Albany 2015:Book of Abstracts
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.
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).
1Department of Chemistry