Colorimetric Aptasensor for Detecting Bacillus carboniphilus Using Aptamer Isolated with a Non-SELEX-Based Method
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains and Culture
2.2. Isolation of Bacillus carboniphilus-Specific Aptamers Using a Centrifugation-Based Partitioning Method
2.3. Affinity Test and Specificity Test
2.4. Colorimetric Aptasensor Detection of B. carboniphilus
2.5. Detection of the Target in Bacterial Mixture and Biofilm
3. Results and Discussion
3.1. Selection and Characterization of Bacillus carboniphilus-Specific Aptamer
3.2. Optimization of a Colorimetric Aptasensor for Detecting B. carboniphilus
3.3. The Performance of a Two-Stage Label-Free Aptasensor for Detecting B. carbonihpilus
3.4. Specific Detection of B. carboniphilus in Bacterial Mixture and Biofilm
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Fujita, T.; Shida, O.; Takagi, H.; Kunugita, K.; Pankrushina, A.N.; Matsuhashi, M. Description of Bacillus carboniphilus sp. nov. Int. J. Syst. Bacteriol. 1996, 46, 116–118. [Google Scholar] [CrossRef] [Green Version]
- Al-Mailem, D.M.; Kansour, M.K.; Radwan, S.S. Moderately thermophilic, hydrocarbonoclastic bacterial communities in Kuwaiti desert soil: Enhanced activity via Ca2+ and dipicolinic acid amendment. Extremophiles 2015, 19, 573–583. [Google Scholar] [CrossRef] [PubMed]
- Rahul, K.; Moamongba, K.S.; Rabha, M.; Sivaprasad, V. Identification and characterization of bacteria causing flacherie in mulberry silkworm, Bombyx mori L. J. Crop Weed 2019, 15, 178–181. [Google Scholar] [CrossRef]
- Rajasekar, A.; Ponmariappan, S.; Maruthamuthu, S.; Palaniswamy, N. Bacterial Degradation and Corrosion of Naphtha in Transporting Pipeline. Curr. Microbiol. 2007, 55, 374–381. [Google Scholar] [CrossRef]
- Rajasekar, A.; Anandkumar, B.; Maruthamuthu, S.; Ting, Y.-P.; Rahman, P.K.S.M. Characterization of corrosive bacterial consortia isolated from petroleum-product-transporting pipelines. Appl. Microbiol. Biotechnol. 2010, 85, 1175–1188. [Google Scholar] [CrossRef] [PubMed]
- Kannan, P.; Kotu, S.P.; Pasman, H.; Vaddiraju, S.; Jayaraman, A.; Mannan, M.S. A systems-based approach for modeling of microbiologically influenced corrosion implemented using static and dynamic Bayesian networks. J. Loss Prev. Process Ind. 2020, 65, 104108. [Google Scholar] [CrossRef]
- Ahmed, A.; Rushworth, J.V.; Hirst, N.A.; Millner, P.A. Biosensors for Whole-Cell Bacterial Detection. Clin. Microbiol. Rev. 2014, 27, 631–646. [Google Scholar] [CrossRef] [Green Version]
- Templier, V.; Roux, A.; Roupioz, Y.; Livache, T. Ligands for label-free detection of whole bacteria on biosensors: A review. TrAC Trends Anal. Chem. 2016, 79, 71–79. [Google Scholar] [CrossRef]
- Altintas, Z.; Akgun, M.; Kokturk, G.; Uludag, Y. A fully automated microfluidic-based electrochemical sensor for real-time bacteria detection. Biosens. Bioelectron. 2018, 100, 541–548. [Google Scholar] [CrossRef]
- Otto, M. Bacterial Sensing of Antimicrobial Peptides. Bact. Sens. Signal. 2009, 136–149. [Google Scholar] [CrossRef] [Green Version]
- Mahlapuu, M.; Björn, C.; Ekblom, J. Antimicrobial peptides as therapeutic agents: Opportunities and challenges. Crit. Rev. Biotechnol. 2020, 40, 978–992. [Google Scholar] [CrossRef] [PubMed]
