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Through the NSF Future Manufacturing research program at Pasadena City College (PCC), students engaged in authentic research to explore aspects of DNA nanotechnology and gain experience in the research process. Emphasizing the scientific method and workforce development, students collaborated with our scientific community at UCLA, UCSB and Caltech as they learned how to use the tools of synthetic biology to build nanoscale bioreactors. Toward this goal, students set out to investigate various parameters to couple a DNAzyme-catalyzed redox reaction to DNA condensates with the aim of localizing the reaction. DNAzymes, guanine-rich sequences of DNA that fold into a G4 quadruplex structure, bind hemin, and catalyze a peroxidation reaction, were formed in vitro and used to catalyze a colorimetric redox reaction. Substrates ABTS (2,2’-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) and Amplifu Red were explored for their ability to ‘turn on’ or change color when oxidized by hydrogen peroxide in the presence of the peroxidase-like DNAzyme. In efforts to compartmentalize this reaction, the sequence for the G4 quadruplex was extended from one arm of a fluorescent 4-armed DNA nanostar, which contained either 15, 20, or 25 base pairs per arm and palindromic sticky ends. Upon annealing the DNA strands to form 4-armed DNA nanostars, with one of the strands containing the G4 sequence, the folded G4 quadruplex was tested for its ability to catalyze colorimetric peroxidation localized to DNA condensates. Students made important choices regarding the concentration of DNAzyme that would result in observable color change when localized to condensates; they carefully studied buffer compatibility between peroxidation and condensate formation; they tested two fluorogenic substrates in DNAzyme-catalyzed peroxidation, ABTS and Amplifu Red; and they meticulusly analyzed the results, using what they learned to inform future decisions. The results of these localization studies will be leveraged in the next steps of this research project aimed at building nanoscale bioreactors from DNA. This high-impact educational experience taught students about the iterative nature of science and the significance of exploring the literature. Through research, they learned the important higher-order skills of experimental design and effective scientific communication, facilitating their development as scientists. This synthetic biology research was translated into lessons and implemented in PCC courses and through outreach, which inspired the students taught in outreach and the PCC researchers who served as learning assistants in this equitable and accessible STEM education. 

Through the NSF Future Manufacturing undergraduate research program at Pasadena City College (PCC), students utilize the tools of synthetic biology to build sustainable, DNA-based materials. The manipulation of DNA enables the construction of microscopic biochemical reactors through the formation of liquid-liquid phase-separated droplets, or DNA condensates. This research investigates the potential of DNA nanostars fused with G-tetraplexes, which can bind hemin, an iron-containing porphyrin co-factor, to form a DNAzyme capable of catalyzing peroxidation reactions within single condensate layers. The in vitro component of this research was enhanced by in silico coarse-grained molecular dynamics simulations, which generated 3D models of the DNA nanostars that allowed student researchers to visualize the behavior of the structures created in the laboratory. Leveraging this computational technique, student researchers developed educational resources and modular lessons to introduce these molecular simulations to a broad student audience at PCC. The simulation programs used, oxDNA and oxView, were instrumental in making this research accessible and engaging for diverse student groups. DNA nanostar simulations were integrated into the General, Organic, and Biochemistry curriculum at PCC, as well as during outreach events such as Girls Science Day, offering students insights into DNA nanostar dynamics and potential applications of DNA-based inventions. This paper details the use of simulation programs to recreate nucleic acid-based nanostructures, advancing the field of DNA nanotechnology. Molecular simulations helped the PCC research students develop experiments that demonstrate how enzymatic activity within DNA droplets can be achieved through G4 complexing. Simulating DNA nanostars with G4s was a profound educational exercise for students, as it taught them about the powerful synergy between in silico and in vitro experimentation. Students also learned about the limitations of modeling biomolecules using computational software, and our G4 simulation results may even inspire the integration of guanine-guanine interactions into the oxDNA program. These findings underscore the significant implications of in silico modeling and structural analysis in biochemical manufacturing and industrial applications, paving the way for further innovations in programmable biomolecular systems. By developing YouTube tutorials that teach students how to carry out nucleic acid simulations on any standard computer, the exploration of DNA dynamics and molecular programming is now widely accessible to both students and educators. 

Protein-functionalized nanoparticles introduce a potentially novel drug delivery method for medical therapeutics, including involvement in cancer therapies and as contrast agents in imaging. Gold and silver nanoparticles are of particular interest due to their distinctive properties. Extensive research shows that gold nanoparticles demonstrate incredible photothermal properties and non-toxic behavior, while silver nanoparticles exhibit antibacterial properties but increase toxicity for human use. However, little is known regarding the properties or applications of hybrid silver-gold particles. This study measured the UV-Vis absorbance spectrum for 40 nm diameter Au, streptavidin-conjugated Au, Ag@Au hybrid, Ag nanoparticles, and Transient Absorbance Spectra of Au. Analysis indicates that the hybrid particles exhibit characteristics of both Ag and Au particles, implying potential applications similar to both Ag and Au nanoparticles.