Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

Topological Bonding of DNA Nanostructures

The properties of DNA that allow it to act as the storage medium of genetic information also make it an outstanding molecule for use in nanotechnology. This fact has led to the development of DNA nanotechnology which is based on Watson-Crick base pairing. The backbone structures involved these constructs are complex species, not simple linear duplex molecules. These motifs and various programmable structures in one, two and three dimensions are constructed by using sticky-ends which are short-linear extensions that hold complementary structures together. The PX (Paranemic Crossover) motif (1) has also been reported as another form of cohesion for large DNA structures. It may be useful in overcoming some of the weaknesses of sticky-ended cohesion (2). Both sticky-ended and PX cohesion are based on hydrogen-bonded interactions that cannot withstand denaturing conditions (3). In the work presented, we used two approaches to demonstrate that the hydrogen-bonded cohesion of DNA nanostructures can be transformed into a topological interaction. In the first case, we created a topological interaction between DNA structures that cohere via both PX and sticky-ends. Covalent linkages were created between the functionalized 3’ and 5’ ends of the sticky-ends. The torus-like structures were obtained via enzymatic ligation. In the second case, we converted the PX interaction of DNA circles containing cohesive loops into catenated structures via the use of Topo I enzyme by creating a linkage between the loops. The two methods were used to construct topologically linked one-dimensional DNA arrays assembled from different types of PX cohering tiles. The construction of these poly-catenated scaffolds allowed for a new method to position nano-particles on linear structures. The program Knotilus (4, 5) was used to determine and display the topology of the catenated DNA structures.

This work is supported by the grants from the National Institute of General Medical Sciences, the National Science Foundation, the Army Research Office and the Office of Naval Research.


  1. Z. Shen, H. Yan, T. Wang, N. C. Seeman, J. Am. Chem. Soc. 126, 1666–1674 (2004).
  2. X. Zhang, H. Yan, Z. Shen, and N. C. Seeman, J. Am. Chem. Soc. 124, 12940–12941 (2002).
  3. C.H. Spink, L. Ding, Q. Yang, R.D. Sheardy, N.C. Seeman, Biophys. J. 97, 528-538 (2009)
  4. Flint, O. "The Master Array, a complete invariant for prime alternating links" (Thesis, 2007)
  5. http://knotilus.math.uwo.ca/

Yoel Ohayon1
Ruojie Sha1
Ortho Flint, 2
Nadrian C. Seeman1

1Department of Chemistry
New York University
New York, NY 10003, USA
2Department of Mathematics
University of Western Ontario
London, ON, N6A 5B7 Canada

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