Interfacing DNA Oligonucleotides with Calcium Phosphate and Other Metal Phosphates

Equilibrium interactions of biomimetic DNA aptamers produce intrafibrillar calcium phosphate mineralization of collagen

Native and biomimetic DNA structures have been demonstrated to impact materials synthesis under a variety of conditions but have only just begun to be explored in this role compared to other biopolymers such as peptides, proteins, polysaccharides, and glycopolymers. One selected DNA aptamer has been explored in calcium phosphate and calcium carbonate mineralization, demonstrating sequence-dependent control of kinetics, morphology, and crystallinity. This aptamer is here applied to a biologically-relevant bone model system that uses collagen hydrogels. In the presence of the aptamer, intrafibrillar collagen mineralization is observed compared to negative controls and a positive control using well-studied poly-aspartic acid. The mechanism of interaction is explored through affinity measurements, kinetics of calcium uptake, and kinetics of aptamer uptake into the forming mineral. There is a marked difference observed between the selected aptamer containing a G-quadruplex secondary structure compared to a control sequence with no G-quadruplex. It is hypothesized that the equilibrium interaction of the aptamer with calcium-phosphate precursors and with the collagen itself leads to slow kinetic mineral formation and a morphology appropriate to bone. This points to new uses for DNA aptamers in biologically-relevant mineralization systems and the possibility of future biomedical applications. STATEMENT OF SIGNIFICANCE: Collagen is the protein structural component that mineralizes with calcium phosphate to form durable bone. Crystalline calcium phosphate must be infused throughout the collagen fiber structure to produce a strong material. This process is assisted by soluble proteins that interact with both calcium phosphate precursors and the collagen protein and has been proposed to follow a polymer-induce liquid precursor (PILP) model. Further understanding of this model and control of the process through synthetic, biomimetic molecules could have significant advantages in biomedical, restorative procedures. For the first time, synthetic DNA aptamers with specific secondary structures are here shown to influence and direct collagen mineralization. The mechanism of this process has been studied to demonstrate an important equilibrium between the DNA aptamer, calcium phosphate precursors, and collagen.

Polydopamine functionalized dendritic fibrous silica nanoparticles as a generic platform for nucleic acid-based biosensing

Accurate and rapid detection of nucleic acid sequences is of utmost importance in various fields, including disease monitoring, clinical treatment, gene analysis and drug discovery. In this study, we developed a "turn-on" fluorescence biosensor that enables simple and highly efficient detection of nucleic acid biomarkers. Our approach involves the utilization of 6-carboxyfluorescein modified single-stranded DNA (FAM-ssDNA) as molecular recognition element, along with polydopamine-functionalized dendritic fibrous nanosilica (DFNS). FAM-ssDNA serves as both specific molecular recognition element for the target analyte and reporter capable of transducing a detectable signal through Watson-Crick base pairing. The polydopamine-functionalized DFNS (DFNS@DA) exhibits strong binding to FAM-ssDNA via polyvalent metal mediated coordination leading to effective quenching by fluorescence resonance energy transfer. In the presence of a complementary target sequence, FAM-ssDNA forms hybridized structure and detaches from DFNS@DA, which causes an increased fluorescence emission. The analytical system based on FAM-ssDNA and DFNS@DA demonstrates exceptional sensitivity, selectivity, and rapid response for the detection of nucleic acid sequences, leveraging the high adsorption and quenching properties of DFNS@DA. For the first proof of concept, we demonstrated the successful detection of microRNA (miR-21) in cancer cells using the FAM-ssDNA/DFNS@DA system. Our results highlight the promising capabilities of DFNS@DA and nucleic acid-based biosensors, offering a generic and cost-effective solution for the detection of nucleic acid-related biomarkers.

New discovery of extremely high adsorption of environmental DNA on cuttlefish bone pyrolysis derivative via large pore structure and carbon film

Environmental DNA (eDNA) carrying antibiotic resistance gene (ARG) has attracted a great deal of attention because of its threat to the ecology and human health. Traditional porous adsorbents, such as microporous biochar and natural mineral, are low-effective in removing eDNA from sewage. This study used cuttlefish-bone (CB), a fishery waste, as an anticipated material to adsorb a model compound of eDNA from herring sperm (hsDNA). An interesting result was firstly observed that extremely high DNA adsorption on cuttlefish-bone pyrolysis derivative (CCB) was up to 88.7 mg/g, 3-10 folds higher than that of most other adsorbents in the existing literatures, which was attributed to the carbon film and large pores. To achieve an adsorption rate of 75 %, hsDNA adsorption took 96 h on CB but only 24 h on CCB, which was attributed to the fluent channel of CCB. The ligand exchange, Ca2+ bridge and π-π interaction were identified as dominated adsorption mechanisms, based on FTIR and phosphate competition experiments. This study exploited a high-efficient, environmentally friendly, and low-cost adsorbent for treating ARG-contaminated soil and water.

