ArticleJournal of molecular graphics & modelling2006
Architecture with GIDEON, a program for design in structural DNA nanotechnology.
Article in Journal of molecular graphics & modelling, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- DNA Origami and Their Application in Biosensors.Biosensors · 2026Review
- Engineering tertiary chirality in helical biopolymers.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Generation of DNA oligomers with similar chemical kinetics via in-silico optimization.Communications chemistry · 2023Article
- Non-Viral Carriers for Nucleic Acids Delivery: Fundamentals and Current Applications.Life (Basel, Switzerland) · 2023Review
- The Art of Designing DNA Nanostructures with CAD Software.Molecules (Basel, Switzerland) · 2021Review
- DNA Transformations for Diagnosis and Therapy.Advanced functional materials · 2021Review
- Design Approaches and Computational Tools for DNA Nanostructures.IEEE open journal of nanotechnology · 2021Article
- Dynamic DNA Assemblies in Biomedical Applications.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2020Review
- Overview of DNA Self-Assembling: Progresses in Biomedical Applications.Pharmaceutics · 2018Review
- DNA origami applications in cancer therapy.Cancer science · 2017Review
- Synthesizing topological structures containing RNA.Nature communications · 2017Article
- Creating complex molecular topologies by configuring DNA four-way junctions.Nature chemistry · 2016Article
- Hierarchical Self Assembly of Patterns from the Robinson Tilings: DNA Tile Design in an Enhanced Tile Assembly Model.Natural computing · 2012Article
- A DNA-based nanomechanical device used to characterize the distortion of DNA by Apo-SoxR protein.Biochemistry · 2012Article
- Structural DNA nanotechnology: from design to applications.International journal of molecular sciences · 2012Review
- Article
- Blunt-ended DNA stacking interactions in a 3-helix motif.Chemical communications (Cambridge, England) · 2010Article
- Construction of a DNA nano-object directly demonstrates computation.Bio Systems · 2009Article
- From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal.Nature · 2009Article
- Rapid prototyping of 3D DNA-origami shapes with caDNAno.Nucleic acids research · 2009Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.