| Description |
Present-day organisms recruit flavin as a redox cofactor for various metabolic transformations. In present-day metabolism, it is biosynthesized via several enzyme-catalyzed steps from guanosine triphosphate (GTP). It is hypothesized that life originated from RNA on the primordial Earth. If this hypothesis holds true for the so-called "RNA World", there should be a counterpart for the most critical molecules we encounter in present-day biology. Thus, we asked what molecule(s) could predate a present-day flavin to support primitive metabolisms. We also try to answer why Mother Nature selected flavin over many other potential candidate molecules from the photophysical perspective. Toward these goals, we studied the photoredox properties of some oxidatively modified nucleobases. Specifically, we studied 5-hydroxypyrimidine and its ability to photochemically repair a thymine dimer in double stranded DNA. It was found that the repair rate is dependent on many factors, including pH, base pairing, and its position relative to the thymine dimer. For these candidate molecules to carry out functions similar to what flavin does in photolyase, we investigated the concept of noncovalent interaction between a free 8-oxoguanine as a flavin mimic and an abasic site in double stranded DNA as a ribozyme model, and found that it can accelerate thymine dimer repair. Not surprisingly, noncovalent interactions that bind the photocatalyst to the DNA duplex can accelerate thymine dimer repair compared to a bimolecular reaction. However, the repair efficiency is still lower than that of photolyase. We thus studied the photophysical proper-ties of one candidate molecule, 8-oxoguanine. To study the excited-state decay of 8-oxoguanine in the presence of base stacking, we optimized a synthetic methodology to prepare an 8-oxoguanine-containing dinucleotide. Pump-probe experiments performed by collaborators demonstrated that a deactivation channel through charge-transfer state formation between 8-oxoguanine and adenine exists in the dinucleotide, and potentially also exists in oligonucleotides. To study 8-oxoguanine excited-state decay in the more relevant double-stranded DNA, we explored various methodologies of circularizing short dsDNA and developed a postsynthetic modification method featuring click chemistry to synthesize a minicircle of DNA. The synthesized minicircle DNA is only two base-pairs long and very stable at room temperature. Through circular dichroism experiments, we found that the conformation of minicircle DNA is not necessarily B-form and is sequence-dependent. Pump-probe experiments were also performed on these molecules. |