Secondary Structure of DNA Aptamer Influences Biomimetic Mineralization of Calcium Carbonate

Calcium materials, such as calcium carbonate, are produced in natural and industrial settings that range from oceanic to biomedical. An array of biological and biomimetic template molecules have been employed in controlling and understanding the mineralization reaction but have largely focused on small molecule additives or disordered polyelectrolytes. DNA aptamers are synthetic and programmable biomolecules with polyelectrolyte characteristics but with predictable and controllable secondary structure akin to native extracellular moieties. This work demonstrates for the first time the influence of DNA aptamers with known G-quadruplex structures on calcium carbonate mineralization. Aptamers demonstrate kinetic inhibition of mineral formation, sequence and pH-dependent uptake into the mineral, and morphological control of the primarily calcite material in controlled solution conditions. In reactions initiated from the complex matrix of ocean water, DNA aptamers demonstrated enhancement of mineralization kinetics and resulting amorphous material. This work provides new biomimetic tools to employ in controlled mineralization and demonstrates the influence that template secondary structure can have in material formation.

Polyvalent Metal Ion Promoted Adsorption of DNA Oligonucleotides by Montmorillonite

Montmorillonite (MMT) is a two-dimensional (2D) clay material. Its abundance on the early earth has attracted studies for its role in prebiotic reactions, and adsorption of DNA to MMT is potentially important for understanding the origin of life. Although several possible models of DNA adsorption on MMT have been established, a consensus on the adsorption mechanism has yet to be formed, thereby a fundamental adsorption study is performed here. Adding up to 300 mM NaCl failed to promote DNA adsorption on MMT, Al₂O₃, or SiO₂ nanoparticles. For polyvalent metals, DNA adsorption was achieved following the order Ce³⁺ > Cu²⁺ > Ni²⁺ > Zn²⁺. Among them, Ce³⁺ and Cu²⁺ inverted the surface charge of MMT to positive. In addition, using washing experiments, Cu²⁺- and Ce³⁺-mediated adsorption mainly depended on the DNA phosphate backbone, while Ni²⁺ and Zn²⁺ interacted with the backbone phosphate groups and adenine bases of DNA. Overall, these polyvalent metal ions promoted DNA adsorption via a cation bridge model. This research provides new insights into the surface interactions of MMT and DNA, which is conducive to future work on the interaction between clays and biopolymers.

Stronger Adsorption of Phosphorothioate DNA Oligonucleotides on Graphene Oxide by van der Waals Forces

Finding DNA sequences that can adsorb strongly on nanomaterials is critical for bioconjugate and biointerface chemistry. In most previous work, unmodified DNA with a phosphodiester backbone (PO DNA) were screened or selected for adsorption on inorganic surfaces. In this work, the adsorption of phosphorothioate (PS)-modified DNA (PS DNA) on graphene oxide (GO) is studied. By use of fluorescently labeled oligonucleotides as probes, all the tested PS DNA strands are adsorbed more strongly on GO compared to the PO DNA of the same sequence. The adsorption mechanism is probed by washing the adsorbed DNA with proteins, surfactants, and urea. Molecular dynamics simulations show that van der Waals forces are responsible for the tighter adsorption of PS DNA. Polycytosine (poly-C) DNA, in general, has a high affinity for the GO surface, and PS poly-C DNA can adsorb even stronger, making it an ideal anchoring sequence on GO. With this knowledge, noncovalent functionalization of GO with a diblock DNA is demonstrated, where a PS poly-C block is used to anchor on the surface. This conjugate achieves better hybridization than the PO DNA of the same sequence for hybridization with the complementary DNA.

Struvite crystallization induced the discrepant transports of antibiotics and antibiotic resistance genes in phosphorus recovery from swine wastewater

Struvite (MgNH₄PO₃·6H₂O) crystallization is one of important methods of phosphorus recovery from wastewater. As to livestock wastewater, the high-strength occurrence of antibiotics and antibiotic resistance genes might induce struvite recovery to spread antibiotic resistance to the environment. However, limited information has been reported on the simultaneous transport of antibiotics and ARGs in struvite recovery. In the present study, tetracyclines (TCs) and tetracyclines antibiotic resistance genes (ARGs) were selected as the targeted pollutants, and their discrepant residues in struvite recovery from swine wastewater were investigated. TCs and ARGs were obviously detected, with their contents of 4.88-79.5 mg/kg and 6.99 × 10⁷-2.14 × 10¹¹ copies/g, notably higher than those of TCs 0.550-1.94 mg/kg and ARGs 3.98 × 10⁴-5.66 × 10⁷ copies/g obtained from synthetic wastewater. The correlational relationship revealed that predominant factors affecting TCs and ARGs transports were different. Results from network analyses indicated that among the total edges, the negative correlations between TCs and ARGs predominately occupied 18.0%. The redundancy analysis revealed that mineral components in the recovered products, including struvite, K-struvite and amorphous calcium phosphate, coupling with organic contents, displayed insignificant roles on TCs residues, where heavy metals exerted positive and remarkable functions to boost TCs migration. Unexpectedly, mineral components and heavy metals did not displayed significant promotion on ARGs transport as a whole.

