Side chain-dependent binding of antitumor indoloquinoxaline derivatives to DNA: comparative spectroscopic and viscometric measurements.

NCA0424 (1) and its side chain positional isomer, NCA0465 (2), are indoloquinoxaline derivatives with potent antitumor activity. To investigate the effect of side chain position for binding with DNA, the interactions of 2 with various B-form DNAs were studied by spectroscopic (circular dichroism (CD), fluorescence and UV) and viscosity measurements and were compared with those of 1. The binding preference for the base sequence was different in each case. The CD spectra showed that 2 formed an asymmetric binding of indoloquinoxaline ring with adenine in DNA, whereas such a base selectivity was not found with 1. The binding features are discussed based on association constants and thermodynamic parameters, indicating the importance of the side chain position for binding specificity for DNA.