A recent proposal for a nucleic-acid sensing device exploits the sensitivity of fluorescence by diamond N-valence (NV) centers to the local concentration of paramagnetic cations such as Mn2+. Hybridization of target DNA or RNA sequences to diamond-surface anchored peptide nucleic acid (PNA) would result in accumulation of Mn2+ ions. This in turn may lead to detectable change in the fluorescence of local NV centers, and, thereby, to label-free DNA/RNA detection.
To investigate the feasibility of this scheme and to help in the interpretation of the experiments we set up a molecular dynamics study of the hybrid duplex on a diamond surface (pictured). In particular we are addressing the following questions: How do PNA and DNA/RNA interact with the OH and COOH functionalized diamond surface? How do Mn2+ ions interact with these NAs, and how does this interaction modifies Mn2+ dynamics? A preliminary step involves building a model of the diamond surface, according to experimental characterization, and then its force-field parametrization for subsequent MD simulations.
| People | Luca Bellucci, Riccardo Nifosì*, Giuseppe Sacco, Valentina Tozzini |
| Keywords | RNA/DNA detection, PNA, surface hybridization reactions, Mn2+ interaction with DNA and RNA |
| Methods, techniques | DFT, Molecular dynamics simulations |
| Collaborations | Justas Zalieckas, Martin M Greve, University of Bergen, Norway |
| Publications | |
| J Zalieckas, MM Greve, L Bellucci, G Sacco, Verner Håkonsen, V Tozzini, R Nifosì Quantum sensing of microRNAs with nitrogen-vacancy centers in diamond Comm Chem 2024 | |
| F Trovato, V Tozzini Supercoiling and local denaturation of plasmids with a minimalist DNA model J Phys Chem B 2008 |