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

FEBS Letters

Nakanishi, Isao²  Rich, Alexander⁵  Hakoshima, Toshio²  Tomita, Ken-ichi³  Van Boom, Jacques H.⁴  Ohishi, Hirofumi³  Terasoma, Noriko³  van der Marel, Gijs⁴  Wang, Andrew H.-J.¹ 

[1] Department of Physiology and Biophysics, University of Illinois, Urbana, IL 61801, USA;Faculty of Pharmaceutical Sciences, Osaka University, 1–6 Yamada-oka, Suita, Osaka 565, Japan;Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-11, Japan;Gorlaeus Laboratories, University of Leiden, 2300 RA Leiden, The Netherlands;Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

关键词: Z-DNA;    Polyamine;    Crystal structure;    d(CG)3-thermospermine complex;    Molecular interaction;    Molecular conformation;   

DOI  :  10.1016/S0014-5793(96)01225-2

学科分类：生物化学/生物物理

来源: John Wiley & Sons Ltd.

【 摘 要 】

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 × 0.5 × 0.5 mm³, X-ray intensity data were collected up to 1.0 Å resolution. Two thermospermine molecules and a magnesium cation were bound to the left-handed double-helical d(CG)₃ molecule. The d(CG)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.

【 授权许可】

Unknown