Book of Abstracts: Albany 2009

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

Braided DNA

On the macroscopic scale, braided materials are regarded as stronger than materials that are just wrapped together. It is not very hard to braid various strands on this scale, where the operations needed to produce braids are readily performed. However, on the molecular scale it is difficult to perform such an operation. The key issue is that braiding requires the use of both positive and negative nodes, as indicated in the image on the left. If one chooses to work with DNA, it turns out that B-DNA, which is right-handed, provides negative nodes, and Z-DNA, which is left-handed, provides positive nodes. Mixed B-DNA and Z-DNA species have been made in the past, including knots, Borromean rings and a nanomechanical device. However, it is more convenient to be able to work with any sequence, rather than to work with the set of sequences that can be induced to form Z-DNA. To that end, we have sought to make a braided structure that contains both conventional DNA made from D-nucleosides and its mirror image, which is made from L-nucleosides. One minor complication of using that approach to making braided materials, unless they are wrapped into a cylindrical tube, is that one must use 5?,5? and 3?,3? linkages to make the constituent strands. We have synthesized the appropriate strands, both out of conventional DNA and out of DNA containing strategically placed L-nucleosides. The design is shown on the right of the figure. Whereas the complex is stable when made from conventional DNA, the circular strands separate upon denaturation. In contrast, the structure containing the L-nucleotides is stable under denaturing conditions. We show by restriction analysis that the braided structure consists of the two circles, in agreement with the design.

The drawing on the left shows the design of the denatured braided complex. The signs of its nodes are indicated. The drawing on the right illustrates the design of the same complex from DNA in its native state. Nucleotides containing D-deoxyribose are drawn in black and those containing L-deoxyribose are drawn in red. The signs of the nodes are indicated. Double filled circles indicate 5?,5? linkages and double arrowheads indicate 3?,3? linkages.

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

Tanashaya Ciengshin
Ruojie Sha
Nadrian C. Seeman*

Dept of Chemistry
New York University
New York NY 10003

ph: 212-998-8395
fx: 212-260-7905