Albany 2015:Book of Abstracts

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

Programmable Crystal Contacts Used to Improve the Resolution of Self-Assembled 3D DNA Crystals

Synthetic branched DNA motifs have been used for the construction of nanoscale objects and periodic arrays in one-, two- and three dimensions. The tensegrity triangle is a stiff DNA motif with three-fold rotational symmetry (Liu et al. 2004), consisting of three B-DNA double helices whose axes are directed along linearly independent directions. Triangles with edges two turns long form a crystalline lattice stabilized via sticky ends. The length of the sticky ends (GA:TC) reported previously was two nucleotides (nt), and the design demonstrated the ability to program the generation of crystalline DNA assemblies (Zheng et al., 2009). These crystals exhibit limited diffracting ability (4.9 Å at beam line NSLS-X25). Recently, we reported that the addition of 5'-phosphate (P) groups improved resolution to 4.1 Å at the same beam line (Sha et al., 2013). In this study, we analyzed the effect of sticky end length and sequence as well as 5'-P position on crystal formation and resolution. Crystals with 1-nt (G:C) sticky ends diffracted to 3.3 Å at the same beam line. We also crystallized the 1-nt and 2-nt motifs with 5'-P on the crossover (1), helical (2) or central (3) strands. The best crystal resolution (2.62 Å) was obtained from the 1-nt system with the 1P-2-3 combination at beam line APS-ID19. Thus, the programmability of intermolecular contacts has facilitated the optimization of diffracting ability for this system.

We acknowledge support of the following grants to NCS: grant no. GM-29554 from the National Institute of General Medical Sciences, grants CMMI-1120890 and CCF-1117210 from the National Science Foundation, MURI W911NF-11-1- 0024 from the Army Research Office, and grants N000141110729 and N000140911118 from the Office of Naval Research.

    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).

    Sha, R., Birktoft, J. J., Nguyen, N., Chandrasekaran, A. R., Zheng, J., Zhao, X., Mao, C., and Seeman, N. C. (2013). Self-assembled DNA crystals: the impact on resolution of 5' phosphates and the DNA source. Nano letters, 13(2), 793-797.

Yoel P. Ohayon1
Arun Richard Chandrasekaran1
Carina Hernandez1
Jens J. Birktoft1
Ruojie Sha, 1
Steve Ginell2
Phil Lukeman3
Chengde Mao4
Paul M. Chaikin5
Nadrian C. Seeman1*

1 Department of Chemistry
New York University
New York, NY 10003, USA
2 Structural Biology Center
Argonne National Laboratory
Argonne, IL, 60439 USA
3 Department of Chemistry
St. John's University
New York, NY, 11439 USA
4 Department of Chemistry
Purdue University
West Lafayette, IN, 47907 USA
5 Department of Physics
New York University
New York, NY 10003, USA.

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