Polymorphic crystal structures of an all-AT DNA dodecamer

Francisco J. Acosta-Reyes, Juan A. Subirana, Joan Pous, Raquel Sánchez-Giraldo, Núria Condom, Roberto Baldini, Lucy Malinina, J. Lourdes Campos

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

In this work, we explore the influence of different solvents and ions on the crystallization behavior of an all-AT dodecamer d(AATAAATTTATT)2 In all cases, the oligonucleotides are found as continuous columns of stacked duplexes. The spatial organization of such columns is variable; consequently we have obtained seven different crystal forms. The duplexes can be made to crystallize in either parallel or crossed columns. Such versatility in the formation of a variety of crystal forms is characteristic for this sequence. It had not been previously reported for any other sequence. In all cases, the oligonucleotide duplexes have been found to crystallize in the B form. The crystallization conditions determine the organization of the crystal, although no clear local interactions have been detected. Mg(2+) and Ni(2+) can be used in order to obtain compact crossed structures. DNA-DNA interactions in the crystals of our all-AT duplexes present crossovers which are different from those previously reported for mixed sequence oligonucleotides. Our results demonstrate that changes in the ionic atmosphere and the crystallization solvent have a strong influence on the DNA-DNA interactions. Similar ionic changes will certainly influence the biological activity of DNA. Modulation of the crystal structure by ions should also be explored in DNA crystal engineering. Liquid crystals with a peculiar macroscopic shape have also been observed.

Original languageEnglish (US)
Pages (from-to)123-133
Number of pages11
JournalBiopolymers
Volume103
Issue number3
DOIs
StatePublished - Mar 1 2015

Bibliographical note

Publisher Copyright:
© 2014 Wiley Periodicals, Inc.

Keywords

  • AT-rich DNA
  • DNA
  • X-ray crystallography
  • crossed DNA structures
  • inorganic cations
  • liquid crystals
  • oligonucleotides

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