Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Two Dimensional DNA Parallelogram Crystals

Two-dimensional DNA crystals have been designed and constructed from Holliday junction analogues that have been combined in groups of four to form parallelogram-like structures. The Holliday junction is not an inherently rigid system, but it can be made less flexible if it is combined into a larger construct (1). Here, we describe 2D lattices formed from three such motifs. In the first motif, we have fused four junctions into a rhombus-like molecule consisting of four eight-turn helices, two on an upper layer and two on a lower layer; the branch points, which define vertices, are separated by four double helical turns each. The rhombuses can be directed to self-assemble by hydrogen bonding of sticky ends to form a two-dimensional periodic array, whose spacing is eight turns in each direction, with a pseudo-spacing of 4 turns in each direction. The expected pseudo-spacing is seen when the array is observed by atomic force microscopy (AFM). A related motif of the same dimensions has been constructed previously with these dimensions; in that case the crossover points consisted of Bowtie junctions.

A qualitatively different array is visualized when the eight?turn spacing consists of a six-turn component and a two-turn component. The two turn spacing is hard to visualize, but the six turn cavities are evident in the AFM images obtained. Hence, it is possible to assemble periodic arrays with tunable cavities using these components. The new size of the motif is expected to serve as a better surface for the deposition of metals. This system also provides the opportunity to measure directly the angles or torsion angles between the arms of branched junctions; here we measure the torsion angle between the helical domains of the Holliday junction analog. We find by AFM that the torsion angles between helices are 68° in the 4-turn array and 60° in the 6+2 turn array.

This research supported by NIGMS, ONR, DARPA/AFOSR, and NSF.

Lisa B. Israel
Nadrian C. Seeman

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

Reference and Footnotes
  1. Mao, C., Sun W., & Seeman, N.C., Designed Two-Dimensional DNA Holliday Junction Arrays Visualized by Atomic Force Microscopy, J. Am. Chem. Soc. 121, 5437-5443 (1999).