Pau Turon

Modeling biominerals formed by apatites and DNA

Different aspects of biominerals formed by apatite and DNA have been investigated using computer modeling tools. Firstly, the structure and stability of biominerals in which DNA molecules are embedded into hydroxyapatite and fluoroapatite nanopores have been examined by combining different molecular mechanics methods. After this, the early processes in the nucleation of hydroxyapatite at a DNA template have been investigated using molecular dynamics simulations. Results indicate that duplexes of DNA adopting a B double helix can be encapsulated inside nanopores of hydroxyapatite without undergoing significant distortions in the inter-strand hydrogen bonds and the intra-strand stacking. This ability of hydroxyapatite is practically independent of the DNA sequence, which has been attributed to the stabilizing role of the interactions between the calcium atoms of the mineral and the phosphate groups of the biomolecule. In contrast, the fluorine atoms of fluoroapatite induce pronounced structural distortions in the double helix when embedded in a pore of the same dimensions, resulting in the loss of its most relevant characteristics. On the other hand, molecular dynamics simulations have allowed us to observe the formation of calcium phosphate clusters at the surface of the B-DNA template. Electrostatic interactions between the phosphate groups of DNA and Ca2+ have been found to essential for the formation of stable ion complexes, which were the starting point of calcium phosphate clusters by incorporating from the solution.

DNA adsorbed on hydroxyapatite surfaces

Hydroxyapatite (HAp) particles with very different surface charges and compositions (i.e. different Ca/P and CO3 2-/PO4 3- ratios) have been obtained by varying the experimental conditions used during the chemical precipitation process. The DNA adsorption capacity and protection imparted against the attack of nucleases of HAp particles have been proved to depend on the surface charge while the buffering capacity is affected by the chemical composition. On the basis of both the surface charge and the crystallinity, the predominant planes at the surfaces of HAp particles have been identified. Atomistic molecular dynamics simulations of surfaces constructed with these planes (i.e. (001) and the two terminations of (010)) with the adsorbed B-DNA double helix have been performed to get microscopic understanding of the influence of the mineral in the biomolecule structure and the interaction energies. The results indicate that the DNA secondary structure is perfectly preserved on the (001) surface, this stability being accompanied by an attractive binding energy. In contrast, the (010) surface with PO4 3-, OH- and Ca2+ ions in the termination induces significant local and global deformations in the double helix, repulsive OH-(HAp)PO4 3- (DNA) interactions provoking the desorption of the biomolecule. Finally, although the termination of the (010) surface with PO4 3- and Ca2+ ions also deforms the double helix, it forms very strong attractive interactions with the biomolecule. These binding characteristics are in excellent agreement with the DNA adsorption and protection abilities experimentally determined for the HAp samples. Finally, the surface charge has been found less decisive than the chemical composition in the efficacy of the transfection process.

Synergistic Approach to Elucidate the Incorporation of Magnesium Ions into Hydroxyapatite

Although the content of Mg(2+) in hard tissues is very low (typically ≤1.5 wt %), its incorporation into synthetic hydroxyapatite (HAp) particles and its role in the minerals properties are still subject of intensive debate. A combined experimental-computational approach is used to answer many of the open questions. Mg(2+) -enriched HAp particles are prepared using different synthetic approaches and considering different concentrations of Mg(2+) in the reaction medium. The composition, morphology and structure of the resulting particles are investigated using X-ray photoelectron spectroscopy, energy dispersive X-ray spectroscopy, scanning and transmission electron microscopies, FTIR, and wide-angle X-ray diffraction. After this scrutiny, the role of the Mg(2+) in the first nucleation stages, before HAp formation, is investigated using atomistic molecular dynamics simulations. Saturated solutions are simulated with and without the presence of DNA, which has been recently used as a soft template in the biomineralization process. This synergistic investigation provides a complete picture of how Mg(2+) ions affect the mineralization from the first stages onwards.

Dissolving Hydroxyolite: A DNA Molecule into Its Hydroxyapatite Mold

In spite of the clinical importance of hydroxyapatite (HAp), the mechanism that controls its dissolution in acidic environments remains unclear. Knowledge of such a process is highly desirable to provide better understanding of different pathologies, as for example osteoporosis, and of the HAp potential as vehicle for gene delivery to replace damaged DNA. In this work, the mechanism of dissolution in acid conditions of HAp nanoparticles encapsulating double-stranded DNA has been investigated at the atomistic level using computer simulations. For this purpose, four consecutive (multi-step) molecular dynamics simulations, involving different temperatures and proton transfer processes, have been carried out. Results are consistent with a polynuclear decalcification mechanism in which proton transfer processes, from the surface to the internal regions of the particle, play a crucial role. In addition, the DNA remains protected by the mineral mold and transferred proton from both temperature and chemicals. These results, which indicate that biomineralization imparts very effective protection to DNA, also have important implications in other biomedical fields, as for example in the design of artificial bones or in the fight against osteoporosis by promoting the fixation of Ca(2+) ions.

