An improved DNA force field for ssDNA interactions with gold nanoparticles

The Selective Function of Quantum Biological Electron Transfer between DNA Bases and Metal Ions in DNA Replication

Metal ions play vital roles in the electron transfer between biological molecules in humans, animals, and plants. However, the electron transfer between metal ions and nucleic acids and its impact on DNA-ion binding during DNA replication has been ignored. Here, we present a long-range quantum biological electron transfer (QBET) between DNA bases and metal ions and its selective function of DNA-ion binding in DNA replication. We discover biophysical DNA-ion binding and create biological filters that allow selective DNA replication by dual modulators of the valence and concentration of metal ions. QBET-based DNA replication filters provide powerful tools for ultrasensitive polymerase chain reaction (PCR) to selectively amplify target sequences with a discrete concentration window of metal ions; for example, Au³⁺ exhibits a concentration window that is approximately 3 orders of magnitude lower than that of Na⁺. DNA-ion filters provide new perspectives into metal ion-mediated QBET in DNA replication and hold great potential in life sciences and medical applications.

Molecular Structure of Single-Stranded DNA on the ZnS Surface of Quantum Dots

DNA-based nanoparticle assemblies have emerged as leading candidates in the development of bioimaging materials, photonic devices, and computing materials. Here, we combine atomistic simulations and experiments to characterize the wrapping mechanism of chimeric single-stranded DNA (ssDNA) on CdSe-ZnS (core-shell) quantum dots (QDs) at different ratios of the phosphorothioate (PS) modification of the bases. We use an implicit solvent, all-atom ssDNA model to match the experimentally calculated ssDNA conformation at low salt concentrations. Through simulation, we find that 3-mercaptopropionic acid (MPA) induces electrostatic repulsion and O-(2-mercaptoethyl)-Ó-methyl-hexa (ethylene glycol) (mPEG) induces steric exclusion, and both reduce the binding affinity of ssDNA. In both simulation and experiment, we find that ssDNA is closer to the QD surface when the QD size is larger. The effect of the PS-base ratio on the conformation of ssDNA is also elaborated in this work. We found through MD simulations, and confirmed by transmission electron microscopy, that the maximum valence numbers are 1, 2, and 3 on QDs of 6, 9, and 14 nm in diameter, respectively. We conclude that the maximum ssDNA valence number is linearly related to the QD size, n ∝ R, and justify this finding through an electrostatic repulsion mechanism.

Hydrophobic collapse-driven nanoparticle coating with poly-adenine adhesives

The mechanism underlying the strong adhesion between DNA with consecutive adenines (polyA) and Au nanoparticles (AuNPs) is experimentally and theoretically studied. We elucidate that the consecutive adenines collectively result in hydrophobic collapse in the adhesion process, which plays a pivotal role for the high adhesion affinity and specificity.

Uniform, Anticorrosive, and Antiabrasive Coatings on Metallic Surfaces for Cation-Metal and Cation-π Interactions

Metals are widely used, from daily life to modern industry. Great efforts have been made to protect the metals with various coatings. However, the well-known conventional electrochemical corrosion induced by cations and the ubiquitous nature of the coffee-ring effect make these processes very difficult. Here, a scheme by two bridges of cations and ethylenediamine (EDA) is proposed to overcome the coffee-ring effect and electrochemical corrosion and experimentally achieve uniform, anticorrosive, and antiabrasive coatings on metallic surfaces. Anticorrosive capability reaches about 26 times higher than that without cation-controlled coatings at 12 h in extremely acidic, high-temperature, and high-humidity conditions and still enhances to 2.7 times over a week. Antiabrasive capability also reaches 2.5 times. Theoretical calculations show that the suspended materials are uniformly adsorbed on the surface mediated by complexed cations through strong cation-metal and cation-π interactions. Notably, the well-known conventional electrochemical corrosion induced by cations is avoided by EDA to control cations solubility in different coating processes. These findings provide a new efficient, cost-effective, facile, and scalable method to fabricate protective coatings on metallic materials and a methodology to study metallic nanostructures in solutions, benefitting practical applications including coatings, printing, dyeing, electrochemical protection, and biosensors.

Molecular Dynamics Simulations of DNA Adsorption on Graphene Oxide and Reduced Graphene Oxide-PEG-NH2 in the Presence of Mg2+ and Cl− ions

Graphene and its functionalised derivatives are transforming the development of biosensors that are capable of detecting nucleic acid hybridization. Using a Molecular Dynamics (MD) approach, we explored single-stranded or double-stranded deoxyribose nucleic acid (ssDNA or dsDNA) adsorption on two graphenic species: graphene oxide (GO) and reduced graphene oxide functionalized with aminated polyethylene glycol (rGO-PEG-NH2). Innovatively, we included chloride (Cl−) and magnesium (Mg2+) ions that influenced both the ssDNA and dsDNA adsorption on GO and rGO-PEG-NH2 surfaces. Unlike Cl−, divalent Mg2+ ions formed bridges between the GO surface and DNA molecules, promoting adsorption through electrostatic interactions. For rGO-PEG-NH2, the Mg2+ ions were repulsed from the graphenic surface. The subsequent ssDNA adsorption, mainly influenced by electrostatic forces and hydrogen bonds, could be supported by π–π stacking interactions that were absent in the case of dsDNA. We provide a novel insight for guiding biosensor development.

Anomalous behavior of membrane fluidity caused by copper-copper bond coupled phospholipids

Membrane fluidity, essential for cell functions, is obviously affected by copper, but the molecular mechanism is poorly understood. Here, we unexpectedly observed that a decrease in phospholipid (PL) bilayer fluidity caused by Cu²⁺ was more significant than those by Zn²⁺ and Ca²⁺, while a comparable reduction occurred in the last two ions. This finding disagrees with the placement in the periodic table of Cu just next to Zn and far from Ca. The physical nature was revealed to be an anomalous attraction between Cu⁺ cations, as well as the induced motif of two phospholipids coupled by Cu-Cu bond (PL-diCu-PL). Namely, upon Cu²⁺ ion binding to a negatively charged phosphate group of lipid, Cu²⁺ was reduced to Cu⁺. The attraction of the cations then caused one Cu⁺ ion simultaneously binding to two lipids and another Cu⁺, resulting in the formation of PL-diCu-PL structure. In contrast, this attraction cannot occur in the cases of Zn and Ca ions. Remarkably, besides lipids, the phosphate group also widely exists in other biological molecules, including DNA, RNA, ADP and ATP. Our findings thus provide a new view for understanding the biological functions of copper and the mechanism underlying copper-related diseases, as well as lipid assembly.

Understanding and Designing the Gold-Bio Interface: Insights from Simulations

Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochemical interactions occurring between these inorganic materials, their functional layers, and the biological species they interact with. Computational approaches are instrumental in providing the necessary molecular insight into the structural and dynamic behavior of the Au-bio interface with spatial and temporal resolutions not yet achievable in the laboratory, and are able to facilitate a rational approach to AuNP design for specific applications. A perspective of the current successes and challenges associated with the multiscale computational treatment of Au-bio interfacial systems, from electronic structure calculations to force field methods, is provided to illustrate the links between different approaches and their relationship to experiment and applications.