Book of Abstracts: Albany 2009

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

Exploring the Rigidity of DNA Nanotubes

DNA nanotubes are cyclic arrangements of DNA motifs that form cylinders. It is possible to design cyclic species with a specific number of helices, most prominently the six-helix bundle (6HB).1 In this case, a series of six DNA double helices are joined together laterally, so that the dihedral angle between any adjacent pairs is 120?. This is an easy angle to achieve for 10.5-fold DNA, because crossover separations of 7 or 14 nucleotide pairs correspond to 2/3 or 4/3 of a turn, respectively. In addition to the direct formation of the 6HB molecule from a group of strands, we have recently reported the formation of 6HB molecules from the lateral cohesion of pairs of bent three-helix (BTX) molecules, thus potentially facilitating the sheathing of a nanorod.2

It is easy to make long tubes from 6HB molecules, by adding sticky ends to both ends of each helix. Such long DNA nanotubes are expected to have structural applications in DNA nanotechnology. It is therefore important to characterize their physical properties. Prominent among these is their rigidity, described by the persistence length. Here, we report on the rigidity of 6HB tubes and two variations, in which the 6HB motif is flanked with either two or three more DNA helices. The 6HB molecule flanked by two helices is pictured below (left) alongside a fluorescence snapshot of a corresponding nanotube (right). The snapshot was taken as the nanotube diffused freely while confined to the focal plane of a microscope by two polymer-coated pieces of glass. Comparison of the average end-to-end distance of a dozen such nanotubes, with contour lengths ranging from 3 to 16 μm, indicates that the persistence length of the 6HB+2 tube is around 3.5 μm, consistent with a mechanical model based on rigidly linked dsDNA (known persistence length ~50 nm). We find that the relative placement of sticky ends is a key factor in the rigidity of the motif.

This research has been supported by a grant from NSF to DKF, and grants from NIGMS, NSF, ARO, ONR and the W.M. Keck Foundation to NCS.

References and Footnotes
  1. Mathieu, F., Liao, S., Mao, C., Kopatsch, J., Wang, T., Seeman, N.C., NanoLett. 5, 661-665 (2005).
  2. Kuzuya, A., Wang, R., Sha, R., Seeman, N.C., NanoLett. 7, 1757-1763 (2007).

Tong Wang
Sergio Martinez
Deborah Kuchnir Fygenson*
Nadrian C. Seeman*

Dept of Chemistry
New York University
New York NY 10003

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