Stacking interaction of guanine with netropsin in the minor groove of d(CGTATATACG)2

Nicola G.A. Abrescia, Lucy Malinina, Juan A. Subirana

Research output: Contribution to journalArticlepeer-review

29 Scopus citations

Abstract

We present the structure of the decanucleotide d(CGTATATACG) determined by single crystal X-ray diffraction at 1.58 Å resolution. A netropsin drug is found in the minor groove with guanine stacked on a pyrrole ring of the drug, a feature described here for the first time. The stacked guanine is an extra-helical base coming from the end of a neighbour oligonucleotide. This observation may open the may to the development of minor groove binding drugs with a higher sequence selectivity. The oligonucleotide is in the B-conformation, but the terminal base-pairs are disrupted: the cytosine residues are disordered while the guanine residues penetrate into the minor groove of neighbouring duplexes. Four hydrated Ni ions with octahedral co-ordination are found associated with the N7 atoms of each guanine. The high affinity of these ions with guanine suggests that they may be used as probes for specific guanine residues.

Original languageEnglish (US)
Pages (from-to)657-666
Number of pages10
JournalJournal of Molecular Biology
Volume294
Issue number3
DOIs
StatePublished - Dec 3 1999

Bibliographical note

Funding Information:
This work was supported by a DGICYT (PB93-1067) grant, the Generalitat de Catalunya (1997-SGR00135) and the TMR/LSF program to the EMBL Hamburg Outstation, reference number ERBFMGECT980134. N.G.A.A. acknowledges a grant from the TMR program ERB4001GT973367.

Keywords

  • DNA/Ni interactions
  • Guanine
  • Netropsin
  • Oligonucleotide structure
  • X-ray diffraction

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