DNA adsorption on nanoscale zeolitic imidazolate framework-8 enabling rational design of a DNA-based nanoprobe for gene detection and regulation in living cells

DNA functionalized nanomaterials have attracted tremendous attention for bioanalytical applications. Owing to exceptional fluorescence quenching ability, most DNA-based nanoprobes were designed with turn-on signals for target gene detection, while only a few of them could simultaneously achieve gene detection and regulation in one system. In this study, we explored the use of nanoscale zeolitic imidazolate framework-8 (ZIF-8) as a building block to construct a DNA-based nanoprobe. We found ZIF-8 could stably adsorb DNA to resist the dissociation by various biological ligands, enabling potential biological applications. However, ZIF-8 was not a nano-quencher to turn off the fluorophore labeling on the adsorbed DNA. We therefore designed a DNAzyme embedded molecular beacon (DMB) to functionalize ZIF-8. After endocytosis, ZIF-8 was disintegrated to release DMB for target mRNA detection, and the co-released Zn2+ acted as an effective cofactor to activate the embedded DNAzyme for mRNA regulation. This study provides a versatile nano-platform to realize multiple functions inside cells by using functional nucleic acids, which holds great promise for theranostic applications.

The CpG molecular structure controls the mineralization of calcium phosphate nanoparticles and their immunostimulation efficacy as vaccine adjuvants

The co-precipitation of calcium phosphate nanoparticles (CaPs) in the presence of nucleotide chains such as polynucleotides (i.e., plasmid DNA and siRNA) and oligonucleotides has been extensively used for pre-clinical gene or drug delivery and immunotherapy studies. However, the exact role of these molecules in mineralization and tuning the physicochemical characteristics of the synthesized CaPs is still not entirely clear. In this study, we evaluated the effects of three different CpG oligodeoxynucleotides (ODN) and two representative nucleic acids (siRNA and DNA), when used as templates for the formation of CaPs. We examined the influence of CpGs with naturally-occurring phosphodiester or modified phosphorothioate backbones on the homogeneous formation of CaPs from a modified simulated body fluid solution. The hydrodynamic size, size polydispersity, morphology and surface charge of the CaPs were used as the most critical checkpoints to unravel the involved mechanisms. Our results show that the characteristics of CaPs are highly dependent on the composition, backbone, sequence and concentrations of the CpGs. The CpG type and concentration control the size distribution of the mineralized CaPs and their immunostimulation performance as verified by the activation of dendritic cells and secretion of the pro-inflammatory interleukin-6 (IL-6) cytokine, type I interferon-α (IFN-α) and co-stimulatory CD80, CD86 and CD40 markers. This study paves the way for better design of more efficient CaPs loaded with different types of CpGs for immunostimulation applications as vaccine adjuvants.

Selected DNA aptamers as hydroxyapatite affinity reagents

DNA aptamers were selected for their ability to bind specifically and quickly to crystalline hydroxyapatite (Ca₁₀(PO₄)₆(OH)₂; HAP), the primary mineral component of enamel and bone. Aptamers were found to have an enhanced percent of G-nucleotides and a propensity for forming a G-quadruplex secondary structure. One aptamer was studied in comparison to control sequences and was found to bind with high affinity and at high loading capacity, with enhanced binding kinetics, and with specificity for crystalline HAP material over amorphous calcium phosphate (ACP) and β-tricalcium phosphate (TCP). The fluorescently-functionalized aptamer was demonstrated to specifically label HAP in a surface binding experiment and suggests the usefulness of this selected aptamer in biomedical or biotechnology fields where the labeling of specific calcium phosphate materials is required.

Fluorescein-Stabilized i-Motif DNA and Its Unfolding Leading to a Stronger Adsorption Affinity

Several previous studies have indicated that polydeoxycytidine (poly-C) DNA has an anomalously high affinity for different types of surfaces. It was hypothesized that the formation of an i-motif structure could be a factor responsible for this enhanced affinity, but this is against the notion that a folded molecule should have fewer interactions with a surface. Herein, the properties of poly-C DNA were examined in detail, focusing on the presence or absence of a FAM (carboxyfluorescein) label and its subsequent adsorption on graphene oxide. Fluorescence and CD spectroscopy studies indicated that FAM can stabilize an i-motif structure in C15 DNA. In particular, the fluorescence of FAM is drastically quenched when the DNA is folded. This structure is irreversibly unfolded upon heating. Furthermore, the unfolded structure has an even higher affinity for graphene oxide than the folded structure. Finally, a large portion of the folded C15 unfolds upon desorption from graphene oxide, and unfolding could happen upon adsorption or desorption of the DNA. This study provides a method to further enhance the adsorption stability of poly-C DNA and calls for care when investigating the potential effects of dye labels on DNA.

