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

LaBean, Thomas H. and Yan, Hao and Kopatsch, Jens and Liu, Furong and Winfree, Erik and Reif, John H. and Seeman, Nadrian C. (2000) Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. Journal of the American Chemical Society, 122 (9). pp. 1848-1860. ISSN 0002-7863. https://resolver.caltech.edu/CaltechAUTHORS:20110309-104204822

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1021/ja993393eDOIArticle
http://pubs.acs.org/doi/full/10.1021/ja993393ePublisherArticle
ORCID:
AuthorORCID
Winfree, Erik0000-0002-5899-7523
Seeman, Nadrian C.0000-0002-9680-4649
Additional Information:© 2000 American Chemical Society. Received September 20, 1999. Published on Web 02/09/2000. We thank Dr. Brad Chaires for useful advice about DNA melting experiments. This work has been supported by grants NSF-CCR-97-25021 and CCR-96-33567 from DARPA and the National Science Foundation to J.H.R. and N.C.S., IRI-9619647 from NSF to J.H.R., ARO contract DAAH-0496-1-0448 to J.H.R., N00014-89-J-3078 from the Office of Naval Research to N.C.S., GM-29554 from the National Institute of General Medical Sciences to N.C.S., and F30602-98-C-0148 from the Air Force Research Laboratory Located at Rome, NY, to N.C.S.
Funders:
Funding AgencyGrant Number
NSFCCR-97-25021
NSCCR-96-33567
NSFIRI-9619647
Army Research Office (ARO)DAAH-0496-1-0448
Office of Naval Research (ONR)N00014-89-J-3078
NIHGM-29554
Air Force Research LaboratoryF30602-98-C-0148
Defense Advanced Research Projects Agency (DARPA)UNSPECIFIED
Issue or Number:9
Record Number:CaltechAUTHORS:20110309-104204822
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20110309-104204822
Official Citation: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,, and, Nadrian C. Seeman, Journal of the American Chemical Society 2000 122 (9), 1848-1860
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:22775
Collection:CaltechAUTHORS
Deposited By: Lucinda Acosta
Deposited On:10 Mar 2011 17:51
Last Modified:09 Mar 2020 13:19

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