The phosphate clamp: a small and independent motif for nucleic acid backbone recognition.

ABSTRACT: The 1.7?Å X-ray crystal structure of the B-DNA dodecamer, [d(CGCGAATTCGCG)]? (DDD)-bound non-covalently to a platinum(II) complex, [{Pt(NH?)?}?-µ-{trans-Pt(NH?)?(NH?(CH?)?NH?)?}](NO?)? (1, TriplatinNC-A,) shows the trinuclear cation extended along the phosphate backbone and bridging the minor groove. The square planar tetra-am(m)ine Pt(II) units form bidentate N-O-N complexes with OP atoms, in a Phosphate Clamp motif. The geometry is conserved and the interaction prefers O2P over O1P atoms (frequency of interaction is O2P?>?O1P, base and sugar oxygens?>?N). The binding mode is very similar to that reported for the DDD and [{trans-Pt(NH?)?(NH?(CH?)?(NH?(+))}?-µ-{trans-Pt(NH?)?(NH?(CH?)?NH?)?}](NO?)? (3, TriplatinNC), which exhibits in vivo anti-tumour activity. In the present case, only three sets of Phosphate Clamps were found because one of the three Pt(II) coordination spheres was not clearly observed and was characterized as a bare Pt²(+) ion. Based on the electron density, the relative occupancy of DDD and the sum of three Pt(II) atoms in the DDD-1 complex was 1:1.69, whereas the ratio for DDD-2 was 1:2.85, almost the mixing ratio in the crystallization drop. The high repetition and geometric regularity of the motif suggests that it can be developed as a modular nucleic acid binding device with general utility.

SUBMITTER: Komeda S 

PROVIDER: S-EPMC3017591 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature