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A theoretical investigation of the intercalative binding of 7‐H pyrido[4.3C]carbazole chromophore into a d(CpG) 2 minihelix
Author(s) -
Maroun Rachid,
Gresh Nohad
Publication year - 1989
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360280405
Subject(s) - chemistry , intercalation (chemistry) , ab initio , carbazole , crystallography , nucleic acid , cpg site , stereochemistry , nucleotide , computational chemistry , photochemistry , inorganic chemistry , biochemistry , gene expression , organic chemistry , dna methylation , gene
Theoretical computations are performed of the intercalative binding to a model d(CpG) 2 minihelix of 7‐H pyrido[4.3C]carbazole, the precursor of the antitumor bisintercalating drug ditercalinium. The conformations of the intercalation site are generated by the AGNAS procedure (algorithm to generate nucleic acid structures) of Miller and co‐workers. The ligand‐nucleotide interactions and the nucleotide conformational energies are computed with the SIBFA procedures (sum of interactions between fragments ab intio computed), which use formulas of empirical origin that reproduce ab initio SCF (self‐consistent field) computations. Among the candidate intercalation sites most favored energetically, one has a pattern of conformational angles related to the one determined crystallographically by Sobell et al. in a series of x‐ray structural studies of small intercalator–dinucleotide monophosphate complexes. Optimal values of the unwinding angle, found in the range of −12° to −14°, are consistent with available experimental data on DNA.