• microrna
• mirna
• nucleic acid sensing
• nv centers
• nitrogen-vacancy centers
• pna
• peptide nucleic acid
• molecular dynamics

Accurate detection of specific oligonucleotide sequences is of crucial importance in biomedical research and in the early diagnosis of disorders whose action is regulated by microRNA/DNA. We discuss a label-free setup that does not involve chemical processes, thus being potentially simpler and more robust, while ensuring high selectivity and sensitivity to many target sequences at once in a compact device. Peptide Nucleic Acid are linked at one end to the diamond substrate and are in solution with water, Cl− and Mn2+ ions. The main idea is that, if target RNA/DNA sequences are present in solution, upon duplex formation, Mn2+ ions will coordinate around the nucleic acid due to electrostatic interaction with phosphate groups, resulting in the accumulation of manganese cations in the proximity of the substrate. This setup exploits the sensitivity of fluorescence of a particular type of color centers in diamond, called Nitrogen-Vacancy centers, to the local concentrations of paramagnetic species such as Mn2+, which is how the presence of target nucleic acid (NA) sequences can ultimately be revealed. In particular, this work addresses the computational modeling of this system, through molecular dynamics simulations and subsequent data analysis. The study of the system is carried in collaboration with experimentalists Justas Zalieckas and Martin M. Greve from the Department of Physics and Technology of the University of Bergen, Norway.