Volume 24, Issue 11, Pages e2 (November 2017)

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Volume 24, Issue 11, Pages 1401-1406.e2 (November 2017) Self-Assembly of 3D DNA Crystals Containing a Torsionally Stressed Component Carina Hernandez, Jens J. Birktoft, Yoel P. Ohayon, Arun Richard Chandrasekaran, Hatem Abdallah, Ruojie Sha, Vivian Stojanoff, Chengde Mao, Nadrian C. Seeman Cell Chemical Biology Volume 24, Issue 11, Pages 1401-1406.e2 (November 2017) DOI: 10.1016/j.chembiol.2017.08.018 Copyright © 2017 Elsevier Ltd Terms and Conditions

Cell Chemical Biology 2017 24, 1401-1406. e2DOI: (10. 1016/j. chembiol Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 1 Torsionally Stressed Two-Turn Tensegrity Triangle (A) The schematic is shown along with the sequence (blunt end 5′-end and arrow 3′-end). The motif is composed of three helical strands (pink), three crossover strands (green), and one circular strand (blue). Iodine atoms in the form of 5-iodouracil or 5-iodocytosine were placed throughout the motif for use in SAD phasing (indicated by red arrows). The stressed region is composed of eight nucleotide pairs. (B) Simplified structural model of the torsionally stressed (PDB: 5EOS) tensegrity triangle showing nucleotide pairs and the molecular surface (Humphrey et al., 1996). (C) Crystals of the iodinated torsionally stressed tensegrity triangle. Most of the crystals were rhombohedral and were around 100 μm in size. Under polarized light, the crystals appear colored but are in fact clear. Cell Chemical Biology 2017 24, 1401-1406.e2DOI: (10.1016/j.chembiol.2017.08.018) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 2 Crystal Structure of PDB: 5EOS, the Under-Twisted Tensegrity Triangle Motif (A) The image shows a stereoscopic projection of the full triangle (three asymmetric units). Visualization was done by PyMol (PyMOL Molecular Graphics System, 2014). (B) This is a stereoscopic projection of the structure with electron density (2Fo − Fc map) contoured at sigma = 1.10. Note the absence of any electron density corresponding to an extruded nucleotide between branched junctions. The junction structures also appear to be undistorted. Cell Chemical Biology 2017 24, 1401-1406.e2DOI: (10.1016/j.chembiol.2017.08.018) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 3 Superimposed Portion between Crossover Points (A) Overlap of PDB: 5EOS, which is the stressed duplex (red) with idealized B-DNA (blue). (B) Overlap of PDB: 3GBI (green) with idealized B-DNA (blue). (C) Overlay of PDB: 5EOS (red) with PDB: 3GBI (green). This figure shows the structural basis for the relation between torsional strain experienced when adding an extra nucleotide pair. It also shows that when compared with ideal B-DNA, the stressed structure still keeps its B-form conformation. The above image was visualized on PyMol (PyMOL Molecular Graphics System, 2014). The B-DNA model was built using TURBO-FRODO (Roussel and Cambillau, 1991) according to idealized B-DNA parameters and is very similar to PDB: 1ZFG (Hays et al., 2005), an ideal B-DNA structure. Cell Chemical Biology 2017 24, 1401-1406.e2DOI: (10.1016/j.chembiol.2017.08.018) Copyright © 2017 Elsevier Ltd Terms and Conditions