Challenges and applications for self-assembled DNA nanostructures

John H. Reif, Thomas H. LaBean, Nadrian Seeman

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

DNA self-assembly is a methodology for the construction of molecular scale structures. In this method, artificially synthesized single stranded DNA self-assemble into DNA crossover molecules (tiles). These DNA tiles have sticky ends that preferentially match the sticky ends of certain other DNA tiles, facilitating the further assembly into tiling lattices. We discuss key theoretical and practical challenges of DNA self-assembly, as well as numerous potential applications. The self-assembly of large 2D lattices consisting of up to thousands of tiles have been recently demonstrated, and 3D DNA lattices may soon be feasible to construct. We describe various novel DNA tiles with properties that facilitate self-assembly and their visualization by imaging devices such as atomic force microscope. We discuss bounds on the speed and error rates of the various types of self-assembly reactions, as well as methods that may minimize errors in self-assembly. We briefly discuss the ongoing development of attachment chemistry from DNA lattices to various types of molecules, and consider application of DNA lattices (assuming the development of such appropriate attachment chemistry from DNA lattices to these objects) as a substrate for: (a) layout of molecular electronic circuit components, (b) surface chemistry, for example ultra compact annealing arrays, (c) molecular robotics; for manipulation of molecules using molecular motor devices. DNA self-assembly can, using only a small number of component tiles, provide arbitrarily complex assemblies. It can be used to execute computation, using tiles that specify individual steps of the computation. In this emerging new methodology for computation: -input is provided by sets of single stranded DNA that serve as nucleation sites for assemblies, and -output can be made by the ligation of reporter strands of DNA that run though the resulting assembly, and then released by denaturing. DNA self-assembly can be used to execute massively parallel computations at the molecular scale, with concurrent assemblies that may execute computations independently. Due to the very compact form of DNA molecules, the degree of parallelism (due to distinct tiling assemblies) may be up to 1015 to possibly 1018. We describe various DNA tiling assemblies that execute various basic computational tasks, such as sequences of arithmetic and logical computations executed in massively parallel fashion. We also consider extensions of these computational methods to 3D DNA tiling lattices and to assemblies that hold state.

Original languageEnglish (US)
Title of host publicationDNA Computing - 6th International Workshop on DNA-Based Computers, DNA 2000 Leiden, The Netherlands, June 13-17, 2000 Revised Papers
PublisherSpringer Verlag
Pages173-198
Number of pages26
Volume2054
ISBN (Print)3540420762, 9783540420767
DOIs
StatePublished - 2001
Event6th International Workshop on DNA-Based Computers, DNA 2000 - Leiden, Netherlands
Duration: Jun 13 2000Jun 17 2000

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume2054
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other6th International Workshop on DNA-Based Computers, DNA 2000
CountryNetherlands
CityLeiden
Period6/13/006/17/00

Fingerprint

Self-assembly
Nanostructures
Tile
DNA
Tiling
Self assembly
Molecules
Chemistry
Molecular Motor
Atomic Force Microscope
Methodology
Number of Components
Parallel Computation
Annealing
Nucleation
Computational Methods
Parallelism
Crossover
Error Rate
Robotics

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

Cite this

Reif, J. H., LaBean, T. H., & Seeman, N. (2001). Challenges and applications for self-assembled DNA nanostructures. In DNA Computing - 6th International Workshop on DNA-Based Computers, DNA 2000 Leiden, The Netherlands, June 13-17, 2000 Revised Papers (Vol. 2054, pp. 173-198). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2054). Springer Verlag. https://doi.org/10.1007/3-540-44992-2_12

Challenges and applications for self-assembled DNA nanostructures. / Reif, John H.; LaBean, Thomas H.; Seeman, Nadrian.

