Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

A PX DNA Triangle Oligomerized Using a Novel Three-Domain Motif

Structural DNA nanotechnology is directed at building objects, lattices and arrays from cohesive interactions between DNA molecules. The predominant means of doing this takes advantage of the information inherent in Watson-Crick base pairing in duplex formation and in sticky-ended cohesion. Nevertheless, other forms of nucleic acid cohesion are also known, particularly paranemic edge-sharing interactions (PX). Here we report the formation of a triangular species that has four strands per edge, held together by PX interactions. We demonstrate by non-denaturing gel electrophoresis and by atomic force microscopy (AFM) that we can combine a partial triangle with other strands to form a four-stranded molecule that is robust. By combining them with a new mixed-fusion type of three-domain (TX) molecule called PATX, we demonstrate by AFM that these triangles can be self-assembled into a linear array.

Schematic Drawings of the motifs used in this work. (a) The PX motif. The four strands are colored red, purple, green and blue; base pairs and helix axes are indicated. (b) Top and side views of the PX triangle are shown, using the same colors as in (a). Only the blue strand is a cyclic molecule. (c) The formation of a linear array. The left side of the upper panel shows the sticky ends on the triangle as A and B; the right side shows the PATX motif (base pairs and helix axes indicated); complementary sticky ends, A' B' are shown; the top two domains are parallel, the bottom two antiparallel. The array incorporating both motifs is shown at the bottom of the panel.

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

Wenyan Liu
Xing Wang
Tong Wang
Ruojie Sha
Nadrian C. Seeman*

Dept of Chemistry
New York University
New York NY 10003

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