain in the phosphate-backbone linkages between the domains and the identification of any steric clashes that might occur as a result.

This stereoscopic image gives the user full depth perception while they inspect and modify the model.

GIDEON has been used to build detailed models of double crossover and triple crossover molecules, evaluating the non-planarity associated with base tilt and junction misalignments.

Detailed analysis of 3D triangles yields clear predictions of the strains associated with triangles of different sizes.

Experiments 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