Literature DB >> 29095165

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

Zhipu Luo1, Zbigniew Dauter1, Miroslaw Gilski2.   

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.

Entities:  

Keywords:  Z-DNA crystal structure; Z-DNA hexamer duplex; hectohedral twinning; pseudomerohedral twinning

Mesh:

Substances:

Year:  2017        PMID: 29095165      PMCID: PMC5683016          DOI: 10.1107/S2059798317014954

Source DB:  PubMed          Journal:  Acta Crystallogr D Struct Biol        ISSN: 2059-7983            Impact factor:   7.652


  26 in total

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Authors:  Jennifer E Padilla; Todd O Yeates
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2003-06-27

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Authors:  P Andrew Karplus; Kay Diederichs
Journal:  Science       Date:  2012-05-25       Impact factor: 47.728

4.  Crystal structure of the self-complementary 5'-purine start decamer d(GCGCGCGCGC) in the Z-DNA conformation. I.

Authors:  C Ban; B Ramakrishnan; M Sundaralingam
Journal:  Biophys J       Date:  1996-09       Impact factor: 4.033

5.  Molecular structure of a left-handed double helical DNA fragment at atomic resolution.

Authors:  A H Wang; G J Quigley; F J Kolpak; J L Crawford; J H van Boom; G van der Marel; A Rich
Journal:  Nature       Date:  1979-12-13       Impact factor: 49.962

6.  Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals the massive presence of alternate conformations.

Authors:  Pawel Drozdzal; Miroslaw Gilski; Mariusz Jaskolski
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-10-28       Impact factor: 7.652

7.  Atomic resolution structure of a chimeric DNA-RNA Z-type duplex in complex with Ba(2+) ions: a case of complicated multi-domain twinning.

Authors:  Miroslaw Gilski; Pawel Drozdzal; Ryszard Kierzek; Mariusz Jaskolski
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-01-22       Impact factor: 7.652

8.  Features and development of Coot.

Authors:  P Emsley; B Lohkamp; W G Scott; K Cowtan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

9.  Left-handed double helical DNA: variations in the backbone conformation.

Authors:  A J Wang; G J Quigley; F J Kolpak; G van der Marel; J H van Boom; A Rich
Journal:  Science       Date:  1981-01-09       Impact factor: 47.728

10.  Phaser crystallographic software.

Authors:  Airlie J McCoy; Ralf W Grosse-Kunstleve; Paul D Adams; Martyn D Winn; Laurent C Storoni; Randy J Read
Journal:  J Appl Crystallogr       Date:  2007-07-13       Impact factor: 3.304

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  2 in total

1.  Modeling the vibrational couplings of nucleobases.

Authors:  Yaoyukun Jiang; Lu Wang
Journal:  J Chem Phys       Date:  2020-02-28       Impact factor: 3.488

2.  Nucleobase carbonyl groups are poor Mg2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey.

Authors:  Filip Leonarski; Luigi D'Ascenzo; Pascal Auffinger
Journal:  RNA       Date:  2018-11-08       Impact factor: 4.942

  2 in total

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