Molecular Recognition Mechanisms: Thermodynamics and Polarization Spectroscopy of DNA--Intercalator Complexes
Doctoral thesis, 2000
Mechanisms for molecular recognition in DNA--intercalator complexes have been investigated by optical spectroscopy. The effect of electrical charge on binding geometry and binding thermodynamics was studied using 2,7-diazapyrene (DAP) and its N-methylated cations DAP+ and DAP2+ as model ligands. It was found that increased charge leads to reduced rotational mobility of the intercalator in the intercalation pocket. In conjunction with this, the driving force for intercalation is shifted from enthalpy to entropy. The unfavorable binding enthalpy found for the dication DAP2+ is interpreted as a combined effect of the enthalpic penalties of inserting a charge into the DNA helix and simultaneously releasing the solvation shell on intercalation.
The interaction of the diazapyrenes with DNA was further characterized by investigating diazapyrene--adenine complexes. Semi-empirical and ab initio calculations suggested that electrostatic interaction of the cations with adenine is significant. The geometry of the complexes in aqueous solution is from NMR measurements and absorption spectra concluded to be of a face-to-face type. Calculations of the electronic spectra of the diazapyrenium--adenine complexes indicate the presence of low-lying charge-transfer transitions. This result helps explain an observed unpolarized absorption tail of the DAP2+--DNA complex.
AT-specific binding has been achieved with piperazinylcarbonyloxyethyl substituted anthracene and pyrene. The specificity is attributed to steric interference of the piperazinium tail with the exocyclic amino groups in the minor groove of GC. Specificity is enhanced through synergism of intercalation and groove binding. However, because the compounds bind more tightly to AT, the ratio K(AT)/K(GC) is reduced by enthalpy--entropy compensation. By introducing a methyl group, the effects of increased steric demand and chirality have been investigated. Chiral discrimination was found to be negligible due to a lack of polarity in the binding.