DEVISING AN EFFECTIVE SILVER ION-CAPTURING SCAFFOLD WITH A CBD-SA LINKER-ENHANCED APTAMER: A SYNTHETIC BIOLOGY APPROACH

Supplementary Files

PDF

Keywords

Metal Ion Recycling
Bacterial Cellulose Nanofiber
Biotin-based Aptamer
Cellulose Binding Domain
Streptavidin

How to Cite

Zhou, H., Che, H., Yao, G., Fan, J., Xu, Z., & Fan, H. (2025). DEVISING AN EFFECTIVE SILVER ION-CAPTURING SCAFFOLD WITH A CBD-SA LINKER-ENHANCED APTAMER: A SYNTHETIC BIOLOGY APPROACH. Journal of Engineering & Technological Advances , 10(1), 17 - 35. https://doi.org/10.35934/segi.v10i1.126

Abstract

Recycling is an important approach to preserving the world’s valuable resources for the good and longevity of the planet, as well as to continue to live the way that humans are accustomed to. In this study, a silver ion capture and reusable platform was successfully assembled via a synthetic biology method to recycle metal ions in wastewater. Three modules exist in this platform: (1) a bacterial cellulose nanofiber block (BCNF), which is a structural module; (2) a fusion protein cellulose-binding domain (CBD) and streptavidin (SA)-based linker (CBD-SA-CBD); and (3) a biotin aptamer for metal ion capture blocks. The cellulose BCNF block showed the optimal glucose concentrations for cultivating the bacterial cellulose block. The optimal conditions were identified to induce proteins for the construction of the CBD-SA-CBD linker block. In general, the linker block binds effectively to the metal ion-capturing aptamer, and Aptamers 3 and 4 bind most effectively with silver ions. The reusability of this metal ion-catching aptamer maintained 99.16 to 99.56% binding affinity after four repeated tests. The calculated silver binding efficiency (BE) of the complete assembly remained as high as 99.95%. This consistent binding affinity is a valuable asset in environmental applications. Owing to the diversity of aptamers and versatility of fusion proteins, this genetic engineering design has great potential for diverse future applications, such as heavy metals, antibiotics, pheromones, and even nuclear waste treatment and removal.

https://doi.org/10.35934/segi.v10i1.126

References

Ayan, E., Yuksel, B., Destan, E., Ertem, F. B., Yildirim, G., Eren, M., Yefanov, O. M., Barty, A., Tolstikova, A., & Ketawala, G. K. (2022). Cooperative allostery and structural dynamics of streptavidin at cryogenic-and ambient-temperature. Communications biology, 5(1), 73. https://doi.org/10.1038/s42003-021-02903-7

Barbosa, M., Simões, H., & Prazeres, D. M. F. (2021). Functionalization of cellulose-based hydrogels with bi-functional fusion proteins containing carbohydrate-binding modules. Materials, 14(12), 3175. https://doi.org/10.3390/ma14123175

Barnard, E., & Timson, D. J. (2010). Split-EGFP Screens for the Detection and Localisation of Protein–Protein Interactions in Living Yeast Cells. Molecular and Cell Biology Methods for Fungi, 303-317. https://doi.org/10.1007/978-1-60761-611-5_23

Bartels, J., Lo?pez Castellanos, S. n., Radeck, J., & Mascher, T. (2018). Sporobeads: The utilization of the Bacillus subtilis endospore crust as a protein display platform. ACS synthetic biology, 7(2), 452-461. https://doi.org/10.1021/acssynbio.7b00285

Bhargava, A., Pareek, V., Roy Choudhury, S., Panwar, J., & Karmakar, S. (2018). Superior bactericidal efficacy of fucose-functionalized silver nanoparticles against Pseudomonas aeruginosa PAO1 and prevention of its colonization on urinary catheters. ACS applied materials & interfaces, 10(35), 29325-29337. https://doi.org/10.1021/acsami.8b09475

Blaha, U., Basavaiah, N., Deenadayalan, K., Borole, D., & Mohite, R. (2011). Onset of industrial pollution recorded in Mumbai mudflat sediments, using integrated magnetic, chemical, 210Pb dating, and microscopic methods. Environmental science & technology, 45(2), 686-692. https://doi.org/10.1021/es1025905

