Deoxyribonucleic acid (DNA), the carrier of genetic information in living organisms, is highly flexible and displays conformational polymorphism. Besides the classic Watson-Crick B-form double helix, it can also adopt other structures like A-form, Z-form, G-quadruplexes, and i-motifs. This flexibility in DNA structure is essential for many important biological processes. The two main forces that determine the unique shape of DNA are base stacking and hydrogen bonding. Therefore, a conformational change involves breaking and reordering these forces within the molecule. We employed optical spectroscopy methods using CD-active (Circular Dichroism-active) fluorescent base analogs, 2-Aminopurine (2-AP) and 6-methylisoxanthopterine (6MI), site-specifically placed into nucleic acid frameworks to monitor both global and more specific local conformational changes. The uniqueness of the site-specific CD-active fluorescent base analog approach is that it allows tracking of local conformational changes in individual base pairs at specific locations on the DNA duplex construct without the interference from canonical bases. The results showed that, in addition to the global structure, the local structures of non-canonical structures, such as G-quadruplex (GQ) and A-form DNA, can be monitored using this method. We further explored ligand interactions with GQs by monitoring spectral changes of the fluorescent bases at both local and global conformational levels, demonstrating that ligand interactions were location-specific.
Jugan et al. (Sun,) studied this question.