- Chen, C.H.; Lu, T.K. Development and Challenges of Antimicrobial Peptides for Therapeutic Applications. Antibiotics 2020, 9, 24. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Yasir, M.; Willcox, M.D.P.; Dutta, D. Action of Antimicrobial Peptides against Bacterial Biofilms. Materials 2018, 11, 2468. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Pardoux, E.; Boturyn, D.; Roupioz, Y. Antimicrobial Peptides as Probes in Biosensors Detecting Whole Bacteria: A Review. Molecules 2020, 25, 1998. [Google Scholar] [CrossRef] [PubMed]
- Hoyos-Nogués, M.; Gil, F.J.; Mas-Moruno, C. Antimicrobial Peptides: Powerful Biorecognition Elements to Detect Bacteria in Biosensing Technologies. Molecules 2018, 23, 1683. [Google Scholar] [CrossRef] [Green Version]
- Pardoux, É.; Roux, A.; Mathey, R.; Boturyn, D.; Roupioz, Y. Antimicrobial peptide arrays for wide spectrum sensing of pathogenic bacteria. Talanta 2019, 203, 322–327. [Google Scholar] [CrossRef]
- Kim, H.-S.; Kim, Y.-J.; Chon, J.-W.; Kim, D.-H.; Yim, J.-H.; Kim, H.; Seo, K.-H. Two-stage label-free aptasensing platform for rapid detection of Cronobacter sakazakii in powdered infant formula. Sens. Actuators B Chem. 2017, 239, 94–99. [Google Scholar] [CrossRef]
- Wang, T.; Chen, C.; Larcher, L.M.; Barrero, R.A.; Veedu, R.N. Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development. Biotechnol. Adv. 2019, 37, 28–50. [Google Scholar] [CrossRef] [PubMed]
- Li, H.; Rothberg, L. Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles. Proc. Natl. Acad. Sci. USA 2004, 101, 14036–14039. [Google Scholar] [CrossRef] [Green Version]
- Zhang, Y.; Lai, B.S.; Juhas, M. Recent Advances in Aptamer Discovery and Applications. Molecules 2019, 24, 941. [Google Scholar] [CrossRef] [Green Version]
- Zhou, J.; Rossi, J. Aptamers as targeted therapeutics: Current potential and challenges. Nat. Rev. Drug Discov. 2017, 16, 181–202. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Tuerk, C.; Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249, 505–510. [Google Scholar] [CrossRef] [PubMed]
- Davydova, A.; Vorobjeva, M.; Pyshnyi, D.; Altman, S.; Vlassov, V.; Venyaminova, A. Aptamers against pathogenic microorganisms. Crit. Rev. Microbiol. 2016, 42, 847–865. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Sola, M.; Menon, A.P.; Moreno, B.; Meraviglia-Crivelli, D.; Soldevilla, M.M.; Cartón-García, F.; Pastor, F. Aptamers Against Live Targets: Is In Vivo SELEX Finally Coming to the Edge? Mol. Ther. Nucleic Acids 2020, 21, 192–204. [Google Scholar] [CrossRef]
- Ohuchi, S. Cell-SELEX Technology. Biores. Open Access 2012, 1, 265–272. [Google Scholar] [CrossRef]
- Quang, N.N.; Miodek, A.; Cibiel, A.; Ducongé, F. Selection of Aptamers Against Whole Living Cells: From Cell-SELEX to Identification of Biomarkers; Springer: New York, NY, USA, 2017; pp. 253–272. [Google Scholar] [CrossRef]
- Kim, H.R.; Song, M.Y.; Chan Kim, B. Rapid isolation of bacteria-specific aptamers with a non-SELEX-based method. Anal. Biochem. 2020, 591, 113542. [Google Scholar] [CrossRef]
- Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31, 3406–3415. [Google Scholar] [CrossRef]
- Huang, J.; Liu, S.; Zhang, C.; Wang, X.; Pu, J.; Ba, F.; Xue, S.; Ye, H.; Zhao, T.; Li, K.; et al. Programmable and printable Bacillus subtilis biofilms as engineered living materials. Nat. Chem. Biol. 2019, 15, 34–41. [Google Scholar] [CrossRef]
- Merritt, J.H.; Kadouri, D.E.; O’Toole, G.A. Growing and Analyzing Static Biofilms. Curr. Protoc. Microbiol. 2005. [Google Scholar] [CrossRef] [Green Version]