Cai, S., Yan, J., Xiong, H., Liu, Y., Peng, D., & Liu, Z. (2018). Investigations on the interface of nucleic acid aptamers and binding targets. Analyst, 143(22), 5317-5338. https://doi.org/10.1039/C8AN01467A

Cantwell, F. F., Nielsen, J. S., & Hrudey, S. E. (1982). Free nickel ion concentration in sewage by an ion exchange column-equilibration method. Analytical Chemistry, 54(9), 1498-1503. https://doi.org/10.1021/ac00246a012

Christianson, A. M., & Waters, C. A. (2021). Silver chloride waste recycling as a guided-inquiry experiment for the instrumental analysis laboratory. Journal of Chemical Education, 99(2), 1014-1020. https://doi.org/10.1021/acs.jchemed.1c00871

Fu, F., & Wang, Q. (2011). Removal of heavy metal ions from wastewaters: A review. Journal of Environmental Management, 92(3), 407-418. https://doi.org/https://doi.org/10.1016/j.jenvman.2010.11.011

Golovlev, V., Lee, S., Allman, S., Taranenko, N., Isola, N., & Chen, C. (2001). Nonresonant MALDI of oligonucleotides: Mechanism of ion desorption. Analytical Chemistry, 73(4), 809-812. https://doi.org/10.1021/ac001006

Hamad, A., Giswantara, G., Pusapawiningtyas, E., Pamungkas, R. B., & Mulyadi, A. H. (2023). Optimization Of process parameters for microbial cellulose production from rice-washing wastewater (NATA-DE-LERI) By Acetobacter Xylinum. Techno (Jurnal Fakultas Teknik, Universitas Muhammadiyah Purwokerto), 24(1), 51-58. https://doi.org/10.30595/techno.v24i1.16988

He, X., Qing, Z., Wang, K., Zou, Z., Shi, H., & Huang, J. (2012). Engineering a unimolecular multifunctional DNA probe for analysis of Hg 2+ and Ag+. Analytical Methods, 4(2), 345-347. https://doi.org/10.1039/C2AY05823E

Hileman, B. (1999). EU, US clash over environmental policies-Conflicts over climate change, biotech crops, and beef hormones are leading to difficult negotiations, trade wars. In (Vol. 77, pp. 21-26): AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA.

Janc, T., Korb, J.-P., Luksic, M., Vlachy, V., Bryant, R. G., Mériguet, G., Malikova, N., & Rollet, A.-L. (2021). Multiscale water dynamics on protein surfaces: protein-specific response to surface ions. The Journal of Physical Chemistry B, 125(31), 8673-8681. https://doi.org/10.1021/acs.jpcb.1c02513

Jung, J. K., Alam, K. K., Verosloff, M. S., Capdevila, D. A., Desmau, M., Clauer, P. R., Lee, J. W., Nguyen, P. Q., Pastén, P. A., & Matiasek, S. J. (2020). Cell-free biosensors for rapid detection of water contaminants. Nature biotechnology, 38(12), 1451-1459. https://doi.org/10.1038/s41587-020-0571-7

Li, Q., Ma, Q., Wu, Y., Li, Y., Li, B., Luo, X., & Liu, S. (2020). Oleogel films through the Pickering effect of bacterial cellulose nanofibrils featuring interfacial network stabilization. Journal of Agricultural and Food Chemistry, 68(34), 9150-9157. https://doi.org/10.1021/acs.jafc.0c03214

Lin, Y., Zhou, Q., Tang, D., Niessner, R., Yang, H., & Knopp, D. (2016). Silver nanolabels-assisted ion-exchange reaction with CdTe quantum dots mediated exciton trapping for signal-on photoelectrochemical immunoassay of mycotoxins. Analytical Chemistry, 88(15), 7858-7866. https://doi.org/10.1021/acs.analchem.6b02124

