Oxide- and Silicate-Water Interfaces and Their Roles in Technology and the Environment.

Interfacial reactions drive all elemental cycling on Earth and play pivotal roles in human activities such as agriculture, water purification, energy production and storage, environmental contaminant remediation, and nuclear waste repository management. The onset of the 21st century marked the beginning of a more detailed understanding of mineral aqueous interfaces enabled by advances in techniques that use tunable high-flux focused ultrafast laser and X-ray sources to provide near-atomic measurement resolution, as well as by nanofabrication approaches that enable transmission electron microscopy in a liquid cell. This leap into atomic- and nanometer-scale measurements has uncovered scale-dependent phenomena whose reaction thermodynamics, kinetics, and pathways deviate from previous observations made on larger systems. A second key advance is new experimental evidence for what scientists hypothesized but could not test previously, namely, interfacial chemical reactions are frequently driven by "anomalies" or "non-idealities" such as defects, nanoconfinement, and other nontypical chemical structures. Third, progress in computational chemistry has yielded new insights that allow a move beyond simple schematics, leading to a molecular model of these complex interfaces. In combination with surface-sensitive measurements, we have gained knowledge of the interfacial structure and dynamics, including the underlying solid surface and the immediately adjacent water and aqueous ions, enabling a better definition of what constitutes the oxide- and silicate-water interfaces. This critical review discusses how science progresses from understanding ideal solid-water interfaces to more realistic systems, focusing on accomplishments in the last 20 years and identifying challenges and future opportunities for the community to address. We anticipate that the next 20 years will focus on understanding and predicting dynamic transient and reactive structures over greater spatial and temporal ranges as well as systems of greater structural and chemical complexity. Closer collaborations of theoretical and experimental experts across disciplines will continue to be critical to achieving this great aspiration.

Self-Replicating DNA-Based Nanoassemblies.

The properties of DNA that make it an effective genetic material also allow it to be ideal for programmed self-assembly. Such DNA-programmed assembly has been utilized to construct responsive DNA origami and wireframe nanoassemblies, yet replicating these hybrid nanomaterials remains challenging. Here we report a strategy for replicating DNA wireframe nanoassemblies using the isothermal ligase chain reaction lesion-induced DNA amplification (LIDA). We designed a triangle wireframe structure that can be formed in one step by ring-closing of its linear analog. Introducing a small amount of the wireframe triangle to an excess of the linear analog and complementary fragments, one of which contains a destabilizing abasic lesion, leads to rapid, sigmoidal self-replication of the wireframe triangle via cross-catalysis. Using the same cross-catalytic strategy we also demonstrate rapid self-replication of a hybrid wireframe triangle containing synthetic vertices as well as the self-replication of circular DNA. This work reveals the suitability of isothermal ligase chain reactions such as LIDA to self-replicate complex DNA architectures, opening the door to incorporating self-replication, a hallmark of life, into biomimetic DNA nanotechnology.

Minimizing Product Inhibition in DNA Self-Replication: Insights for Prebiotic Replication from the Role of the Enzyme in Lesion-Induced DNA Amplification.

Self-replication of nucleic acids in the absence of enzymes represents an important and poorly understood step in the origin of life as such reported systems are strongly hindered by product inhibition. Studying one of the few successful examples of enzymatic DNA self-replication based on a simple ligation chain reaction, lesion-induced DNA amplification (LIDA), can shed light on how this fundamental process may have originally evolved. To identify the unknown factors that lead LIDA to overcome product inhibition we have employed isothermal titration calorimetry and global fitting of time-dependent ligation data to characterize the individual steps of the amplification process. We find that incorporating the abasic lesion into one of the four primers substantially decreases the stability difference between the product and intermediate complexes compared with complexes without the abasic group. In the presence of T4 DNA ligase this stability gap is further reduced by two orders of magnitude revealing that the ligase also helps overcome product inhibition. Kinetic simulations reveal that the intermediate complex stability and the magnitude of the ligation rate constant significantly impact the rate of self-replication, suggesting that catalysts that both facilitate ligation and stabilize the intermediate complex might be a route to efficient nonenzymatic replication.

Relating the phase in vibrational sum frequency spectroscopy and second harmonic generation with the maximum entropy method.

