Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes

Thomas H. LaBean, Hao Yan, Jens Kopatsch, Furong Liu, Erik Winfree, John H. Reif, Nadrian Seeman

Research output: Contribution to journalArticle

Abstract

This paper extends the study and prototyping of unusual DNA motifs, unknown in nature, but founded on principles derived from biological structures. Artificially designed DNA complexes show promise as building blocks for the construction of useful nanoscale structures, devices, and computers. The DNA triple crossover (TX) complex described here extends the set of experimentally characterized building blocks. It consists of four oligonucleotides hybridized to form three double-stranded DNA helices lying in a plane and linked by strand exchange at four immobile crossover points. The topology selected for this TX molecule allows for the presence of reporter strands along the molecular diagonal that can be used to relate the inputs and outputs of DNA-based computation. Nucleotide sequence design for the synthetic strands was assisted by the application of algorithms that minimize possible alternative base-pairing structures. Synthetic oligonucleotides were purified, stoichiometric mixtures were annealed by slow cooling, and the resulting DNA structures were analyzed by nondenaturing gel electrophoresis and heat-induced unfolding. Ferguson analysis and hydroxyl radical autofootprinting provide strong evidence for the assembly of the strands to the target TX structure. Ligation of reporter strands has been demonstrated with this motif, as well as the self-assembly of hydrogen-bonded two-dimensional crystals in two different arrangements. Future applications of TX units include the construction of larger structures from multiple TX units, and DNA-based computation. In addition to the presence of reporter strands, potential advantages of TX units over other DNA structures include space for gaps in molecular arrays larger spatial displacements in nanodevices, and the incorporation of well-structured out-of-plane components in two-dimensional arrays.

Original languageEnglish (US)
Pages (from-to)1848-1860
Number of pages13
JournalJournal of the American Chemical Society
Volume122
Issue number9
DOIs
StatePublished - Mar 8 2000

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Self assembly
Ligation
DNA
Molecular Computers
Oligonucleotides
Nucleotide Motifs
Base Pairing
Hydroxyl Radical
Electrophoresis
Hydrogen
Hot Temperature
Gels
Nucleotides
Equipment and Supplies
Topology
Cooling
Crystals
Molecules

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. / LaBean, Thomas H.; Yan, Hao; Kopatsch, Jens; Liu, Furong; Winfree, Erik; Reif, John H.; Seeman, Nadrian.

In: Journal of the American Chemical Society, Vol. 122, No. 9, 08.03.2000, p. 1848-1860.

Research output: Contribution to journalArticle

LaBean, Thomas H. ; Yan, Hao ; Kopatsch, Jens ; Liu, Furong ; Winfree, Erik ; Reif, John H. ; Seeman, Nadrian. / Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. In: Journal of the American Chemical Society. 2000 ; Vol. 122, No. 9. pp. 1848-1860.
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