By Kiara N. Villa Del Valle
This paper focuses reports how through a change in the pH, their compound gets protonated and through hydrogen bonds, the compound and the base binds. Lastly, the better-known DNA structure the double helix, but there are other varieties such as hairpin loops, interior loops, multi-branched loops and bulge loops. Bulge loops, are when an extra base winds up on one side of the DNA strand. This can happen when the helix missing a base or an extra one was inserted during the DNA copying process. This anomaly can cause cancer or triplet diseases. They first performed experiments to determine the pH dependence if the azaDANP. They changed the pH from 1.0 to 9.0 and it shows a hypochromic and hypsochromic shifts as the pH was changing. They also plotted the absorption in terms of the pH and determined a pKaH (pKa of the protonated form) of 4.3, a lower pKaH of 6.8 for a previously described compound. This decrease was due to the decreased basicity of the ring nitrogen by the substitution at C4-N. To get information about the azaDANP binding to the C-bulge, they simulated possible complexes between azaDANP and cytosine, it showed that the protonation likely occurs at N1 for the complex formation. They performed more experiments to measure the absorption spectra of azaDANP in presence of T, G, A and C bulged DNA, at pH 7.0 and 5.5 at room temperature. We want to focus in this, at 5.5 pH there is a new absorption band at 407 nm that in neutral pH is not observed and therefore suggesting that the formation is pH sensitive. The thermal stability of the azaDANP-C-bulge was investigated with absorption with variable temperature. We can see that the peak observed at 407 nm at 2 °C decreases as the temperature is increased to 80 °C. This shows the equilibrium of azaDANP and GCG/CC DNA to form a binary complex and, therefore, appearing to be temperature dependent.