Nonlinear optical methods, such as vibrational sum frequency generation (vSFG) and second harmonic generation (SHG), are powerful techniques to study elusive structures at charged buried interfaces. However, for the separation and determination of the Stern and diffuse layer spectra at these charged interfaces, complex vSFG spectra and, hence, the absolute phase need to be retrieved. The maximum entropy method is a useful tool for the retrieval of complex spectra from the intensity spectra; however, one caveat is that an understanding of the error phase is required. Here, for the first time, we provide a physically motivated understanding of the error phase. Determining the error phase from simulated spectra of oscillators with a spectral overlap, we show that for broadband vSFG spectra, such as for the silica/water interface, the diffuse and Stern layers' spectral overlap within the O-H stretching window results in a correlation between the error phase and the phase shift between the responses of these layers. This correlation makes the error phase sensitive to changes in Debye length from varying the ionic strength among other variations at the interface. Furthermore, the change in the magnitude of the error phase can be related to the absolute SHG phase, permitting the use of an error phase model that can utilize the SHG phase to predict the error phase and, hence, the complex vSFG spectra. Finally, we highlight limitations of this model for vSFG spectra with a poor overlap between the diffuse and Stern layer spectra (silica/HOD in D2O system).

Water Structure in the Electrical Double Layer and the Contributions to the Total Interfacial Potential at Different Surface Charge Densities.

The electric double layer governs the processes of all charged surfaces in aqueous solutions; however, elucidating the structure of the water molecules is challenging for even the most advanced spectroscopic techniques. Here, we present the individual Stern layer and diffuse layer OH stretching spectra at the silica/water interface in the presence of NaCl over a wide pH range using a combination of vibrational sum frequency generation spectroscopy, heterodyned second harmonic generation, and streaming potential measurements. We find that the Stern layer water molecules and diffuse layer water molecules respond differently to pH changes: unlike the diffuse layer, whose water molecules remain net-oriented in one direction, water molecules in the Stern layer flip their net orientation as the solution pH is reduced from basic to acidic. We obtain an experimental estimate of the non-Gouy-Chapman (Stern) potential contribution to the total potential drop across the insulator/electrolyte interface and discuss it in the context of dipolar, quadrupolar, and higher order potential contributions that vary with the observed changes in the net orientation of water in the Stern layer. Our findings show that a purely Gouy-Chapman (Stern) view is insufficient to accurately describe the electrical double layer of aqueous interfaces.

CRISPR-Click Enables Dual-Gene Editing with Modular Synthetic sgRNAs.

Gene-editing systems such as CRISPR-Cas9 readily enable individual gene phenotypes to be studied through loss of function. However, in certain instances, gene compensation can obfuscate the results of these studies, necessitating the editing of multiple genes to properly identify biological pathways and protein function. Performing multiple genetic modifications in cells remains difficult due to the requirement for multiple rounds of gene editing. While fluorescently labeled guide RNAs (gRNAs) are routinely used in laboratories for targeting CRISPR-Cas9 to disrupt individual loci, technical limitations in single gRNA (sgRNA) synthesis hinder the expansion of this approach to multicolor cell sorting. Here, we describe a modular strategy for synthesizing sgRNAs where each target sequence is conjugated to a unique fluorescent label, which enables fluorescence-activated cell sorting (FACS) to isolate cells that incorporate the desired combination of gene-editing constructs. We demonstrate that three short strands of RNA functionalized with strategically placed 5'-azide and 3'-alkyne terminal deoxyribonucleotides can be assembled in a one-step, template-assisted, copper-catalyzed alkyne-azide cycloaddition to generate fully functional, fluorophore-modified sgRNAs. Using these synthetic sgRNAs in combination with FACS, we achieved selective cleavage of two targeted genes, either separately as a single-color experiment or in combination as a dual-color experiment. These data indicate that our strategy for generating double-clicked sgRNA allows for Cas9 activity in cells. By minimizing the size of each RNA fragment to 41 nucleotides or less, this strategy is well suited for custom, scalable synthesis of sgRNAs.

Probing Silica-Kaolinite Interactions with Sum Frequency Generation Spectroscopy.

