Despite being the fundament of life for living organisms, many functionalities of DNA and RNA still present as challenging targets for scientists. One such aspect is the elucidation of the complete mechanism behind the hydrolysis of the nucleic acids’ backbone, comprised of repeated phosphodiester bond segments linking adjacent nucleosides. Indeed, the phosphate bond is known for its superb stability, which allows RNA and DNA to remain intact at 25°C, pH 7.0 for hundreds and millions of years, respectively. However, enzymes called nucleases perform the phosphodiester cleavage in seconds, a result yet to be surpassed by artificial competitors.
To date, not even the most meticulously designed molecules have approached the efficiency demonstrated by nucleases and researchers are still trying to understand the underlying hydrolytic mechanisms behind these enzymes. Accordingly, we decided to challenge ourselves with that issue and by using the principles of nano and supramolecular chemistry we attempted to reach enzymes’ efficacy and elucidate the mechanism of phosphodiester cleavage.
In our recent work we reported surface-passivated gold nanoparticles behaving like artificial nanonucleases, cleaving plasmid DNA pBR322 with the highest efficiency reported thus far based on a single metal ion mechanism.1 Inspired by nature’s nucleases, we created a pocket comprising one Zn(II) ion, one arginine and one serine, precisely mimicking the active site suggested for natural metallonucleases grounding their efficiency on a monometallic mechanism. Experimental studies supported by MD calculations revealed a key role of a positively charged arginine, which assists in the transition state stabilization and reduces the pKa of the nucleophilic alcohol of serine, followed by one Zn(II) ion coordinating a phosphate diester of DNA.
Our additional studies performed with commonly used DNA model BNP (bis-p-nitrophenyl phosphate) demonstrated how by designing an artificial catalyst just based on experiments with a simple model substrate can lead to misguided conclusions when compared with a real target such as plasmid DNA.
1. Scrimin, P. M.; Czescik, J.; Zamolo, S.; Darbre, T.; Rigo, R.; Sissi, C.; Pecina, A.; Riccardi, L.; De Vivo, M.; Mancin, F., A Gold Nanoparticle Nanonuclease Relying on a Zn(II) Mononuclear Complex. Angewandte Chemie International Edition (just accepted); doi: 10.1002/anie.202012513
