Deoxyribozymes that catalyze photochemistry: cofactor-dependent and -independent photorepair of thymine dimers.

Abstract

Experimental strategies involving in vitro selection, designed to test the validity of the "RNA World Hypothesis", have demonstrated a significantly broader catalytic range for RNA (and, nucleic acids in general) than found in naturally occurring ribozymes. We wished to explore whether photochemical reactions could be catalyzed by nucleic acid enzymes. In vitro selection experiments were carried out to obtain "photolyase" deoxyribozymes, capable of photoreversing thymine cyclobutane dimers in the presence of a cofactor, serotonin. During in vitro selection from a thymine-dimer containing random DNA library, irradiated with light >300 nm, two pools of catalytic nucleic molecules emerged--one that required serotonin for activity, and another pool that, surprisingly, did not. Characterization of the serotonin-independent clones indicated the optimal wavelength for its repair activity (approximately 1,400-fold) to be approximately 300 nm, notably red-shifted from the absorption maximum of the DNA itself. The folded enzyme may contain a G-quadruplex (whose spectra have red-shifted tails relative to duplex absorbance), and our hypothesis has the folded enzyme as an antenna for the efficient channelling of light or electrons to the thymine dimer, much in the manner of protein photolyases.