- Hasegawa, H.; Savory, N.; Abe, K.; Ikebukuro, K. Methods for Improving Aptamer Binding Affinity. Molecules 2016, 21, 421. [Google Scholar] [CrossRef]
- Ghisolfi-Nieto, L.; Joseph, G.; Puvion-Dutilleul, F.; Amalric, F.; Bouvet, P. Nucleolin is a Sequence-specific RNA-binding Protein: Characterization of Targets on Pre-ribosomal RNA. J. Mol. Biol. 1996, 260, 34–53. [Google Scholar] [CrossRef]
- Pajerski, W.; Ochonska, D.; Brzychczy-Wloch, M.; Indyka, P.; Jarosz, M.; Golda-Cepa, M.; Sojka, Z.; Kotarba, A. Attachment efficiency of gold nanoparticles by Gram-positive and Gram-negative bacterial strains governed by surface charges. J. Nanopart. Res. 2019, 21. [Google Scholar] [CrossRef] [Green Version]
- Park, J.-W.; Shumaker-Parry, J.S. Structural Study of Citrate Layers on Gold Nanoparticles: Role of Intermolecular Interactions in Stabilizing Nanoparticles. J. Am. Chem. Soc. 2014, 136, 1907–1921. [Google Scholar] [CrossRef] [PubMed]
- Pamies, R.; Cifre, J.G.H.; Espín, V.F.; Collado-González, M.; Baños, F.G.D.; De La Torre, J.G. Aggregation behaviour of gold nanoparticles in saline aqueous media. J. Nanopart. Res. 2014, 16. [Google Scholar] [CrossRef]
- Kim, Y.J.; Kim, H.S.; Chon, J.W.; Kim, D.H.; Hyeon, J.Y.; Seo, K.H. New colorimetric aptasensor for rapid on-site detection of Campylobacter jejuni and Campylobacter coli in chicken carcass samples. Anal. Chim. Acta 2018, 1029, 78–85. [Google Scholar] [CrossRef] [PubMed]
- Kannan, P.; Su, S.S.; Mannan, M.S.; Castaneda, H.; Vaddiraju, S. A Review of Characterization and Quantification Tools for Microbiologically Influenced Corrosion in the Oil and Gas Industry: Current and Future Trends. Ind. Eng. Chem. Res. 2018, 57, 13895–13922. [Google Scholar] [CrossRef]
- Skovhus, T.L.; Eckert, R.B.; Rodrigues, E. Management and control of microbiologically influenced corrosion (MIC) in the oil and gas industry—Overview and a North Sea case study. J. Biotechnol. 2017, 256, 31–45. [Google Scholar] [CrossRef]
- Little, B.J.; Blackwood, D.J.; Hinks, J.; Lauro, F.M.; Marsili, E.; Okamoto, A.; Rice, S.A.; Wade, S.A.; Flemming, H.C. Microbially influenced corrosion—Any progress? Corros. Sci. 2020, 170, 108641. [Google Scholar] [CrossRef]
Aptamer | Sequences of Random Region |
---|---|
BCA-05 | CGG ACG GCT CTC GGG TTC TGC GGG TGT AAC CGA GAA ATA TCT ACG |
BCA-14 | TGA TTT GGT TCC ACT GTT GCG GAG GGG TCT TAC TGC TAG TGG TTT |
BCA-23 | TTG TCG CAT CAA TTT TTT TTT CAT CTG GTA GGC TCG CGA TTT C |
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Kim, H.-K.; Kim, H.-R.; Yoon, S.-J.; Lee, K.-B.; Kim, J.; Kim, B.-C. Colorimetric Aptasensor for Detecting Bacillus carboniphilus Using Aptamer Isolated with a Non-SELEX-Based Method. Chemosensors 2021, 9, 121. https://doi.org/10.3390/chemosensors9060121
Kim H-K, Kim H-R, Yoon S-J, Lee K-B, Kim J, Kim B-C. Colorimetric Aptasensor for Detecting Bacillus carboniphilus Using Aptamer Isolated with a Non-SELEX-Based Method. Chemosensors. 2021; 9(6):121. https://doi.org/10.3390/chemosensors9060121
Chicago/Turabian StyleKim, Ho-Kyeong, Hye-Ri Kim, Su-Jin Yoon, Kang-Bong Lee, Jungbae Kim, and Byoung-Chan Kim. 2021. "Colorimetric Aptasensor for Detecting Bacillus carboniphilus Using Aptamer Isolated with a Non-SELEX-Based Method" Chemosensors 9, no. 6: 121. https://doi.org/10.3390/chemosensors9060121