Structural and Dynamic Aspects of the Sequence Specific Binding of Netropsin and Its Bis-Imidazole Analogue on the Decadeoxyribonucleotide d-[CGCAATTGCG]2

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Abstract
High field 1H-NMR techniques have been used to examine the sequence dependent binding of a lexitropsin, the bis-imidazole analogue of netropsin 1, to the decadeoxyribonuceotide d- [CGCAATTGCG]2. The non-exchangeable and imino protons of the 1:1 lexitropsin: DNA complex are assigned by 1D-NOE difference and COSY methods. Addition of 1 to the DNA resulted in marked drug induced chemical shift changes of both the non-exchangeable and imino protons of A(4,5) and T(6,7). These results suggest that the lexitropsin is located in the minor groove along A(4) to T(7) of the DNA. Weaker chemical shift changes are observed for C(3) and G(8) which suggest that the bisimidazole moiety of 1 can also accept G.C sites. Specific NOEs seen between the lexitropsin (H2, H14 and H15) and DNA (AH2(4) and AH2(5)) confirmed that the N to C-terminii of 1 is, on average, bound centrally to the sequence in the direction 5′-AATT-3′. However, netropsin 2 is shown to bind tightly only to the AATT sequence. Exchange NMR effects permit the estimate of the rate of exchange of the lexitropsin 1 between the two equivalent sites on the DNA to be approximately 160 s1 and 24 s1 for netropsin under comparable conditions. Several factors contributing to the sequence specificity of lexitropsin binding are discussed.

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