Treating the oil sands tailings ponds is a major challenge because of the vast amounts of tailings and the need for a reliable treatment technique for releasing water and generating the highly consolidated material required for land reclamation. Treatment with chemicals such as lime (calcium (hydr)oxide) is a promising technology for tailings dewatering and consolidation, particularly at higher pH. Given that kaolinite and silica minerals are the main constituents of many oil sands, we have investigated the influence of lime and NaOH addition on the silica/aqueous kaolinite interface over the pH range 7.4-12.4 using vibrational sum frequency generation spectroscopy (SFG). With lime addition, at pH 12.0 and above we observe a complete disappearance of the vibrational features of the interfacial water molecules for planar silica in contact with an aqueous dispersion of kaolinite particles. A concurrent increase in the amount of adsorbed kaolinite on the silica surface at pH 12.0 and above is observed, shown in the increased intensity of the kaolinite SFG peak at 3694 cm-1. This suggests that the absence of water features in the SFG spectra is associated with conditions that facilitate dewatering. With NaOH addition, however, the interfacial water SF intensity is still significant even under highly alkaline conditions despite the increase in adsorbed kaolinite at high pH. To better understand the SFG observations and get a deeper insight into the chemistry of the silica/aqueous kaolinite interface, we measure the ζ-potential on the planar silica/aqueous interface and kaolinite aqueous dispersions under the same pH conditions with NaOH and lime addition.

Enhanced mismatch selectivity of T4 DNA ligase far above the probe: Target duplex dissociation temperature.

T4 DNA ligase is a widely used ligase in many applications; yet in single nucleotide polymorphism analysis, it has been found generally lacking owing to its tendency to ligate mismatches quite efficiently. To address this lack of selectivity, we explored the effect of temperature on the selectivity of the ligase in discriminating single base pair mismatches at the 3'-terminus of the ligating strand using short ligation probes (9-mers). Remarkably, we observe outstanding selectivities when the assay temperature is increased to 7 °C to 13 °C above the dissociation temperature of the matched probe:target duplexes using commercially available enzyme at low concentration. Higher enzyme concentration shifts the temperature range to 13 °C to 19 °C above the probe:target dissociation temperatures. Finally, substituting the 5'-phosphate terminus with an abasic nucleotide decreases the optimal temperature range to 7 °C to 10 °C above the matched probe:target duplex. We compare the temperature dependence of the T4 DNA ligase catalyzed ligation and a nonenzymatic ligation system to contrast the origin of their modes of selectivity. For the latter, temperatures above the probe:target duplex dissociation lead to lower ligation conversions even for the perfect matched system. This difference between the two ligation systems reveals the uniqueness of the T4 DNA ligase's ability to maintain excellent ligation yields for the matched system at elevated temperatures. Although our observations are consistent with previous mechanistic work on T4 DNA ligase, by mapping out the temperature dependence for different ligase concentrations and probe modifications, we identify simple strategies for introducing greater selectivity into SNP discrimination based on ligation yields.

Silica Surface Charge Enhancement at Elevated Temperatures Revealed by Interfacial Water Signals.

The structure of water adjacent to silica is sensitive to the degree of deprotonation of surface silanol groups. As a result, close inspection of signals originating from these water molecules can be used to reveal the surface charge density. We have used nonlinear vibrational spectroscopy of the water O-H stretching band over a temperature range of 10-75 °C to account for the increase in surface potential from deprotonation. We demonstrate that the behavior at the silica surface is a balance between increasing surface charge and a decreasing contribution of water molecules aligned by the surface charge. Together with a model that accounts for two different types of silanol sites, we use our data to report the changes in enthalpy and entropy for deprotonation at each site. This is the first experimental determination of these thermodynamic parameters for hydrated silanol groups at the silica surface, critical to a wide range of geochemical and technological applications.

Quick Click: The DNA-Templated Ligation of 3'-O-Propargyl- and 5'-Azide-Modified Strands Is as Rapid as and More Selective than Ligase.

The copper(I)-mediated azide-alkyne cycloaddition (CuAAC) of 3'-propargyl ether and 5'-azide oligonucleotides is a particularly promising ligation system because it results in triazole linkages that effectively mimic the phosphate-sugar backbone of DNA, leading to unprecedented tolerance of the ligated strands by polymerases. However, for a chemical ligation strategy to be a viable alternative to enzymatic systems, it must be equally as rapid, as discriminating, and as easy to use. We found that the DNA-templated reaction with these modifications was rapid under aerobic conditions, with nearly quantitative conversion in 5 min, resulting in a kobs value of 1.1 min-1 , comparable with that measured in an enzymatic ligation system by using the highest commercially available concentration of T4 DNA ligase. Moreover, the CuAAC reaction also exhibited greater selectivity in discriminating C:A or C:T mismatches from the C:G match than that of T4 DNA ligase at 29 °C; a temperature slightly below the perfect nicked duplex dissociation temperature, but above that of the mismatched duplexes. These results suggest that the CuAAC reaction of 3'-propargyl ether and 5'-azide-terminated oligonucleotides represents a complementary alternative to T4 DNA ligase, with similar reaction rates, ease of setup and even enhanced selectivity for certain mismatches.

