Design and binding of a distamycin A analog to d(CGCAAGTTGGC)路d(GCCAACTTGCG): synthesis, NMR studies, and implications for the design of sequence-specific minor groove binding oligopeptides was written by Dwyer, Tammy J.;Geierstanger, Bernhard H.;Bathini, Yadagiri;Lown, J. William;Wemmer, David E.. And the article was included in Journal of the American Chemical Society in 1992.Electric Literature of C7H9N3O4 This article mentions the following:
Distamycin A analog I was prepared in which an imidazole ring is substituted for the central pyrrole ring of distamycin A. A key step in the synthesis was the coupling of acid II with amine III by EDCI to give the corresponding peptide. The latter peptide was converted into I in 3 steps. Two-dimensional NMR spectroscopy was used to characterize the complex formed between I and d(CGCAAGTTGGC)路d(GCCAACTTGCG). Titration of the AAGTT duplex with I yielded a single complex with a ligand:DNA stoichiometry of 2:1. The nuclear Overhauser effect (NOESY) experiment in D2O was used to assign the aromatic and C1’H DNA protons and to identify intermol. ligand-DNA contacts between nonlabile protons. The NOESY experiment in H2O was used to assign the imino and amino DNA protons and the amide protons of the ligands and to identify ligand-DNA contacts involving these labile protons. These data indicate that two ligand mols. bind simultaneously to the minor groove of the central 5′-AAGTT-3′ sequence in a head-to-tail orientation. Mol. modeling, using 35 ligand-DNA distance constraints derived from a semiquant. anal. of the NOESY data, shows that the imidazole N3 of one of the ligands forms a hydrogen bond with the C2 amino group of the guanine in the binding site. Addnl., the titration of d(CGCAAATTGGC)路d(GCCAATTTGCG) with I was performed. No specific complex was detected by NMR spectroscopy between I and the AAATT duplex. This result emphasizes the importance of the imidazole N3 atom of I in the recognition of the AAGTT binding site. In the experiment, the researchers used many compounds, for example, Ethyl 1-methyl-4-nitro-1H-imidazole-2-carboxylate (cas: 109012-23-9Electric Literature of C7H9N3O4).
Ethyl 1-methyl-4-nitro-1H-imidazole-2-carboxylate (cas: 109012-23-9) belongs to imidazole derivatives. 1H-imidazole is an imidazole tautomer which has the migrating hydrogen at position 1. It is a conjugate base of an imidazolium cation. It is a conjugate acid of an imidazolide. It is a tautomer of a 4H-imidazole. Many drugs contain an imidazole ring, such as certain antifungal drugs, the nitroimidazole series of antibiotics, and the sedative midazolam.Electric Literature of C7H9N3O4
Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem