Enhanced Binding of a Non‐hydrogen Bond Ligand to DNA by Introducing an Apurine/Apyrimidine Site

Abstract

AbstractIntercalators are well known for their DNA binding specificity by inserting between base pairs, whereas the binding event occurring to apurine/apyrimidine site (AP site)‐containing DNA for this type of noncovalent interaction is still not highlighted although AP site is frequently in vivo produced in living cells. Here proflavine (PF) as an example is used to investigate the binding specificity of the AP site in DNA for a non‐hydrogen bond ligand. Experimental results indicate that the AP site should be the preferential binding site for PF. The intrinsic binding constant of PF for the AP site is one order of magnitude greater than that occurring for PF intercalation. Additionally, the thermostability of the AP site‐containing DNA is significantly increased after PF binding. The PF bound to the AP site should adopt a specific binding orientation distinguishable from that by which PF intercalated into base pairs. The results obtained here should be very useful for judging biochemical and biophysical effectiveness of small molecules based on their different binding behavior to DNA.