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

Hirofumi Ohishi, Noriko Terasoma, Isao Nakanishi, 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

22 Citations (Scopus)


The DNA fragment, d(CG)3, was co-crystallized with N-(3-amino-propyl)-N-(5-aminopropyl)-1,4-diaminobutane (thermospermine; PA(334)), a polyamine metabolized from the nucleic acid. By using a good crystal with dimensions of 0.5 x 0.5 x 0.5 mm3, X-ray intensity data were collected up to 1.0 Å resolution. Two thermospermine molecules and a magnesium cation mere bound to the left-handed double-helical d(CG)3 molecule. The d(CC)3 molecule adopted the left-handed Z-conformation and two thermospermine molecules and a magnesium cation neutralized the negative charges of the phosphate groups of the d(CG)3 molecule. Furthermore, the binding modes between d(CG)3 and thermospermine were different from those of d(CG)3 complexes with PA(24), spermidine and spermine. This is the first case in which it was determined by X-ray crystallographic analysis that one of two thermospermine molecules bound three d(CG)3 duplexes which were symmetrically related to each other, and the other formed two hydrogen bonds at the N(5) and N(9) atoms with two adjacent nucleotide phosphate groups of a single d(CG)3 strand at the minor groove. Furthermore, no direct coordination bond was found between the d(CG)3 molecule and the magnesium cation.

Original languageEnglish
Pages (from-to)291-296
Number of pages6
JournalFEBS Letters
Issue number2-3
Publication statusPublished - Dec 2 1996
Externally publishedYes


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

ASJC Scopus subject areas

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


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