Study of Non-Isothermal Crystallization of Polydioxanone and Analysis of Morphological Changes Occurring during Heating and Cooling Processes

Non-isothermal crystallization kinetics of polydioxanone (PDO), a polymer with well-established applications as bioabsorbable monofilar suture, was investigated by Avrami, Mo, and isoconversional methodologies. Results showed Avrami exponents appearing in a relatively narrow range (i.e., between 3.76 and 2.77), which suggested a three-dimensional spherulitic growth and instantaneous nucleation at high cooling rates. The nucleation mechanism changed to sporadic at low rates, with both crystallization processes being detected in the differential scanning calorimetry (DSC) cooling traces. Formation of crystals was hindered as the material crystallized because of a decrease in the motion of molecular chains. Two secondary nucleation constants were derived from calorimetric data by applying the methodology proposed by Vyazovkin and Sbirrazzuoli through the estimation of effective activation energies. In fact, typical non-isothermal crystallization analysis based on the determination of crystal growth by optical microscopy allowed secondary nucleation constants of 3.07 × 105 K2 and 1.42 × 105 K2 to be estimated. Microstructure of sutures was characterized by a stacking of lamellae perpendicularly oriented to the fiber axis and the presence of interlamellar and interfibrillar amorphous regions. The latter became enhanced during heating treatments due to loss of partial chain orientation and decrease of electronic density. Degradation under various pH media revealed different macroscopic morphologies and even a distinct evolution of lamellar microstructure during subsequent heating treatments.

Restricted puckering of mineralized RNA-like riboses.

The pseudorotational motions of highly hydroxylated pentafuranose sugars in the free state and tethered to hydroxyapatite have been compared. The conformation pentafuranose ring remains restricted at the North region of the pseudorotational wheel, which is the one typically observed for nucleosides and nucleotides in the double helix A-RNA, when the phosphate-bearing sugar is anchored to the mineral surface. Results indicate that the severe restrictions imposed by the mineral are responsible of the double helix preservation when DNA and RNA are encapsulated in crystalline nanorods.

Surviving Mass Extinctions through Biomineralized DNA

Even in the worst of conditions, such as those which occurred during mass extinction events, life on Earth never totally stopped. Aggressive chemical and physical attacks able to sterilize or poison living organisms occurred repeatedly. Surprisingly, DNA was not degraded, denatured or modified to the point of losing the capability of transferring the genetic information to the next generations. After the events of mass extinction life was able to survive and thrive. DNA was passed on despite being an extremely fragile biomolecule. The potential implications of hydroxyapatite protection of DNA are discussed in this Concept article including how DNA acts as a template for hydroxyapatite (HAp) formation, how cell death can trigger biomineralization, and how DNA can be successfully released from HAp when the conditions are favorable for life.

Sustainable synthesis of amino acids by catalytic fixation of molecular dinitrogen and carbon dioxide

The industrial process of nitrogen fixation is complex and results in a huge economic and environmental impact. It requires a catalyst and high temperature and pressure to induce the rupture of the strong N–N bond and subsequent hydrogenation. On the other hand, carbon dioxide removal from the atmosphere has become a priority objective due to the high amount of global carbon dioxide emissions (i.e. 36 200 million tons in 2015). In this work, we fix nitrogen from N2 and carbon from CO2 and CH4 to obtain both glycine and alanine (D/L racemic mixture), the two simplest amino acids. The synthesis, catalyzed by polarized hydroxyapatite under UV light irradiation and conducted in an inert reaction chamber, starts from a simple gas mixture containing N2, CO2, CH4 and H2O and uses mild reaction conditions. At atmospheric pressure and 95 °C, the glycine and alanine molar yields with respect to CH4 or CO2 are about 1.9% and 1.6%, respectively, but they grow to 3.4% and 2.4%, when the pressure increases to 6 bar and the temperature is maintained at 95 °C. Besides, the minimum temperature required for the successful production of detectable amounts of amino acids is 75 °C. Accordingly, an artificial photosynthetic process has been developed by using an electrophotocatalyst based on hydroxyapatite thermally and electrically stimulated and coated with zirconyl chloride and a phosphonate. The synthesis of amino acids by direct fixation of nitrogen and carbon from gas mixtures opens new avenues regarding the nitrogen fixation for industrial purposes and the recycling of carbon dioxide.

Grafting of Hydroxyapatite for Biomedical Applications

Hydroxyapatite (HAp) is a bioceramic material that is the main inorganic component of hard and connective tissues (e.g., bones and teeth). Therefore efforts to develop novel biomaterials as bone substitute are currently based on HAp composites. A good interaction and adhesion between HAp and the selected polymeric matrix is required to achieve good mechanical properties. The affinity between these two phases can be improved by chemical reaction of coupling agents with the hydroxyl groups on the surface of HAp. The present review is focused to describe the main grafting processes and surface modifications carried out on HAp surfaces and the repercussions on biomineralization and osteogenesis processes.

Effects of hydroxyapatite (0001) Ca2+/Mg2+ substitution on adsorbed D-ribose ring puckering

Advanced Molecular Dynamics (MD) simulation protocols have been used to assess the ring puckering of cyclic D-ribose when the sugar is adsorbed on the most stable (0001) facet of calcium hydroxyapatite (HAp). In addition, sugar⋯mineral interactions, which are crucial for transfection processes and prebiotic chemistry, have been studied for systems in which the Ca2+ ions of the above mentioned HAp facet were totally or partially replaced by Mg2+. The latter replacement is spatially and quantitatively limited and has been found to cause important alterations in the conformational behavior of D-ribose that are similar to those suffered in hairpin RNA from A to B helical structures. Accordingly, replacement of Ca2+ by Mg2+ has a dramatic effect on the functionality of the nucleic acid. These changes have been related to both the substitution site on the surface and the amount of ions. Our results show that when replacement by Mg2+ occurs in OH−-coordinated Ca2+ ions, Mg2+⋯D-ribose interactions are strong enough to prevent the interactions between the hydroxyl groups of the sugar and the remaining Ca2+ ions.