Mn2+-Assisted DNA Oligonucleotide Adsorption on Ti2C MXene Nanosheets

As a new type of 2D nanomaterial, MXene (transition metal carbide/nitride) nanosheets are already widely used in catalysis, sensing, and energy research. DNA is a popular sensing molecule. Compared to other 2D materials such as graphene oxide, MoS₂, and WS₂, few fundamental studies were carried out on DNA adsorption by MXene. Due to its exfoliation and delamination process, the surface of MXene is abundant in -F, -OH, and -O- groups, rendering the surface negatively charged and repelling DNA. In previous studies, surface modification of MXene was performed to promote DNA adsorption. Herein, Mn²⁺ was discovered to promote DNA adsorption on unmodified Ti₂C MXene. Different from Ca²⁺ and Mg²⁺, Mn²⁺ can inverse the ζ-potential of the Ti₂C MXene to positive. DNA mainly uses its phosphate backbone for adsorption, while its bases contribute significantly less. In addition, delayed DNA desorption was observed through the addition of inorganic phosphate due to the formation of manganese phosphate to gradually extract Mn²⁺ from the DNA/MXene complex. Finally, DNA-induced DNA desorption from the Ti₂C MXene can hardly distinguish the complementary DNA from a random DNA, which is very different from that for graphene oxide. This difference is likely due to the distinct surface chemistry between the MXene and graphene oxide.

Bioorthogonal DNA Adsorption on Polydopamine Nanoparticles Mediated by Metal Coordination for Highly Robust Sensing in Serum and Living Cells

DNA-functionalized nanomaterials, such as various 2D materials, metal oxides, and gold nanoparticles, have been extensively explored as biosensors. However, their practical applications for selective sensing and imaging in biological samples remain challenging due to interference from the sample matrix. Bioorthogonal chemistry has allowed specific reactions in cells, and we want to employ this concept to design nanomaterials that can selectively adsorb DNA but not proteins or other abundant biomolecules. In this work, DNA oligonucleotides were found to be adsorbed on polydopamine nanoparticles (PDANs) via polyvalent metal-mediated coordination, and such adsorption bioorthogonally resisted DNA displacement by various biological ligands, showing better performance compared to graphene oxide and metal oxide nanoparticles for DNA detection. Using DNA/PDANs as biosensors, a detection limit of <1 nM target DNA was achieved in serum and other biological samples, and imaging of cancer-related microRNA in cells was demonstrated. The DNA binding mechanism on PDAN was further studied by ligand displacement experiments and X-ray photoelectron spectroscopy characterization, which demonstrated the critical role of polyvalent metal ions to bridge DNA with PDANs. This work provides fundamental insights into the biointerface science of PDANs with DNA, which can benefit applications in biosensor design, directed assembly of nanomaterials, bioimaging, and drug delivery.

Adsorption of Phosphate and Polyphosphate on Nanoceria Probed by DNA Oligonucleotides

Phosphate-containing molecules exist in many forms in biology and the environment, and their interaction with metal oxides is an important aspect of their chemistry and biochemistry. In this work, phosphates with different degrees of polymerization (e.g., orthophosphate, pyrophosphate (PPi), sodium triphosphate (STPP), sodium trimetaphosphate (STMP), and polyphosphate with 25 phosphate units) and phosphates with one or two capping groups were studied. CeO₂ nanoparticles (nanoceria) were used as a model metal oxide. DNA is also a polyphosphate, and a fluorescently labeled DNA oligonucleotide was mixed with nanoceria. These phosphate species were individually added to displace the adsorbed DNA. Longer phosphate chains were more efficient when each molecule was used at the same molar concentration, whereas PPi and STPP were most efficient at the same total phosphorus atom concentration. By capping the phosphate with organic groups, the affinity was significantly decreased. Isothermal titration calorimetry (ITC) was also performed to quantitatively measure thermodynamic parameters. Although STMP was very slow at displacing DNA, it was still adsorbed very strongly by nanoceria from ITC, indicating kinetic effects likely due to its ring structure. This observation allowed us to use the DNA as a probe to study the hydrolysis of STMP to form STPP. In summary, this study provides a systematic understanding of phosphate species interacting with metal oxides, and interestingly, it demonstrates an analytical application as well.