The absence of tertiary interactions in a self-assembled DNA crystal structure

Nam Nguyen, Jens J. Birktoft, Ruojie Sha, Tong Wang, Jianping Zheng, Pamela E. Constantinou, Stephan L. Ginell, Yi Chen, Chengde Mao, Nadrian Seeman

Research output: Contribution to journalArticle

Abstract

DNA is a highly effective molecule for controlling nanometer-scale structure. The convenience of using DNA lies in the programmability of Watson-Crick base-paired secondary interactions, useful both to design branched molecular motifs and to connect them through sticky-ended cohesion. Recently, the tensegrity triangle motif has been used to self-assemble three-dimensional crystals whose structures have been determined; sticky ends were reported to be the only intermolecular cohesive elements in those crystals. A recent communication in this journal suggested that tertiary interactions between phosphates and cytosine N(4) groups are responsible for intermolecular cohesion in these crystals, in addition to the secondary and covalent interactions programmed into the motif. To resolve this issue, we report experiments challenging this contention. Gel electrophoresis demonstrates that the tensegrity triangle exists in conditions where cytosine-PO 4 tertiary interactions seem ineffective. Furthermore, we have crystallized a tensegrity triangle using a junction lacking the cytosine suggested for involvement in tertiary interactions. The unit cell is isomorphous with that of a tensegrity triangle crystal reported earlier. This structure has been solved by molecular replacement and refined. The data presented here leave no doubt that the tensegrity triangle crystal structures reported earlier depend only on base pairing and covalent interactions for their formation.

Original languageEnglish (US)
Pages (from-to)234-237
Number of pages4
JournalJournal of Molecular Recognition
Volume25
Issue number4
DOIs
StatePublished - Apr 2012

Fingerprint

Cytosine
DNA
Base Pairing
Electrophoresis
Gels
Phosphates

Keywords

  • crystal design
  • DNA nanotechnology
  • robust DNA motif
  • self-assembled DNA crystals

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology

Cite this

Nguyen, N., Birktoft, J. J., Sha, R., Wang, T., Zheng, J., Constantinou, P. E., ... Seeman, N. (2012). The absence of tertiary interactions in a self-assembled DNA crystal structure. Journal of Molecular Recognition, 25(4), 234-237. https://doi.org/10.1002/jmr.2183

The absence of tertiary interactions in a self-assembled DNA crystal structure. / Nguyen, Nam; Birktoft, Jens J.; Sha, Ruojie; Wang, Tong; Zheng, Jianping; Constantinou, Pamela E.; Ginell, Stephan L.; Chen, Yi; Mao, Chengde; Seeman, Nadrian.

In: Journal of Molecular Recognition, Vol. 25, No. 4, 04.2012, p. 234-237.

Research output: Contribution to journalArticle

Nguyen, N, Birktoft, JJ, Sha, R, Wang, T, Zheng, J, Constantinou, PE, Ginell, SL, Chen, Y, Mao, C & Seeman, N 2012, 'The absence of tertiary interactions in a self-assembled DNA crystal structure', Journal of Molecular Recognition, vol. 25, no. 4, pp. 234-237. https://doi.org/10.1002/jmr.2183
Nguyen N, Birktoft JJ, Sha R, Wang T, Zheng J, Constantinou PE et al. The absence of tertiary interactions in a self-assembled DNA crystal structure. Journal of Molecular Recognition. 2012 Apr;25(4):234-237. https://doi.org/10.1002/jmr.2183
Nguyen, Nam ; Birktoft, Jens J. ; Sha, Ruojie ; Wang, Tong ; Zheng, Jianping ; Constantinou, Pamela E. ; Ginell, Stephan L. ; Chen, Yi ; Mao, Chengde ; Seeman, Nadrian. / The absence of tertiary interactions in a self-assembled DNA crystal structure. In: Journal of Molecular Recognition. 2012 ; Vol. 25, No. 4. pp. 234-237.
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