Design tools for reporter strands and DNA origami scaffold strands

DOI10.1016/J.TCS.2016.10.007MaRDI QIDQ529038zbMATH OpenOpenAlexFDO

Authors Joanna A. Ellis-Monaghan, Greta Pangborn, Nadrian C. Seeman, Sam Blakeley, Conor Disher, Mary Falcigno, Brianna Healy, Ada Morse, Bharti Singh, Melissa C. Westland

Publication date 18 May 2017

Published in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.tcs.2016.10.007

zbMATH Keywords

augmenting edgesDNA origamiDNA self-assemblyEulerian circuitsknotted DNAreporter strandscaffolding strandturning costs

Mathematics Subject Classification ID

Eulerian and Hamiltonian graphs (05C45) Modes of computation (nondeterministic, parallel, interactive, probabilistic, etc.) (68Q10) Graph theory (including graph drawing) in computer science (68R10) Computer graphics; computational geometry (digital and algorithmic aspects) (68U05) Protein sequences, DNA sequences (92D20)

Recommendations

• DNA origami and the complexity of Eulerian circuits with turning costs
• Unknotted strand routings of triangulated meshes
• On existence of reporter strands in DNA-based graph structures
• DNA origami and unknotted A-trails in torus graphs
• Self-assembling DNA graphs

Cites work

• A Dynamic Programming Approach to Sequencing Problems
• Dynamic Programming Treatment of the Travelling Salesman Problem
• scientific article; zbMATH DE number 1953202 (Why is no real title available?)
• scientific article; zbMATH DE number 791397 (Why is no real title available?)
• Khovanov homology is an unknot-detector
• Maximum matching and a polyhedron with 0,1-vertices
• On existence of reporter strands in DNA-based graph structures
• On the computational complexity of the Jones and Tutte polynomials
• Synthesising topological links
• Synthetic single-stranded DNA topology
• The computational complexity of knot and link problems

Cited in

(10)

• On existence of reporter strands in DNA-based graph structures
• Unknotted strand routings of triangulated meshes
• DNA origami and the complexity of Eulerian circuits with turning costs
• Edge-outer graph embedding and the complexity of the DNA reporter strand problem
• DNA origami words and rewriting systems
• Design formalism for DNA self-assembly of polyhedral skeletons using rigid tiles
• DNA origami and unknotted A-trails in torus graphs
• The topology of scaffold routings on non-spherical mesh wireframes
• Design methods for 3D wireframe DNA nanostructures
• DNA origami words, graphical structures and their rewriting systems

Describes a project that uses

Uses Software

• Stony Brook

This page was built for publication: Design tools for reporter strands and DNA origami scaffold strands

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q529038)