Influence of High pH on the Organization of Acetonitrile at the Silica/Water Interface Studied by Sum Frequency Generation Spectroscopy.

The acetonitrile-water mixture is one of the most commonly used solvents in hydrophilic interaction chromatography, which contains silica as the solid phase. As such, the silica/acetonitrile-water interface plays a large role in the separation of compounds. Varying the pH is one way to influence retention times, particularly of ionizable solutes, yet the influence of high pH is often unpredictable. To determine how the structure of this interface changes with pH, we utilized the surface specific technique sum frequency generation (SFG). Previous SFG studies at neutral pH have suggested the existence of acetonitrile bilayers at the aqueous silica interface even at low acetonitrile mole fractions. Here we find that the SFG signal from 2900 to 3040 cm-1 at the silica/acetonitrile-water interface increased as we adjusted the aqueous pH from near neutral to high values. This increase in signal was attributed to a greater amount of aligned water which is consistent with an increase in silica surface charge at high pH. In contrast, complementary measurements of the silica/acetonitrile-deuterium oxide interface revealed that the acetonitrile methyl mode nearly vanished as the aqueous pH was increased. This loss of methyl mode signal is indicative of a decrease in the number density of acetonitrile molecules at the interface, as orientation analysis indicates no significant change in the net orientation of the outer leaflet of the acetonitrile bilayer over the pH range studied.

Bridging molecular-scale interfacial science with continuum-scale models.

Solid-water interfaces are crucial for clean water, conventional and renewable energy, and effective nuclear waste management. However, reflecting the complexity of reactive interfaces in continuum-scale models is a challenge, leading to oversimplified representations that often fail to predict real-world behavior. This is because these models use fixed parameters derived by averaging across a wide physicochemical range observed at the molecular scale. Recent studies have revealed the stochastic nature of molecular-level surface sites that define a variety of reaction mechanisms, rates, and products even across a single surface. To bridge the molecular knowledge and predictive continuum-scale models, we propose to represent surface properties with probability distributions rather than with discrete constant values derived by averaging across a heterogeneous surface. This conceptual shift in continuum-scale modeling requires exponentially rising computational power. By incorporating our molecular-scale understanding of solid-water interfaces into continuum-scale models we can pave the way for next generation critical technologies and novel environmental solutions.

Hydrolyzable emulsions as a dual release platform for hydrophobic drugs and DNA.

Several challenges need to be overcome when applying nucleic acids as therapeutic agents. We developed a new way to control the onset of the release of cholesterol-conjugated oligonucleotides with a simple, versatile, and cheap platform. Moreover, we combine the platform into a dual-release system that can release a hydrophobic drug with zero-order kinetics, followed by a rapid release of cholesterol-conjugated DNA.

Disrupting Protein Expression with Double-Clicked sgRNA-Cas9 Complexes: A Modular Approach to CRISPR Gene Editing.

CRISPR-Cas9 is currently the most versatile technique to perform gene editing in living organisms. In this approach, the Cas9 endonuclease is guided toward its DNA target sequence by the guide RNA (gRNA). Chemical synthesis of a functional single gRNA (sgRNA) is nontrivial because of the length of the RNA strand. Recently we demonstrated that a sgRNA can be stitched together from three smaller fragments through a copper-catalyzed azide-alkyne cycloaddition, making the process highly modular. Here we further advance this approach by leveraging this modulator platform by incorporating chemically modified nucleotides at both ends of the modular sgRNA to increase resistance against ribonucleases. Modified nucleotides consisted of a 2'-O-Me group and a phosphorothioate backbone in varying number at both the 5'- and 3'-ends of the sgRNA. It was observed that three modified nucleotides at both ends of the sgRNA significantly increased the success of Cas9 in knocking out a gene of interest. Using these chemically stabilized sgRNAs facilitates multigene editing at the protein level, as demonstrated by successful knockout of both Siglec-3 and Siglec-7 using two fluorophores in conjunction with fluorescence-activated cell sorting. These results demonstrate the versatility of this modular platform for assembling sgRNAs from small, chemically modified strands to simultaneously disrupt the gene expression of two proteins.

