Biomineralization of hydroxyapatite on DNA molecules in SBF: morphological features and computer simulation

The cell membrane as biofunctional material for accelerated bone repair

The cell (plasma) membrane is enriched with numerous receptors, ligands, enzymes, and phospholipids that play important roles in cell-cell and cell-extracellular matrix interactions governing, for instance, tissue development and repair. We previously showed that plasma membrane nanofragments (PMNFs) act as nucleation sites for bone formation in vivo, and induce in vitro mineralization within 1 day. In this study, we optimized the methods for generating, isolating, and applying PMNFs as a cell-free therapeutic to expedite bone defect repair. The PMNFs were isolated from different mouse cell lines (chondrocytes, osteoblasts, and fibroblasts), pre-conditioned, lyophilized, and subsequently transplanted into 2 mm critical-sized calvarial defects in mice (n = 75). The PMNFs from chondrocytes, following a 3-day pre-incubation, significantly accelerated bone repair within 2 weeks, through a coordinated attraction of macrophages, endothelial cells, and osteoblasts to the healing site. In vitro experiments confirmed that PMNFs enhanced cell adhesion. Comparison of the PMNF efficacy with phosphatidylserine, amorphous calcium phosphate (ACP), and living cells confirmed the unique ability of PMNFs to promote accelerated bone repair. Importantly, PMNFs promoted nearly complete integration of the regenerated bone with native tissue after 6 weeks (% non-integrated bone area = 15.02), contrasting with the partial integration (% non-integrated bone area = 56.10; p < 0.01, Student's test) with transplantation of ACP. Vickers microhardness tests demonstrated that the regenerated bone after 6 weeks (30.10 ± 1.75) exhibited hardness similar to native bone (31.07 ± 2.46). In conclusion, this is the first study to demonstrate that cell membrane can be a promising cell-free material with multifaceted biofunctional properties that promote accelerated bone repair. STATEMENT OF SIGNIFICANCE.

Effect of Ba2+ on the biomineralization of Ca2+ and Mg2+ ions induced by Bacillus licheniformis

The effect of barium ions on the biomineralization of calcium and magnesium ions is often overlooked when utilizing microbial-induced carbonate precipitation technology for removing barium, calcium, and magnesium ions from oilfield wastewater. In this study, Bacillus licheniformis was used to bio-precipitate calcium, magnesium, and barium ions. The effects of barium ions on the physiological and biochemical characteristics of bacteria, as well as the components of extracellular polymers and mineral characteristics, were also studied in systems containing coexisting barium, calcium, and magnesium ions. The results show that the increasing concentrations of barium ions decreased pH, carbonic anhydrase activity, and concentrations of bicarbonate and carbonate ions, while it increased the contents of humic acids, proteins, polysaccharides, and DNA in extracellular polymers in the systems containing all three types of ions. With increasing concentrations of barium ions, the content of magnesium within magnesium-rich calcite and the size of minerals precipitated decreased, while the full width at half maximum of magnesium-rich calcite, the content of O-C=O and N-C=O, and the diversity of protein secondary structures in the minerals increased in systems containing all three coexisting ions. Barium ions does inhibit the precipitation of calcium and magnesium ions, but the immobilized bacteria can mitigate the inhibitory effect. The precipitation ratios of calcium, magnesium, and barium ions reached 81-94%, 68-82%, and 90-97%. This research provides insights into the formation of barium-enriched carbonate minerals and offers improvements for treating oilfield wastewater.