Lin, Z., Li, X., & Kraatz, H.-B. (2011). Impedimetric immobilized DNA-based sensor for simultaneous detection of Pb2+, Ag+, and Hg2+. Analytical Chemistry, 83(17), 6896-6901. https://doi.org/10.1021/ac2014096

Liu, Z., Lin, D., Shen, R., & Yang, X. (2021). Bacterial cellulose nanofibers improved the emulsifying capacity of soy protein isolate as a stabilizer for pickering high internal-phase emulsions. Food Hydrocolloids, 112, 106279. https://doi.org/10.1016/j.foodhyd.2020.106279

Matlock, M. M., Howerton, B. S., & Atwood, D. A. (2002). Chemical precipitation of lead from lead battery recycling plant wastewater. Industrial & engineering chemistry research, 41(6), 1579-1582. https://doi.org/10.1021/ie010800y

Ng, E. W., Shima, D. T., Calias, P., Cunningham Jr, E. T., Guyer, D. R., & Adamis, A. P. (2006). Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nature reviews drug discovery, 5(2), 123-132. https://doi.org/10.1038/nrd1955

Saran, R., Yao, L., Hoang, P., & Liu, J. (2018). Folding of the silver aptamer in a DNAzyme probed by 2-aminopurine fluorescence. Biochimie, 145, 145-150. https://doi.org/10.1016/j.biochi.2017.07.001

Shen, F., Mao, S., Mathivanan, J., Wu, Y., Chandrasekaran, A. R., Liu, H., Gan, J., & Sheng, J. (2020). Short DNA oligonucleotide as a Ag+ binding detector. ACS omega, 5(44), 28565-28570. https://doi.org/10.1021/acsomega.0c03372

Xie, Y., Yang, M., Zhu, L., Yue, X., Zhai, B., & Xu, W. (2023). Research progress of DNA aptamer-based silver ions detection. Advanced Agrochem, 2(3), 231-235. https://doi.org/10.1016/j.aac.2023.06.006

Yan, N., He, X., Tang, B. Z., & Wang, W.-X. (2019). Differentiating silver nanoparticles and ions in medaka larvae by coupling two aggregation-induced emission fluorophores. Environmental science & technology, 53(10), 5895-5905. https://doi.org/10.1021/acs.est.9b01156

Yan, N., Tsim, S. M. J., He, X., Tang, B. Z., & Wang, W.-X. (2020). Direct visualization and quantification of maternal transfer of silver nanoparticles in zooplankton. Environmental science & technology, 54(17), 10763-10771. https://doi.org/10.1021/acs.est.0c03228

Zhang, H.-L., Lv, C., Li, Z.-H., Jiang, S., Cai, D., Liu, S.-S., Wang, T., & Zhang, K.-H. (2023). Analysis of aptamer-target binding and molecular mechanisms by thermofluorimetric analysis and molecular dynamics simulation. Frontiers in Chemistry, 11, 1144347. https://doi.org/10.3389/fchem.2023.1144347

Zhang, L., Jiang, H., & Wang, W.-X. (2020). Subcellular imaging of localization and transformation of silver nanoparticles in the oyster larvae. Environmental science & technology, 54(18), 11434-11442. https://doi.org/10.1021/acs.est.0c03342

Zhang, L., & Wang, W.-X. (2018). Dominant role of silver ions in silver nanoparticle toxicity to a unicellular alga: evidence from luminogen imaging. Environmental science & technology, 53(1), 494-502. https://doi.org/10.1021/acs.est.8b04918

Zhen, H., Wu, X., Hu, J., Xiao, Y., Yang, M., Hirotsuji, J., Nishikawa, J.-i., Nakanishi, T., & Ike, M. (2009). Identification of retinoic acid receptor agonists in sewage treatment plants. Environmental science & technology, 43(17), 6611-6616. https://doi.org/10.1021/es9000328

Zhou, X., Memon, A. G., Sun, W., Fang, F., & Guo, J. (2020). Fluorescent probe for Ag+ detection using SYBR GREEN I and CC mismatch. Biosensors, 11(1), 6. https://doi.org/10.3390/bios11010006

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Copyright (c) 2025 Array