Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

2D DNA Arrays Used to Organize DNA-Based Devices, DNAzymes and Metallic Nanoparticles

Structural DNA nanotechnology combines branched DNA motifs with cohesive ends to form objects, lattices, and devices. It has been possible for many years to produce 2D arrays from a variety of DNA motifs that tile the plane. One of the chief goals of this approach is not merely to produce DNA arrangements, but to organize functional species. Here, we report three examples of using DNA tiles to organize other materials. In the first case, schematized below, we have used three-domain motifs (TX) connected 1-3 to form a lattice containing gaps that are flanked by sticky ends. We have developed a cassette that we can used to insert the robust sequence PX-JX2 motif into one of these gaps. We demonstrate by atomic force microscopy (AFM) that the device is functional following insertion.

In the second case, we have attached a DNAzyme to a two-domain (DX) motif. The DNAzyme cleaves itself in the presence of cupric cations, and we demonstrate this activity by a change in the pattern, as visualized by AFM. In principle, this system can lead to a 'developmental' pathway. In a third case, we have developed a robust 3-space-spanning motif, the 3D-DX triangle, held together by sticky-ended double cohesion. We use two of the propagation directions to form the 2D array, and then use the third direction as the site to attach a metallic nanoparticle. One strand of DNA is attached to the nanoparticle, and this strand is a strand that is part of the motif. By using two different DNA tiles, and two differently-sized nanoparticles, we can make uniform, gapped, or checkerboard patterns, which are visualized by transmission electron microscopy. The checkerboard pattern is shown schematically below.

This research supported by NIGMS, NSF, ARO and the W.M. Keck Foundation.

Baoquan Ding
Alejandra Garibotti
Jiwen Zheng
Pamela Constantinou
Nadrian C. Seeman*

Department of Chemistry
New York University
New York NY 10003

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