Fabrication of initial trabecular bone-inspired three-dimensional structure with cell membrane nano fragments

The extracellular matrix of trabecular bone has a large surface exposed to the bone marrow and plays important roles such as hematopoietic stem cell niche formation and maintenance. In vitro reproduction of trabecular bone microenvironment would be valuable not only for developing a functional scaffold for bone marrow tissue engineering but also for understanding its biological functions. Herein, we analyzed and reproduced the initial stages of trabecular bone formation in mouse femur epiphysis. We identified that the trabecular bone formation progressed through the following steps: (i) partial rupture of hypertrophic chondrocytes; (ii) calcospherite formation on cell membrane nano fragments (CNFs) derived from the ruptured cells; and (iii) calcospherite growth and fusion to form the initial three-dimensional (3D) structure of trabecular bones. For reproducing the initial trabecular bone formation in vitro, we collected CNFs from cultured cells and used as nucleation sites for biomimetic calcospherite formation. Strikingly, almost the same 3D structure of the initial trabecular bone could be obtained in vitro by using additional CNFs as a binder to fuse biomimetic calcospherites.

Biomineralization from the Perspective of Ion Aggregation: Calcium Phosphate Nucleation in the Physiological Environment

Biomineralization is an important process of bone tissue generation. Calcium (Ca) and phosphate (P) ions aggregate and nucleate under the regulation of biomolecules at the initial mineralization stage. Due to the complexity of the physiological environment, the movement behavior and mineralization mechanism of calcium and phosphate ions, as well as the effect of biomolecules on them, are not clear. In this study, computer simulations and experimental verification were applied to investigate the characteristics of the initial biomineralization from the view of ion aggregation and nucleation. The results prove that P ions play a more important role in mineralization than Ca ions. The guanidyl group and surrounding carboxyl terminal groups are a potential excellent nucleation domain on proteins. The interval distribution of acidic/basic residues on protein is more conductive to the formation of large Ca and P ions clusters. The involvement of protein could increase the probability of hydroxyapatite phase precipitation, especially in the presence of a helical conformation. The detailed information on Ca and P ions behavior provided by the computer simulations is helpful for further understanding the mechanism of biomineralization, which will promote the development of bone repair materials to the biomimetic mineralized materials.

DNA translocation through pH-dependent soft nanopores

Controlling the translocation velocity of DNA is the main challenge in the process of sequencing by means of nanopores. One of the main methods to overcome this challenge is covering the inner walls of the nanopore with a layer of polyelectrolytes, i.e., using soft nanopores. In this paper the translocation of DNA through soft nanopores, whose inner polyelectrolyte layer (PEL) charge is pH-dependent, is theoretically studied. We considered the polyelectrolyte to be made up of either acidic or basic functional groups. It was observed that the electroosmotic flow (EOF) induced by the PEL charge is in the opposite/same direction of DNA electrophoresis (EPH) when the PEL is made up of acidic/basic groups. It was found that, not only the DNA charge and consequently the EPH, but also the EOF are influenced by the electrolyte acidity. The synergy between the changes in the retardation, EOF and EPH, determines how the intensity and direction of DNA translocation alter with pH. In fact, for both cases, at mild values of pH (as long as [Formula: see text] for the case that PEL is of acidic nature), the more the pH, the less the translocation velocity. However, for PELs of acidic nature, higher values of pH increase the intensity of the EOF so much that DNA may experience a change in the translocation direction. Ultimately, conducting the process at a particular range of pH values, and at higher pH values, in the cases of using PELs of acidic nature, and basic nature, respectively, was recommended.

Synthesis and Characterization of Polymer-Based Coatings Modified with Bioactive Ceramic and Bovine Serum Albumin

This study involves the synthesis of hydroxyapatite and describes the preparation and characterization of polymer coatings based on poly(ethylene glycol) diacrylate and poly(ethylene glycol) and modified with bovine serum albumin and hydroxyapatite. Hydroxyapatite was obtained by wet chemical synthesis and characterized by X-ray diffraction and FTIR spectroscopy, and its Ca/P molar ratio was determined (1.69 ± 0.08). The ceramic and bovine serum albumin were used in the preparation of composite materials with the polymeric matrix. The chemical composition of coatings was characterized with FTIR spectroscopy, and their morphology was recorded with SEM imaging. Moreover, the measurements of surface roughness parameters and stereometric research were performed. The prepared coatings were subjected to in vitro studies in simulated body fluid and artificial saliva. Changes in chemical composition and morphology after immersion were examined with FTIR spectroscopy and SEM imaging. Based on the conducted research, it can be stated that applied modifiers promote the biomineralization process. The roughness analysis confirmed prepared materials were characterized by the micrometer-scale topography. The materials morphology and roughness, and the morphology of the newly formed apatite deposit, were dependent on the type of the used modifier, and the artificial fluid used in in vitro studies.

