Abasic site-switched structure conversion of neutral red for selective DNA recognition

DNA-binding-switched conversion of small molecule's structure and property provides a promising tool for achieving a high selectivity in identification of a DNA specific site. Herein, the optical properties of neutral red in response to its abasic site (AP site) binding were investigated for this purpose. At pH 8.4, neutral red exists in solution mainly at the neutral form (NR). However, the presence of an AP site in DNA converts NR to a protonated form (NRH+), following a 100-nm red shift in absorption spectra. This conversion is inefficient for the fully matched DNAs without the AP site. Relative to the absorption spectra, the fluorescence in response to the binding-switched conversion is more dependent on the sequences near the AP site. The AP site's hydrophobic microenvironment and electron transfer between the AP site-bound NRH+ in excited state and the nearby context bases govern the emission behavior. It was found that the AP site having a large void space favors occurrence of dipole interaction between the bound NRH+ and the context bases. This AP site-dependent conversion of neutral red in structure and then its optical properties would find wide applications in the field of DNA assay with a high selectivity and sensitivity.