Selectivity and efficiency in the ligation of the pyrene:abasic base pair by T4 and PBCV-1 DNA ligases.

Remarkable selectivity was observed in the ligation of 5'-phosphate 1-pyrene nucleotide terminated strands across from an abasic lesion in a DNA-templated ligation reaction by two different ligases suggesting that pyrene-terminated strands could be used in abasic site detection. Increasing ATP concentration was critical to enhancing the selectivity for this base pair with T4 DNA ligase.

Role of Ions on the Surface-Bound Water Structure at the Silica/Water Interface: Identifying the Spectral Signature of Stability.

Isolating the hydrogen-bonding structure of water immediately at the surface is challenging, even with surface-specific techniques like sum-frequency generation (SFG), because of the presence of aligned water further away in the diffuse layer. Here, we combine zeta potential and SFG intensity measurements with the maximum entropy method referenced to reported phase-sensitive SFG and second-harmonic generation results to deconvolute the SFG spectral contributions of the surface waters from those in the diffuse layer. Deconvolution reveals that at very low ionic strength, the surface water structure is similar to that of a neutral silica surface near the point-of-zero-charge with waters in different hydrogen-bonding environments oriented in opposite directions. This similarity suggests that the known metastability of silica colloids against aggregation under both conditions could arise from this distinct surface water structure. Upon the addition of salt, significant restructuring of water is observed, leading to a net decrease in order at the surface.

Reverse transcription lesion-induced DNA amplification: An instrument-free isothermal method to detect RNA.

One challenge in point-of-care (POC) diagnostics is the lack of room-temperature methods for RNA detection based on enzymatic amplification and visualization steps. Here we perform reverse transcription lesion-induced DNA amplification (RT-LIDA), an isothermal amplification method that only requires T4 DNA ligase. RT-LIDA involves the RNA-templated ligation of DNA primers to form complementary DNA (cDNA) followed by toehold-mediated strand displacement of the cDNA and its exponential amplification via our isothermal ligase chain reaction LIDA. Each step is tuned to proceed at 28 °C, which falls within the range of global room temperatures. Using RT-LIDA, we can detect as little as ∼100 amol target RNA and can distinguish RNA target from total cellular RNA. Finally, we demonstrate that the resulting DNA amplicons can be detected colorimetrically, also at room temperature, by rapid, target-triggered disassembly of DNA-modified gold nanoparticles. This integrated amplification/detection platform requires no heating or visualization instrumentation, which is an important step towards realizing instrument-free POC testing.

Sharp melting of polymer-DNA hybrids: an associative phase separation approach.

An associative equilibrium theory describing the sharp melting behavior of polymer-DNA hybrids is developed. The theory considers linear polymers with attached DNAs on each polymer that serve as "stickers" and with a two-state model governing the DNA melting equilibrium. For three or more oligonucleotides on each polymer, solutions of polymer-DNA hybrids are found to undergo phase separation at sufficiently low temperatures. The dense phase dissolves as temperature increases, which leads to a sharp increase in the fraction of non-hybridized DNA near the phase transition temperature, in agreement with experimental absorbance profiles at 260 nm. The melting temperature is predicted to have the same dependence on salt concentration as a solution of unattached DNAs and be weakly sensitive to the concentration of DNA in solution. The melting temperature is predicted to be higher than that of unattached DNA in solution, with the magnitude of the increase sensitive to the DNA hybridization cooperativity. The theoretical predictions are generally in good quantitative agreement with new experimental data (also presented here), which show the effect of the polymer-DNA hybrid length and salt concentration on the melting profiles.

pH-Dependent Inversion of Hofmeister Trends in the Water Structure of the Electrical Double Layer.

Specific ion effects (SIEs) are known to influence the acid/base behavior of silica and the interfacial structure of water, yet evidence of the effect of pH on SIEs is lacking. Here broadband vibrational sum frequency generation (SFG) spectroscopy was used to study SIEs on the water structure at the electrical double layer (EDL) of silica as a function of pH and monovalent cation identity from pH 2-12 at 0.5 M salt concentration. SFG results indicate a direct Hofmeister series of cation adsorption at pH 8 (Li+ < Na+ < K+ < Cs+), with an inversion in this series occurring at pH > 10. In addition, an inversion in SFG intensity trends also occurred at pH < 6, which was attributed to contributions from asymmetric cation hydration and EDL overcharging. The highly pH-dependent SIEs for silica/water have implications for EDL models that often assume pH-independent parameters.