Nucleic acids generally reside in cellular aqueous solutions with mixed divalent/monovalent ions, and the competitive binding of divalent and monovalent ions is critical to the structures of nucleic acids because of their polyanionic nature. In this work, we first proposed a general and effective method for simulating a nucleic acid in mixed divalent/monovalent ion solutions with desired bulk ion concentrations via molecular dynamics (MD) simulations and investigated the competitive binding of Mg/Na ions to various nucleic acids by all-atom MD simulations. The extensive MD-based examinations show that single MD simulations conducted using the proposed method can yield desired bulk divalent/monovalent ion concentrations for various nucleic acids, including RNA tertiary structures. Our comprehensive analyses show that the global binding of Mg/Na to a nucleic acid is mainly dependent on its structure compactness, as well as Mg/Na concentrations, rather than the specific structure of the nucleic acid. Specifically, the relative global binding of Mg over Na is stronger for a nucleic acid with higher effective surface charge density and higher relative Mg/Na concentrations. Furthermore, the local binding of Mg/Na to a phosphate of a nucleic acid mainly depends on the local phosphate density in addition to Mg/Na concentrations.

Luminescent lanthanide metal–organic frameworks (Ln-MOFs) draw great interest due to their promising luminescent properties and wide applications in sensor design. In this work, a europium-organic framework (DPQ-Eu) has been synthesized under solvothermal conditions based on the aggregation-induced emission (AIE) ligand 4, 4′-(quinoxaline-2, 3-diyl)dibenzoic acid (H2DPQ). Structural analyses show that DPQ-Eu adopts the monoclinic C2/c space group and forms a 3, 6-connected 2D porous network with a topological symbol of {42·6}2{44·69·82}. The formation of DPQ-Eu contributes an absolute quantum efficiency of 21.49% compared with that of the AIE ligand H2DPQ (0.02%) mainly due to the coordination-induced emission, providing DPQ-Eu with a great potential of being a luminescent sensor. Fluorescent investigations show that DPQ-Eu has a selective and sensitive response to Fe3+ and Hg2+ among various metal ions by ratiometric emission changes of the decreased emission at 415 nm and increased emission at 676 nm, with the detection limits of 25.99 and 39.70 nM and good reusability (5 times). The sensing behaviors probably can be ascribed to the promoted antenna effect from the ligand to the Eu(III) center by the coordination of Fe3+/Hg2+ to the quinoxaline moiety. For anion sensing, DPQ-Eu can respond to Cr2O7 2– by emission quenching at both 415 and 676 nm with a detection limit of 9.88 nM and 5 times reusability, probably associated with the energy competing absorption and reduced energy transfer from the ligand to the Eu(III) center. In addition, DPQ-Eu shows ratiometric emission changes to CN– by the emission enhancement and decrease at 415 and 676 nm, respectively, with a detection limit of 8.19 nM and five-run recycling tests, probably corresponding to the inhibition of energy transfer from the ligand to the Eu(III) center caused by the binding interactions between the CN– and Eu(III) nodes.

Nucleic acids are negatively charged biomolecules, and metal ions in solutions are important to their folding structures and thermodynamics, especially multivalent ions. However, it has been suggested that the binding of multivalent ions to nucleic acids cannot be quantitatively described by the well-established Poisson-Boltzmann (PB) theory. In this work, we made extensive calculations of ion distributions around various RNA-like macroions in divalent and trivalent salt solutions by PB theory and Monte Carlo (MC) simulations. Our calculations show that PB theory appears to underestimate multivalent ion distributions around RNA-like macroions while can reliably predict monovalent ion distributions. Our extensive comparisons between PB theory and MC simulations indicate that when an RNA-like macroion gets ion neutralization beyond a "critical" value, the multivalent ion distribution around that macroion can be approximately described by PB theory. Furthermore, an empirical formula was obtained to approximately quantify the critical ion neutralization for various RNAlike macroions in multivalent salt solutions, and this empirical formula was shown to work well for various real nucleic acids including RNAs and DNAs.