High-field NMR and restrained molecular modeling studies on a DNA heteroduplex containing a modified apurinic abasic site in the form of covalently linked 9-aminoellipticine.

摘要: Two-dimensional NMR methods were used to model the possible solution structure of an intercalative complex 9-aminoellipticine (Aell), a polycyclic pyridocarbazolamine, covalently bound apurinic ring-opened deoxyribose site duplex DNA fragment in reduced Schiff base form. The required oligonucleotide single strand containing attached aminoellipticine was obtained by reductive amination presence sodium cyanoborohydride. combined NMR-energy minimization employed refine structures two distinct forms, intrahelical and extrahelical, control 9-mer DNA, d(CGTG.dr.GTGC).d(GCACTCACG), which contains positioned opposite dT residue on complementary strand. conjugate with same sequence, derivatized via aforementioned covalent attachment, also incorporating intermolecular drug-DNA intra- internucleotide NOE-derived proton-proton distance estimates as restraints energy routines. indole ring system aminoellipticine, is inserted at site, intercalates between parallel flanking GC pairs. pyridinic protonated form, stacks cytidine thymidine bases strand, consistent observation that normal sequential NOE connectivity 5'-C13-T14 step broken indeed diverted through ellipticine moiety, e.g., C13-Aell-T14 connectivities Aell-H4/C5Me protons. Interestingly, partial stacking observed only 5'-CT vs adjacent 5'-TC step, owing inherently weak interactions associated former. In absence any potential groups can participate electrostatic or hydrogen-bonding nucleic acid, pi-pi hydrophobic contacts intercalation appear be important factors determining stability conformation aminoellipticine-DNA conjugate. Stacking such bistranded complexation apparently govern formation form right-handed B-type duplex. overall structural features lead us propose working models for enzyme-like cleavage activity inhibition AP endonuclease-dependent excision-repair pathway.