Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Assembly and Characterization of Eight-Arm and Twelve-Arm DNA Branched Junctions

The connectivity of networks built from DNA branched junctions is a function of the number of arms in the junctions used. To date, junctions containing up to six arms have been reported (1), limiting the possible products to 6-connected networks. Here, we report the construction of DNA branched junctions that contain either eight arms or twelve arms surrounding a branch point. The eight-arm junction is as stable as junctions containing five or six arms, but twelve-arm junction is not. Unlike such smaller junctions as five, six, and eight arms, twelve-arm junction cannot be shown to migrate as a single band on native gel when each of its arms contains sixteen nucleotide pairs. However it can be stabilized if its arms contain twenty-four nucleotide pairs.

Ferguson analysis of these junctions in combination with three, four, five, and six-arm junctions indicates a linear increase in friction constant as the number of arms increases. The four-arm junction migrates anomalously slowly at 4°C, but it migrates as though it consists of four separate cylinders at 25°C or higher. We ascribe this effect to the well-known stacking of the arms of the 4-arm junction at lower temperatures. Ferguson analysis does not show the eight-arm and twelve-arm junctions to have any unusual stacking structure. All strands show similar responses to hydroxyl radical autofootprinting analysis.

The ability to construct eight-arm and twelve-arm junctions vastly increases the number of structures and networks that can be built from branched DNA components. In particular, the classical Buckminster Fuller octet truss structure, the 'stick' version of cubic-close packing, is 12-connected. This highly stable motif is now a realistic target for DNA nanotechnology, as a consequence of the ability to construct the 12-arm junction. In addition, branch migration can be used as the basis for motion in nanomechanical devices (2). In principle, it is possible to have branch migration in these even-armed junctions, suggesting that they could be used in similar systems, with multiple sites of control.

Xing Wang
Nadrian C. Seeman*

Department of Chemistry
New York University
New York, NY 10003, USA

*Phone: 212-998-8395
Fax: 212-260-7905
Email: ned.seeman@nyu.edu


This research supported by NIGMS, ONR, NSF and Nanoscience Technologies, Inc.

References and Footnotes
  1. Y. Wang, J. E. Mueller, B. Kemper, and N. C. Seeman. Biochem. 30, 5667-5674 (1991).
  2. X. Yang, A. Vologodskii, B. Liu, B. Kemper, and N. C. Seeman. Biopols. 45, 69-83 (1998).