A theoretical study of the interaction of monomethylammonium with double-stranded oligonucleotides

Theoretical design of a bis-orthopepetide derivative of a tetracationic porphyrin targeted toward a six-base pair sequence of DNA

Tetra-(4-N-methylpyridyl)-porphyrin, (T4MPyP), is a tetracationic porphyrin that binds to G-C sequences of DNA by means of an intercalative mode. In order to extend its selective sequence recognition capacity for bases beyond the intercalation site, and in the major groove, we have undertaken the theoretical design of bis-ortho peptide derivatives of T4MPyP. In these, two ortho N-methylpiperidinium nitrogens are linked to a cationic residue, L-Lys, L-Orn, or L-Arg. The binding energetics of these novel compounds were compared for six distinct double-stranded palindromic hexanucleotide sequences. Four distinct modes of binding were compared: a) major, b) minor groove binding of both peptidic arms; c) a straddling mode in which each arm is in a different groove of DNA; d) exclusive binding of the arms to the sugar-phosphate backbone. For our most promising compound, that with Lys side-chains, a distinctive energetical advantage was computed in favor of an all-major groove binding to sequence d(CCCGGG)2. The corresponding complex is separated by an energy gap of 12 kcal/mol, with respect to the second-best sequence bound in the major groove, d(GGCGCC)2, and of 20 kcal/mol with respect to minor groove binding to sequence d(TACGTA)2. The results obtained with such a prototypic compound indicate that it is fully possible to design sequence selective (> 6 base-pairs) photosensitizers as peptide derivatives of T4MPyP and prompt the engineering of further, more complex analogs thereof.

A theoretical investigation on the sequence selective binding of daunomycin to double-stranded polynucleotides

Theoretical computations are performed on the structural and energetical factors involved in the sequence selective binding of daunomycin (DNM) to six representative self-complementary double-stranded hexanucleotides: d(CGTACG)2,d(CGATCG)2,d(CITACI)2, d(TATATA)2, d(CGCGCG)2 and d(TACGTA)2. The conformational angles of the hexanucleotides are fixed in values found in the representative crystal structure of the d(CGTACG)2-DNM complex. The intermolecular DNM-hexanucleotide interaction energies and the conformational energy changes of DNM upon binding are computed and optimized in the framework of the SIBFA procedure, which uses empirical formulas based on ab initio SCF computations. Among the two regularly alternating hexanucleotides, d(TATATA)2 and d(CGCGCG)2, a stronger binding is predicted for the former, in agreement with experimental results obtained with poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC). Altogether, however, among the six investigated sequences, the strongest complexes are computed for the mixed hexanucleotides d(CGATCG)2 and d(CGTACG)2, containing the intercalation site between two CG base pairs and an adjacent TA base pair. This situation may be related to the increased affinity of DNM for GC rich DNA's and to the situation in the crystal structure of the DNM-d(CGTACG)2 complex. Analysis of the intrinsic base sequence preferences expressed by the individual constituents of DNM, namely the daunosamine side chain, the chromophore ring and its two 9-hydroxyl and 9-acetoxy substituents, reveals that the overall sequence preference found is the result of a rather intricate interplay of intrinsic sequence preferences, in particular at the level of daunosamine and the 9-hydroxyl substituent.(ABSTRACT TRUNCATED AT 250 WORDS)