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Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

Impact of Sticky End Length on the Diffraction of Self-Assembled DNA Crystals

Our laboratory has reported a self-assembled three-dimensional crystal based on a DNA tensegrity triangle. The tensegrity triangle is a rigid DNA motif with three-fold rotational symmetry, consisting of three helices whose axes are directed along three linearly independent directions (Liu et al. 2004). The triangles form a crystalline lattice stabilized via sticky ends (Zheng et al. 2009). The length of the sticky ends reported previously was two nucleotides (nt) GA:TC. Although diffracting to 4 Å resolution at the APS-ID19 beam line, they diffract only to 4.9 Å at the NSLS-X25 beam line. In the current study, we have analyzed the effect of sticky end length and sequence on crystal formation and the resolution of the X-ray diffraction pattern on NSLS-X25. Tensegrity triangle motifs having 1-, 2-, and 3-nt sticky ends all formed crystals. X-ray diffraction data from the same beam line revealed that the crystal resolution was somewhat better for the 2-nt sticky end having an AA:TT base pair (4.75 Å) than GA:CT and CC:GG (8.0 Å). Moreover the 1-nt sticky end (C:G) yielded a diffraction pattern whose resolution (3.5 Å) compared favorably with all three 2-nt sticky end systems. However the triangle motif having a 1-nt sticky end with an A:T base pair did not yield any crystals. For motifs with 3-nt sticky ends, the sequence GAG:CTC produced small crystals (10-20 µm) while larger crystals (150 µm) were obtained with the sequences TAG:ATC and TAT:ATA. Our results indicate that not only do the lengths and sequences of the sticky ends define the interactions between motifs, but they also have an impact on the resulting resolution. We expect redesigned assemblies to form three-dimensional crystals with better resolution that can aid in the scaffolding of biological macromolecules for crystallographic structure determination. Applications in many areas of DNA nanotechnology are expected to benefit from a complete analysis of the effects of sticky end length, sequence and free energy.

We acknowledge support of the following grants to NCS: grant GM-29554 from NIGMS, grants CTS-0608889 and CCF-0726378 from the NSF, grant W911FF-08-C-0057 from ARO, grants N000140910181 and N000140911118 from ONR and DE-SC0007991 from DOE.

References

    Liu, D., Wang, W., Deng, Z., Walulu, R., Mao, C., Tensegrity: Construction of rigid DNA triangles with flexible four-arm junctions, J. Am. Chem. Soc. 126, 2324-2325 (2004).

    Zheng, J., Birktoft, J.J., Chen, Y., Wang, T., Sha, R., Constantinou, P.E., Ginell, S.L., Mao, C., Seeman, N.C.. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461, 74-77 (2009).


Yoel P. Ohayon 1
Arun Richard Chandrasekaran1
Esra Demirel1
Sabrine I. Obbad1
Rutu C. Shah1
Victoria T. Adesoba1
Matthew Lehmann1
Jens J. Birktoft1
Ruojie Sha1
Paul M. Chaikin2
Nadrian C. Seeman 1*

1Department of Chemistry
New York University
New York, NY 10003, USA
2Department of Physics
New York University
New York, NY 10003, USA

Ph: (212) 998-8395
Fax: (212) 995-4475
ned.seeman@nyu.edu