Interaction between the left-handed Z-DNA and polyamine-2: The crystal structure of the d(CG)3 and spermidine complex

Hirofumi Ohishi, Isao Nakanishi, Kouichi Inubushi, Gijs Van Der Marel, Jacques H. Van Boom, Alexander Rich, Andrew H.J. Wang, Toshio Hakoshima, Ken Ichi Tomita

Research output: Contribution to journalArticlepeer-review

23 Citations (Scopus)

Abstract

This paper deals with the crystal structure of d(CG)3-spermidine complex. The DNA fragment, d(CG)3, was crystallized with N-(2-amino-propyl)- 1,4-diamino-butane, PA(34), spermidine. The results of its X-ray crystallographic analysis showed many intermolecular contacts between d(CG)3 and spermidine, but the binding mode of spermidine to the d(CG)3 molecule is different from that of the d(CG)3 and N-(2-amino-ethyl)-1,4-diamino-butane [PA(24)] complex: a spermidine molecule bound to the d(CG)3 and its symmetrically related neighboring d(CG)3 molecules through the water molecules with hydrogen bonds, while one PA(24) molecule connected directly to one d(CG)3 molecule, but not to its neighboring d(CG)3 molecule. In the crystal, the d(CG)3 molecule was the left-handed Z-form, and three magnesium cations and a sodium cation were observed around the d(CG)3 moiety with different binding modes from the case of the d(CG)3-PA(24) complex.

Original languageEnglish
Pages (from-to)153-156
Number of pages4
JournalFEBS Letters
Volume391
Issue number1-2
DOIs
Publication statusPublished - Aug 5 1996
Externally publishedYes

Keywords

  • Crystal structure
  • Molecular complex
  • Molecular interaction
  • Polyamine
  • Spermidine
  • Z-DNA
  • d(CG)

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Genetics
  • Cell Biology

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