Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Two Dimensional Crystals of DNA DX-Parallelograms

Two-dimensional DNA crystals have been designed and constructed from Holliday junction analogues by combining them 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). Previously, 2D parallelogram lattices have been formed by fusing four junctions into a rhombus-like molecule consisting of four eight-turn helices, two on an upper layer and two on a lower layer. Recently, the parallelogram has been redesigned to have larger cavities. This has been done by forming 2D parallelogram lattices consisting of four twelve turn helices. These parallelograms were not well-behaved at all.

However, we established recently that using double crossover (DX) components, rather than single helices leads to much more robust motifs; the use of DX cohesion is particularly important (2). Consequently, to create these new 2D crystals, each helix of the original parallelogram was replaced by a DX molecule, making it a DX parallelogram. This led both to reinforced components and to double cohesion between units. Two versions of this DX parallelogram were designed. DX molecules are characterized by the relative orientations of their helices and the number of half helical turns between junction points. The orientations of the helices were antiparallel in both designs, but the number of half helical turns between junctions differed. The first version was designed to have all even number of half helical turns between junctions therefore this molecule is called the PDX-E-E. The periodicity of this molecule was 40nm. This design did not yield an extensive, well-ordered array, and the angle could not be accurately measured for this motif. The second version was designed to have a repeating pattern of every other number of half helical turns between junctions being even and odd therefore this molecule is called the PDX-E-O. The periodicity of this molecule was also measured to be 40nm and the torsion angles between the arms of branched junctions were measured to be 50°, as illustrated in the AFM image (left) and its zoom (right). These new designs provide a larger size parallelogram that we expect to find utility in patterning.


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

References and Footnotes
  1. Mao, C., Sun W., and Seeman, N. C. J. Am. Chem. Soc. 121, 5437-5443 (1999).
  2. Ding, B., Sha, R., and Seeman, N.C. J. Am. Chem. Soc. 126, 10230-10231 (2004).

Lisa B. Israel
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