PMID: 8614632Apr 1, 1996Paper

The width of the minor groove affects the binding of the bisquaternary heterocycle SN-6999 to duplex DNA

Nucleic Acids Research
J M RydzewskiW Chazin

Abstract

A complex between d(GGGAAAAACGG).d(CCGTTTTTCCC) and the minor groove binding drug SN-6999 has been studied by 1H nuclear magnetic resonance spectroscopy. The drug is found to bind in the d(A)5 tract, but with interactions extending one residue in the 3'-direction along each strand. Doubling of resonances in the complex indicates slow to intermediate exchange between two binding modes. An orientational preference (7:3) is found, the first such example in an SN-6999 complex. Furthermore, the upper limit of the lifetime for the major species is longer than was found for SN-6999 with other DNA duplexes. The preferred orientation of SN-6999 has the pyridinium ring near the 5'-end of the (+) strand; the minor binding mode has the reverse orientation. The orientational preference and slower exchange rate relative to other SN-6999 complexes is attributed to increased stabilization from van der Waals interactions due to better shape complementarity between the DNA duplex and ligand. The comparison of these results with studies of SN-6999 complexed to other DNA duplexes reveals the sensitivity of the binding properties to the delicate interplay between the molecular structure of the ligand and the specific characteristics of the DNA mino...Continue Reading

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Citations

Dec 24, 2013·Biochemistry·Neil M BellShankar Balasubramanian
Feb 9, 2012·Dalton Transactions : an International Journal of Inorganic Chemistry·Fangfei LiF Richard Keene
Mar 16, 2012·Physical Chemistry Chemical Physics : PCCP·Viktor V KostjukovMaxim P Evstigneev
Dec 2, 1999·Pharmacology & Therapeutics·B S ReddyJ W Lown

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