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Four highly pseudosymmetric and/or twinned structures of d(CGCGCG)2 extend the repertoire of crystal structures of Z-DNA.

Luo Z, Dauter Z, Gilski M
Acta Crystallogr D Struct Biol 73 940-951 (2017)
Related entries: 6aqt, 6aqw, 6aqx

Cited: 5 times
EuropePMC logo PMID: 29095165

Abstract

DNA oligomer duplexes containing alternating cytosines and guanines in their sequences tend to form left-handed helices of the Z-DNA type, with the sugar and phosphate backbone in a zigzag conformation and a helical repeat of two successive nucleotides. Z-DNA duplexes usually crystallize as hexagonally arranged parallel helical tubes, with various relative orientations and translation of neighboring duplexes. Four novel high-resolution crystal structures of d(CGCGCG)2 duplexes are described here. They are characterized by a high degree of pseudosymmetry and/or twinning, with three or four independent duplexes differently oriented in a monoclinic P21 lattice of hexagonal metric. The various twinning criteria give somewhat conflicting indications in these complicated cases of crystal pathology. The details of molecular packing in these crystal structures are compared with other known crystal forms of Z-DNA.

Articles - 6aqv mentioned but not cited (2)

  1. Four highly pseudosymmetric and/or twinned structures of d(CGCGCG)2 extend the repertoire of crystal structures of Z-DNA. Luo Z, Dauter Z, Gilski M. Acta Crystallogr D Struct Biol 73 940-951 (2017)
  2. Modeling the vibrational couplings of nucleobases. Jiang Y, Wang L. J Chem Phys 152 084114 (2020)


Articles citing this publication (3)

  1. Letter Nucleobase carbonyl groups are poor Mg2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey. Leonarski F, D'Ascenzo L, Auffinger P. RNA 25 173-192 (2019)
  2. Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy. Li M, Teng B, Lu W, Zhang JZ. J Mol Model 26 31 (2020)
  3. Predicting accurate ab initio DNA electron densities with equivariant neural networks. Lee AJ, Rackers JA, Bricker WP. Biophys J 121 3883-3895 (2022)


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