Contemporary models of intrafibrillar mineralization mechanisms are established using collagen fibrils as templates without considering the contribution from collagen-bound apatite nucleation inhibitors. However, collagen matrices destined for mineralization in vertebrates contain bound matrix proteins for intrafibrillar mineralization. Negatively charged, high–molecular weight polycarboxylic acid is cross-linked to reconstituted collagen to create a model for examining the contribution of collagen-ligand interaction to intrafibrillar mineralization. Cryogenic electron microscopy and molecular dynamics simulation show that, after cross-linking to collagen, the bound polyelectrolyte caches prenucleation cluster singlets into chain-like aggregates along the fibrillar surface to increase the pool of mineralization precursors available for intrafibrillar mineralization. Higher-quality mineralized scaffolds with better biomechanical properties are achieved compared with mineralization of unmodified scaffolds in polyelectrolyte-stabilized mineralization solution. Collagen-ligand interaction provides insights on the genesis of heterogeneously mineralized tissues and the potential causes of ectopic calcification in nonmineralized body tissues.

The visionary idea that RNA adopts nonbiological roles in today's nanomaterial world has been nothing short of phenomenal. These RNA molecules have ample chemical functionality and self‐assemble to form distinct nanostructures in response to external stimuli. They may be combined with inorganic materials to produce nanomachines that carry cargo to a target site in a controlled manner and respond dynamically to environmental changes. Comparable to biological cells, programmed RNA nanomachines have the potential to replicate bone healing in vitro. Here, an RNA–biomineral nanomachine is developed, which accomplishes intrafibrillar and extrafibrillar mineralization of collagen scaffolds to mimic bone formation in vitro. Molecular dynamics simulation indicates that noncovalent hydrogen bonding provides the energy source that initiates self‐assembly of these nanomachines. Incorporation of the RNA–biomineral nanomachines into collagen scaffolds in vivo creates an osteoinductive microenvironment within a bone defect that is conducive to rapid biomineralization and osteogenesis. Addition of RNA‐degrading enzymes into RNA–biomineral nanomachines further creates a stop signal that inhibits unwarranted bone formation in tissues. The potential of RNA in building functional nanostructures has been underestimated in the past. The concept of RNA–biomineral nanomachines participating in physiological processes may transform the nanoscopic world of life science.

With continually increased computer power, molecular mechanics force field-based approaches, such as the endpoint methods of molecular mechanics Poisson−Boltzmann surface area (MM-PBSA) and molecular mechanics generalized Born surface area (MM-GBSA), have been routinely applied in both drug lead identification and optimization. However, the MM-PB/GBSA method is not as accurate as the pathway-based alchemical free energy methods, such as thermodynamic integration (TI) or free energy perturbation (FEP). Although the pathway-based methods are more rigorous in theory, they suffer from slow convergence and computational cost. Moreover, choosing adequate perturbation routes is also crucial for the pathway-based methods. Recently, we proposed a new method, coined extended linear interaction energy (ELIE) method, to overcome some disadvantages of the MM-PB/GBSA method to improve the accuracy of binding free energy calculation. In this work, we have systematically assessed this approach using in total 229 protein−ligand complexes for eight protein targets. Our results showed that ELIE performed much better than the molecular docking and MM-PBSA method in terms of root-mean-square error (RMSE), correlation coefficient (R), predictive index (PI), and Kendall's τ. The mean values of PI, R, and τ are 0.62, 0.58, and 0.44 for ELIE calculations. We also explored the impact of the length of simulation, ranging from 1 to 100 ns, on the performance of binding free energy calculation. In general, extending simulation length up to 25 ns could significantly improve the performance of ELIE, while longer molecular dynamics (MD) simulation does not always perform better than short MD simulation. Considering both the computational efficiency and achieved accuracy, ELIE is adequate in filling the gap between the efficient docking methods and computationally demanding alchemical free energy methods. Therefore, ELIE provides a practical solution for the routine ranking of compounds in lead optimization.

Although deoxyribonucleic acid (DNA) is the genetic coding for the very essence of life, these macromolecules or components thereof are not necessarily lost after a cell dies. There appears to be a link between extracellular DNA and biomineralization. Here the authors demonstrate that extracellular DNA functions as an initiator of collagen intrafibrillar mineralization. This is confirmed with in vitro and in vivo biological mineralization models. Because of their polyanionic property, extracellular DNA molecules are capable of stabilizing supersaturated calcium phosphate solution and mineralizing 2D and 3D collagen matrices completely as early as 24 h. The effectiveness of extracellular DNA in biomineralization of collagen is attributed to the relatively stable formation of amorphous liquid droplets triggered by attraction of DNA to the collagen fibrils via hydrogen bonding. These findings suggest that extracellular DNA is biomimetically significant for fabricating inorganic-organic hybrid materials for tissue engineering. DNA-induced collagen intrafibrillar mineralization provides a clue to the pathogenesis of ectopic mineralization in different body tissues. The use of DNase for targeting extracellular DNA at destined tissue sites provides a potential solution for treatment of diseases associated with ectopic mineralization.

To achieve the highly emissive features and overcome the troublesome photobleaching for fluorescent organic molecules, a facile and versatile strategy named “self-isolation enhanced emission (SIEE)” was developed to prevent the π–π stacking of organic fluorophores by linking alkyl chains on their conjugated backbones. As a proof-of-concept, one or two octyl groups were grafted onto the backbone of 4,7-di­(thiophen-2-yl)­benzo­[c]­[1,2,5]­thiadiazole (termed as DTBT-0), resulting in two different molecules, termed as DTBT-1 and DTBT-2, respectively. Compared with DTBT-0, DTBT-1 and DTBT-2 exhibited remarkably enhanced fluorescent properties in both aggregated thin films and nanoparticles, demonstrating that the SIEE method could isolate the fluorophores effectively and then prevent their π–π stacking to achieve the impressive fluorescent properties. After proper surface modification, excellent water dispersibility, biocompatibility, and improved resistance to photobleaching were also achieved for highly emissive DTBT-2-based nanoparticles, which were then successfully applied for cellular imaging.