Pyrene as a Sensitive Probe for DNA Conformational Changes Due to Protonation

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Abstract
Planar pyrene molecules can acquire optical activity upon binding to the disymmetric environment of duplex DNA. Positive induced Cotton effects are observed for pyrene in basic and neutral DNA solutions but revert to strongly negative CD bands in moderately acidic solutions. pH titrations indicate that this change over is strongly cooperative until acid denaturation sets in. The negative induced CD for pyrene results from its binding to a protonated duple.x state which shows a striking 40°C decrease in the melting temperature from its neutral counterpart with 0.18 M NaCI. Further studies with synthetic polynucleotidesreveal that pyrene strongly prefers the guanine containing sequences in general and dG-dC (and/or dC-dG) sequence(s) in particular for this protonated duplex state, in distinct contrast to the dA-dT (and/or dT-dA) sequence specificity in the neutral solutions. The observed pyrene CD sign reversal upon protonation is thus the manifestation of DNA conformational change and the accompanied alteration in base sequence specificity.