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Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

Let's Get Twisted: The Crystal Structure of Torsionally Stressed DNA

The self-assembly of 3D crystalline structures is one of the main goals of structural DNA nanotechnology. We have shown previously that it is possible to design and self-assemble a well-ordered macromolecular 3D crystalline lattice (3GBI) (Zheng et al., 2004). The motif used was the tensegrity triangle, a rigid DNA motif with three-fold pseudo-symmetry (Liu et al., 2004). One possible application of such a motif would be to obtain a detailed picture of torsionally stressed DNA, which is the state of DNA within the cell. In this experiment the two-turn DNA tensegrity triangle used previously with 7 nucleotide pairs between crossovers was modified to contain 8 nucleotides between crossovers, thereby producing an under-twisted state. The double helical region between the vertices thus experiences a strain owing to the extra nucleotide pair that has been inserted. The space group is R3, with a = 69.4 Å and α = 104.9°, similar to a = 69.2 Å and α = 101.4° for 3GBI. The crystal structure was solved by single wavelength anomalous techniques to 5.0 Å resolution; Rwork = 0.1960 and Rfree = 0.2114. We find that the DNA tolerates the strain well, and does not appear to extrude any nucleotides, despite the fairly large perturbation on the molecule. This modified design produces under-twisted DNA with an average twist of 31.32 degrees for the torsionally-stressed region. The planes of the bases in the stressed section are tilted on average by 3.22 degrees with respect to the helix axis, giving the helix a slightly curved appearance. The average separation of residues along the helix axis is 3.21 Å in this section. The intra-junction distance is determined to be 26.1 Å whereas for 3GBI it is 23.2 Å.

This research has been supported by he following grants to NCS: GM-29554 from NIGMS, grants CCF-1117210, CMMI-1120890, and EFRI-1332411 from the NSF, MURI W911NF-11-1-0024 from ARO, grants N000141110729 and N000140911118 from ONR, grant 3849 from the Gordon and Betty Moore Foundation.

References
    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).

    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).


Carina Hernandez1
Jens J. Birktoft1
Arun Richard
Chandrasekaran1
Yoel P. Ohayon1
Ruojie Sha1
Chengde Mao2
Nadrian C. Seeman1*

1Department of Chemistry
New York University
New York, NY 10003, USA
2Department of Chemistry
Purdue University
West Lafayette, IN, 47907 USA

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