DNA nanostructures as templates for biomineralization

Nature uses extracellular matrix scaffolds to organize biominerals into hierarchical structures over various length scales. This has inspired the design of biomimetic mineralization scaffolds, with DNA nanostructures being among the most promising. DNA nanotechnology makes use of molecular recognition to controllably give 1D, 2D and 3D nanostructures. The control we have over these structures makes them attractive templates for the synthesis of mineralized tissues, such as bones and teeth. In this Review, we first summarize recent work on the crystallization processes and structural features of biominerals on the nanoscale. We then describe self-assembled DNA nanostructures and come to the intersection of these two themes: recent applications of DNA templates in nanoscale biomineralization, a crucial process to regenerate mineralized tissues.

In vivo self-degradable graphene nanomedicine operated by DNAzyme and photo-switch for controlled anticancer therapy

Although graphene oxide (GO) possesses many beneficial functionalities for biomedical usage as itself, modification of GO surface with several polymers or protein is inevitable for in vivo applications; however, such modification limits the degradability of GO due to the steric hindrance. In that context, designing of a surface modified GO carrier that is going to be degraded after its biological function (i.e., drug delivery) is highly desired, especially at complex in vivo level. Herein, we design an unprecedented "catalytic GO nanomedicine" by applying the catalytic DNA, achieving self-degradation of GO in systemic level in the body after the therapy following surface modification. Once the catalytic GO nanomedicines are taken up by mucin1 (MUC1) aptamer-facilitated endocytosis, a photo-switch triggers the release of doxorubicin from the DNA. The single stranded G-quadruplex sequence on the surface of GO forms a quartet structure and becomes DNAzyme by binding with hemin on the GO surface, exhibiting peroxidase effect. Due to the high H₂O₂ concentration in cancer cells, the catalytic GO nanomedicine generates sufficient amount of strong oxidant, hypochlorous acid (HOCl), inducing GO degradation into small fragments for potential clearance. We demonstrate the potential of our catalytic GO nanomedicine for both therapy and degradation at cellular and complex in vivo environment.

Cellular Fragments as Biomaterial for Rapid In Vitro Bone-Like Tissue Synthesis

Current stem cell-based techniques for bone-like tissue synthesis require at least two to three weeks. Therefore, novel techniques to promote rapid 3D bone-like tissue synthesis in vitro are still required. In this study, we explored the concept of using cell nanofragments as a substrate material to promote rapid bone formation in vitro. The methods for cell nanofragment fabrication were ultrasonication (30 s and 3 min), non-ionic detergent (triton 0.1% and 1%), or freeze-dried powder. The results showed that ultrasonication for 3 min allowed the fabrication of homogeneous nanofragments of less than 150 nm in length, which mineralized surprisingly in just one day, faster than the fragments obtained from all other methods. Further optimization of culture conditions indicated that a concentration of 10 mM or 100 mM of β-glycerophosphate enhanced, whereas fetal bovine serum (FBS) inhibited in a concentration-dependent manner, the mineralization of the cell nanofragments. Finally, a 3D collagen-cell nanofragment-mineral complex mimicking a bone-like structure was generated in just two days by combining the cell nanofragments in collagen gel. In conclusion, sonication for three min could be applied as a novel method to fabricate cell nanofragments of less than 150 nm in length, which can be used as a material for in vitro bone tissue engineering.