DNA Computing - 6th International Workshop on DNA-Based Computers, DNA 2000 Leiden, The Netherlands, June 13-17, 2000 Revised Papers. Vol. 2054 Springer Verlag, 2001. p. 173-198 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2054).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Reif, JH, LaBean, TH & Seeman, N 2001, Challenges and applications for self-assembled DNA nanostructures. in DNA Computing - 6th International Workshop on DNA-Based Computers, DNA 2000 Leiden, The Netherlands, June 13-17, 2000 Revised Papers. vol. 2054, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 2054, Springer Verlag, pp. 173-198, 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, Netherlands, 6/13/00. https://doi.org/10.1007/3-540-44992-2_12
Reif JH, LaBean TH, Seeman N. Challenges and applications for self-assembled DNA nanostructures. In DNA Computing - 6th International Workshop on DNA-Based Computers, DNA 2000 Leiden, The Netherlands, June 13-17, 2000 Revised Papers. Vol. 2054. Springer Verlag. 2001. p. 173-198. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/3-540-44992-2_12
Reif, John H. ; LaBean, Thomas H. ; Seeman, Nadrian. / Challenges and applications for self-assembled DNA nanostructures. DNA Computing - 6th International Workshop on DNA-Based Computers, DNA 2000 Leiden, The Netherlands, June 13-17, 2000 Revised Papers. Vol. 2054 Springer Verlag, 2001. pp. 173-198 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
@inproceedings{4cf6f9dd21da41aaad56668dcfefaaeb,
title = "Challenges and applications for self-assembled DNA nanostructures",
abstract = "DNA self-assembly is a methodology for the construction of molecular scale structures. In this method, artificially synthesized single stranded DNA self-assemble into DNA crossover molecules (tiles). These DNA tiles have sticky ends that preferentially match the sticky ends of certain other DNA tiles, facilitating the further assembly into tiling lattices. We discuss key theoretical and practical challenges of DNA self-assembly, as well as numerous potential applications. The self-assembly of large 2D lattices consisting of up to thousands of tiles have been recently demonstrated, and 3D DNA lattices may soon be feasible to construct. We describe various novel DNA tiles with properties that facilitate self-assembly and their visualization by imaging devices such as atomic force microscope. We discuss bounds on the speed and error rates of the various types of self-assembly reactions, as well as methods that may minimize errors in self-assembly. We briefly discuss the ongoing development of attachment chemistry from DNA lattices to various types of molecules, and consider application of DNA lattices (assuming the development of such appropriate attachment chemistry from DNA lattices to these objects) as a substrate for: (a) layout of molecular electronic circuit components, (b) surface chemistry, for example ultra compact annealing arrays, (c) molecular robotics; for manipulation of molecules using molecular motor devices. DNA self-assembly can, using only a small number of component tiles, provide arbitrarily complex assemblies. It can be used to execute computation, using tiles that specify individual steps of the computation. In this emerging new methodology for computation: -input is provided by sets of single stranded DNA that serve as nucleation sites for assemblies, and -output can be made by the ligation of reporter strands of DNA that run though the resulting assembly, and then released by denaturing. DNA self-assembly can be used to execute massively parallel computations at the molecular scale, with concurrent assemblies that may execute computations independently. Due to the very compact form of DNA molecules, the degree of parallelism (due to distinct tiling assemblies) may be up to 1015 to possibly 1018. We describe various DNA tiling assemblies that execute various basic computational tasks, such as sequences of arithmetic and logical computations executed in massively parallel fashion. We also consider extensions of these computational methods to 3D DNA tiling lattices and to assemblies that hold state.",
author = "Reif, {John H.} and LaBean, {Thomas H.} and Nadrian Seeman",
year = "2001",
doi = "10.1007/3-540-44992-2_12",
language = "English (US)",
isbn = "3540420762",
volume = "2054",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
publisher = "Springer Verlag",
pages = "173--198",
booktitle = "DNA Computing - 6th International Workshop on DNA-Based Computers, DNA 2000 Leiden, The Netherlands, June 13-17, 2000 Revised Papers",

}

TY - GEN

T1 - Challenges and applications for self-assembled DNA nanostructures

AU - Reif, John H.

AU - LaBean, Thomas H.

