NMR Characterization of the DNA Binding Properties of a Novel Hoechst 33258 Analogue Peptide Building Block

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• 作者：Jakob Bunkenborg ; Carsten Behrens ; and Jens Peter Jacobsen
• 刊名：Bioconjugate Chemistry
• 出版年：2002
• 出版时间：September 2002
• 年：2002
• 卷：13
• 期：5
• 页码：927 - 936
• 全文大小：606K
• 年卷期：v.13,no.5(September 2002)
• ISSN：1520-4812

文摘

A novel aryl-bis-benzimidazole amino acid analogue of the DNA-binding compound Hoechst 33258has recently been designed for incorporation in peptide combinatorial libraries by replacing theN-methylpiperazine group with a carboxyl group and the hydroxy group with an amino-methyl group.The DNA-binding properties of the aryl-bis-benzimidazole monomer with the C-terminus derivatizedwith 3-(dimethylamino)-propylamine has been investigated in this paper by ¹H NMR studies of twodifferent complexes with two different DNA sequences: A₅ d(5'-GCCA₅CG-3'):d(5'-CGT₅GGC-3') andA₃T₃ d(5'-CGA₃T₃CG-3')₂. Chemical shift footprinting shows that the ligand binds at the center of theA₃T₃ sequence but at the 3'-end of A₅. A large number of NOEs show a well-defined complex with theligand situated at the center of the palindromic A₃T₃ but with the asymmetric A₅ the ligand bindswith an orientational preference with the bis-benzimidazole moiety displaced toward the 3'-end fromthe center of the duplex. Two families of models of the complexes with A₅ and A₃T₃ were derived withrestrained molecular dynamics based on a large set of 70 and 61, respectively, intermolecular ligandNOEs. Both models give a picture of a tightly fitting ligand with close van der Waals contacts withthe walls of the minor groove and with the two benzimidazole and the amide hydrogens involved inbifurcated cross-strand hydrogen bonds to adenine N3 and thymine O2. The minor groove width ofthe models correlate well with the binding site of the ligand, and the orientational preference is arguedto be a consequence of the minor groove width and hydrogen bonding.