Development of a simple coarse-grained DNA model for analysis of oligonucleotide complex formation

<p>In this paper, we develop a coarse-grained nucleotide model for the purpose of simulating large-scale aptamer-based hydrogel network formation in future research. In the model, each nucleotide is represented by a single interaction site containing sugar, phosphate and base. Discontinuous molecular dynamics (DMD) simulations are performed to simulate formation and denaturation of oligonucleotide duplexes as a function of temperature. The simulated melting temperatures of oligonucleotide duplexes are calculated in simulations of systems with different sequences, lengths and concentrations of oligonucleotides, and compared to data from the OligoAnalyzer tool. The denaturation of oligonucleotide triplexes containing a hybridised structure of three different oligonucleotides is analysed using both simulations and experiments. The nucleotide model is found to be a good predictor of the oligonucleotide’s hybridised state for both duplexes and triplexes. This coarse-grained model has wide ranging applications in the development or optimisation of DNA-based technologies including DNA origami, DNA-enabled hydrogels and DNA-based biosensors.</p

<i>In Vitro</i> Biosynthesis of Metal Nanoparticles in Microdroplets

We report the use of a hydrogel polymer, recombinant <i>Escherichia coli</i> cell extracts, and a microdroplet-based microfluidic device to fabricate artificial cellular bioreactors which act as reactors to synthesize diverse metal nanoparticles (NPs). The combination of cell extracts, microdroplet-based microfluidic device, and hydrogel was able to produce a mass amount of artificial cellular bioreactors with uniform size and shape. For the first time, we report the alternating generation of microdroplets through one orifice for the fabrication of the artificial cellular reactors using the cell extract as inner cellular components and hydrogel as an artificial cellular membrane. Notably, the hydrogels were able to protect the encapsulated cell extracts from the surrounding environment and maintain the functionality of cellular component for the further cellular bioreactor applications. Furthermore, the successful applications of the fabricated artificial cellular bioreactors to synthesize various NPs including quantum dots, iron, and gold was demonstrated. By employing this microfluidic technique, the artificial cellular bioreactors could be applicable for the synthesis of diverse metal NPs through simple dipping of the reactors to the metal precursor solutions. Thus, the different size of NPs can be synthesized through controlling the concentration of metal precursors. This artificial cellular bioreactors offer promising abilities to biofriendly ways to synthesis diverse NPs and can be applicable in chemical, biomedical, and bioengineering applications

<i>In Vitro</i> Biosynthesis of Metal Nanoparticles in Microdroplets

We report the use of a hydrogel polymer, recombinant <i>Escherichia coli</i> cell extracts, and a microdroplet-based microfluidic device to fabricate artificial cellular bioreactors which act as reactors to synthesize diverse metal nanoparticles (NPs). The combination of cell extracts, microdroplet-based microfluidic device, and hydrogel was able to produce a mass amount of artificial cellular bioreactors with uniform size and shape. For the first time, we report the alternating generation of microdroplets through one orifice for the fabrication of the artificial cellular reactors using the cell extract as inner cellular components and hydrogel as an artificial cellular membrane. Notably, the hydrogels were able to protect the encapsulated cell extracts from the surrounding environment and maintain the functionality of cellular component for the further cellular bioreactor applications. Furthermore, the successful applications of the fabricated artificial cellular bioreactors to synthesize various NPs including quantum dots, iron, and gold was demonstrated. By employing this microfluidic technique, the artificial cellular bioreactors could be applicable for the synthesis of diverse metal NPs through simple dipping of the reactors to the metal precursor solutions. Thus, the different size of NPs can be synthesized through controlling the concentration of metal precursors. This artificial cellular bioreactors offer promising abilities to biofriendly ways to synthesis diverse NPs and can be applicable in chemical, biomedical, and bioengineering applications