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Two Dimensions and Two States in DNA Nanotechnology

Seeman, Nadrian C. and Liu, Furong and Mao, Chengde and Yang, Xiaoping and Wenzler, Lisa A. and Sha, Ruojie and Sun, Weiqiong and Shen, Zhiyong and Li, Xiaojun and Qi, Jing and Zhang, Yuwen and Fu, Tsu-Ju and Chen, Junghuei and Winfree, Erik (2000) Two Dimensions and Two States in DNA Nanotechnology. Journal of Biomolecular Structure and Dynamics, 11 (S2). pp. 253-262. ISSN 0739-1102.

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The construction of periodic matter and nanomechanical devices are central goals of DNA nanotechnology. The minimal requirements for components of designed crystals are [1] programmable interactions, [2] predictable local intermolecular structures and [3] rigidity. The sticky-ended association of DNA molecules fulfills the first two criteria, because it is specific and diverse, and it results in the formation of B-DNA. Stable branched DNA molecules permit the formation of networks, but individual single branches are too flexible. Antiparallel DNA double crossover (DX) molecules can provide the necessary rigidity, so we use these components to tile the plane. It is possible to include DNA hairpins that act as topographic labels for this 2-D crystalline array, because they protrude from its plane. By altering sticky ends, it is possible to change the topographic features formed by these hairpins, and to detect these changes by means of AFM. We can modify arrays by restricting hairpins or by adding them to sticking ends protruding from the array. Although individual branched junctions are unsuitable for use as crystalline components, parallelograms of four 4-arm junction molecules are sufficiently rigid that they can be used to produce 2D arrays. The arrays contain cavities whose dimensions are readily tuned by changing the edges of their parallelogram components. We have used these arrays to measure directly the angle between the helices of the Holliday junction. The rigidity of the DX motif can also be exploited to produce a nanomechanical device predicated on the B-Z transition. Two DNA double crossover molecules have been joined by a segment of DNA capable of undergoing the B-Z transition. In the B-conformation, the unconnected helices of the two molecules are on the same side of the connecting helix, whereas in the Z conformation they are on opposite sides, leading to movements of as much as 60Å. This effect is shown by fluorescence resonance energy transfer, because dyes attached to the unconnected helices have different separations in the two states.

Item Type:Article
Related URLs:
URLURL TypeDescription
Seeman, Nadrian C.0000-0002-9680-4649
Mao, Chengde0000-0001-7516-8666
Winfree, Erik0000-0002-5899-7523
Additional Information:© 2000 Adenine Press. This work has been supported by grants GM-29554 from the National Institute of General Medical Sciences, N00014-89-J- 3078 from the Office of Naval Research, NSF-CCR-97-25021 from DARPA/National Science Foundation and F30602-98-C- 0148 from the Information Directorate of the Rome NY Air Force Research Laboratory to N.C.S., by Margaret and Herman Sokol Fellowships to J.C. and X.Y., and by NYU-GSAS Dissertation Fellowships to Y.Z. and C.M.
Funding AgencyGrant Number
Office of Naval Research (ONR)N00014-89-J-3078
Rome NY Air Force Research Laboratory Information DirectorateF30602-98-C-0148
Margaret and Herman Sokol FellowshipsUNSPECIFIED
NYU-GSAS Dissertation FellowshipsUNSPECIFIED
Defense Advanced Research Projects Agency (DARPA)UNSPECIFIED
Issue or Number:S2
Record Number:CaltechAUTHORS:20111024-091114335
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:27366
Deposited By: Tony Diaz
Deposited On:24 Oct 2011 21:48
Last Modified:09 Mar 2020 13:19

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