Architecture with GIDEON, a program for design in structural DNA nanotechnology

Jeffrey J. Birac, William B. Sherman, Jens Kopatsch, Pamela E. Constantinou, Nadrian Seeman

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)470-480
Number of pages11
JournalJournal of Molecular Graphics and Modelling
Volume25
Issue number4
DOIs
StatePublished - Dec 2006

Fingerprint

nanotechnology
Nanotechnology
DNA
deoxyribonucleic acid
triangles
graphical user interface
Graphical user interfaces
crossovers
B-Form DNA
Geometry
oligonucleotides
Oligonucleotides
commands
geometry
linkages
misalignment
manipulators
Nanostructures
phosphates
Phosphates

Keywords

  • DNA
  • DNA double crossover
  • DNA models
  • DNA tensegrity triangle
  • DNA triple crossover
  • Geometrical molecular modeling
  • GIDEON
  • Graphical user interface

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Spectroscopy
  • Atomic and Molecular Physics, and Optics

Cite this

Architecture with GIDEON, a program for design in structural DNA nanotechnology. / Birac, Jeffrey J.; Sherman, William B.; Kopatsch, Jens; Constantinou, Pamela E.; Seeman, Nadrian.

In: Journal of Molecular Graphics and Modelling, Vol. 25, No. 4, 12.2006, p. 470-480.

Research output: Contribution to journalArticle

Birac, Jeffrey J. ; Sherman, William B. ; Kopatsch, Jens ; Constantinou, Pamela E. ; Seeman, Nadrian. / Architecture with GIDEON, a program for design in structural DNA nanotechnology. In: Journal of Molecular Graphics and Modelling. 2006 ; Vol. 25, No. 4. pp. 470-480.
@article{65f2aa6f96b64b6986f69d485f6ed214,
title = "Architecture with GIDEON, a program for design in structural DNA nanotechnology",
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.",
keywords = "DNA, DNA double crossover, DNA models, DNA tensegrity triangle, DNA triple crossover, Geometrical molecular modeling, GIDEON, Graphical user interface",
author = "Birac, {Jeffrey J.} and Sherman, {William B.} and Jens Kopatsch and Constantinou, {Pamela E.} and Nadrian Seeman",
year = "2006",
month = "12",
doi = "10.1016/j.jmgm.2006.03.005",
language = "English (US)",
volume = "25",
pages = "470--480",
journal = "Journal of Molecular Graphics and Modelling",
issn = "1093-3263",
publisher = "Elsevier Inc.",
number = "4",

}

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

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 - Geometrical molecular modeling

KW - GIDEON

KW - Graphical user interface

UR - http://www.scopus.com/inward/record.url?scp=33746587908&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33746587908&partnerID=8YFLogxK

U2 - 10.1016/j.jmgm.2006.03.005

DO - 10.1016/j.jmgm.2006.03.005

M3 - Article

C2 - 16630733

AN - SCOPUS:33746587908

VL - 25

SP - 470

EP - 480

JO - Journal of Molecular Graphics and Modelling

JF - Journal of Molecular Graphics and Modelling

SN - 1093-3263

IS - 4

ER -