Biominerals Formed by DNA and Calcium Oxalate or Hydroxyapatite: A Comparative Study

Biominerals formed by DNA and calcium oxalate (CaOx) or hydroxyapatite (HAp), the most important and stable phase of calcium phosphate) have been examined and compared using a synergistic combination of computer simulation and experimental studies. The interest of this comparison stems from the medical observation that HAp- and CaOx-based microcalcifications are frequently observed in breast cancer tissues, and some of their features are used as part of the diagnosis. Molecular dynamics simulations show that (1) the DNA double helix remains stable when it is adsorbed onto the most stable facet of HAp, whereas it undergoes significant structural distortions when it is adsorbed onto CaOx; (2) DNA acts as a template for the nucleation and growth of HAp but not for the mineralization of CaOx; and (3) the DNA double helix remains stable when it is encapsulated inside HAp nanopores, but it becomes destabilized when the encapsulation occurs into CaOx nanopores. Furthermore, CaOx and HAp minerals containing DNA molecules inside and/or adsorbed on the surface have been prepared in the lab by mixing solutions containing the corresponding ions with fish sperm DNA. Characterization of the formed minerals, which has been focused on the identification of DNA using UV-vis spectroscopy, indicates that the tendency to adsorb and, especially, encapsulate DNA is much smaller for CaOx than for HAp, which is in perfect agreement with results from molecular dynamics simulations. Finally, quantum mechanical calculations have been performed to rationalize these results in terms of molecular interactions, evidencing the high affinity of Ca²⁺ toward oxalate anions in an aqueous environment.

Biomolecule-assisted green synthesis of nanostructured calcium phosphates and their biomedical applications

Calcium phosphates (CaPs) are ubiquitous in nature and vertebrate bones and teeth, and have high biocompatibility and promising applications in various biomedical fields. Nanostructured calcium phosphates (NCaPs) are recognized as promising nanocarriers for drug/gene/protein delivery owing to their high specific surface area, pH-responsive degradability, high drug/gene/protein loading capacity and sustained release performance. In order to control the structure and surface properties of NCaPs, various biomolecules with high biocompatibility such as nucleic acids, proteins, peptides, liposomes and phosphorus-containing biomolecules are used in the synthesis of NCaPs. Moreover, biomolecules play important roles in the synthesis processes, resulting in the formation of various NCaPs with different sizes and morphologies. At room temperature, biomolecules can play the following roles: (1) acting as a biocompatible organic phase to form biomolecule/CaP hybrid nanostructured materials; (2) serving as a biotemplate for the biomimetic mineralization of NCaPs; (3) acting as a biocompatible modifier to coat the surface of NCaPs, preventing their aggregation and increasing their colloidal stability. Under heating conditions, biomolecules can (1) control the crystallization process of NCaPs by forming biomolecule/CaP nanocomposites before heating; (2) prevent the rapid and disordered growth of NCaPs by chelating with Ca2+ ions to form precursors; (3) provide the phosphorus source for the controlled synthesis of NCaPs by using phosphorus-containing biomolecules. This review focuses on the important roles of biomolecules in the synthesis of NCaPs, which are expected to guide the design and controlled synthesis of NCaPs. Moreover, we will also summarize the biomedical applications of NCaPs in nanomedicine and tissue engineering, and discuss their current research trends and future prospects.

Precipitation SELEX: identification of DNA aptamers for calcium phosphate materials synthesis

DNA aptamers that enhance calcium phosphate mineral formation were identified using a novel precipitation SELEX method. The evolved DNA library was substantially enriched in G nucleotides and in predicted G-quadruplex structures, suggesting their importance in the mechanism of mineralization. This work could readily be extended to provide additional novel DNA aptamers for materials synthesis.

A bio-inspired nacre-like layered hybrid structure of calcium carbonate under the control of carboxyl graphene

Schematic illustration of the fabrication of GO-COOH/CaCO₃ multilayer hybrid structures: GO-COOH, the GO-COOH/CaCl₂ multilayer hybrid structure, and the GO-COOH/CaCO₃ hybrid multilayer structure (from left to right).

An experimental-computer modeling study of inorganic phosphates surface adsorption on hydroxyapatite particles

The adsorption of different phosphates and a triphosphonate onto hydroxyapatite has been highlighted combining experiments and theoretical calculations.