AU - Seeman, Nadrian

PY - 2001

Y1 - 2001

N2 - DNA self-assembly is a methodology for the construction of molecular scale structures. In this method, artificially synthesized single stranded DNA self-assemble into DNA crossover molecules (tiles). These DNA tiles have sticky ends that preferentially match the sticky ends of certain other DNA tiles, facilitating the further assembly into tiling lattices. We discuss key theoretical and practical challenges of DNA self-assembly, as well as numerous potential applications. The self-assembly of large 2D lattices consisting of up to thousands of tiles have been recently demonstrated, and 3D DNA lattices may soon be feasible to construct. We describe various novel DNA tiles with properties that facilitate self-assembly and their visualization by imaging devices such as atomic force microscope. We discuss bounds on the speed and error rates of the various types of self-assembly reactions, as well as methods that may minimize errors in self-assembly. We briefly discuss the ongoing development of attachment chemistry from DNA lattices to various types of molecules, and consider application of DNA lattices (assuming the development of such appropriate attachment chemistry from DNA lattices to these objects) as a substrate for: (a) layout of molecular electronic circuit components, (b) surface chemistry, for example ultra compact annealing arrays, (c) molecular robotics; for manipulation of molecules using molecular motor devices. DNA self-assembly can, using only a small number of component tiles, provide arbitrarily complex assemblies. It can be used to execute computation, using tiles that specify individual steps of the computation. In this emerging new methodology for computation: -input is provided by sets of single stranded DNA that serve as nucleation sites for assemblies, and -output can be made by the ligation of reporter strands of DNA that run though the resulting assembly, and then released by denaturing. DNA self-assembly can be used to execute massively parallel computations at the molecular scale, with concurrent assemblies that may execute computations independently. Due to the very compact form of DNA molecules, the degree of parallelism (due to distinct tiling assemblies) may be up to 1015 to possibly 1018. We describe various DNA tiling assemblies that execute various basic computational tasks, such as sequences of arithmetic and logical computations executed in massively parallel fashion. We also consider extensions of these computational methods to 3D DNA tiling lattices and to assemblies that hold state.

AB - DNA self-assembly is a methodology for the construction of molecular scale structures. In this method, artificially synthesized single stranded DNA self-assemble into DNA crossover molecules (tiles). These DNA tiles have sticky ends that preferentially match the sticky ends of certain other DNA tiles, facilitating the further assembly into tiling lattices. We discuss key theoretical and practical challenges of DNA self-assembly, as well as numerous potential applications. The self-assembly of large 2D lattices consisting of up to thousands of tiles have been recently demonstrated, and 3D DNA lattices may soon be feasible to construct. We describe various novel DNA tiles with properties that facilitate self-assembly and their visualization by imaging devices such as atomic force microscope. We discuss bounds on the speed and error rates of the various types of self-assembly reactions, as well as methods that may minimize errors in self-assembly. We briefly discuss the ongoing development of attachment chemistry from DNA lattices to various types of molecules, and consider application of DNA lattices (assuming the development of such appropriate attachment chemistry from DNA lattices to these objects) as a substrate for: (a) layout of molecular electronic circuit components, (b) surface chemistry, for example ultra compact annealing arrays, (c) molecular robotics; for manipulation of molecules using molecular motor devices. DNA self-assembly can, using only a small number of component tiles, provide arbitrarily complex assemblies. It can be used to execute computation, using tiles that specify individual steps of the computation. In this emerging new methodology for computation: -input is provided by sets of single stranded DNA that serve as nucleation sites for assemblies, and -output can be made by the ligation of reporter strands of DNA that run though the resulting assembly, and then released by denaturing. DNA self-assembly can be used to execute massively parallel computations at the molecular scale, with concurrent assemblies that may execute computations independently. Due to the very compact form of DNA molecules, the degree of parallelism (due to distinct tiling assemblies) may be up to 1015 to possibly 1018. We describe various DNA tiling assemblies that execute various basic computational tasks, such as sequences of arithmetic and logical computations executed in massively parallel fashion. We also consider extensions of these computational methods to 3D DNA tiling lattices and to assemblies that hold state.

UR - http://www.scopus.com/inward/record.url?scp=84958981221&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84958981221&partnerID=8YFLogxK

U2 - 10.1007/3-540-44992-2_12

DO - 10.1007/3-540-44992-2_12

M3 - Conference contribution

SN - 3540420762

SN - 9783540420767

VL - 2054

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 173

EP - 198

BT - DNA Computing - 6th International Workshop on DNA-Based Computers, DNA 2000 Leiden, The Netherlands, June 13-17, 2000 Revised Papers

PB - Springer Verlag

ER -