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Goikoetxea G, Akhtar KTK, Prysiazhniuk A, Borsa BA, Aldag ME, Kavruk M, Ozalp VC, Hernandez FJ. Fluorescent and electrochemical detection of nuclease activity associated with Streptococcus pneumoniae using specific oligonucleotide probes. Analyst 2024; 149:1289-1296. [PMID: 38240377 DOI: 10.1039/d3an01532g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
Streptococcus pneumoniae (S. pneumoniae) represents a significant pathogenic threat, often responsible for community-acquired pneumonia with potentially life-threatening consequences if left untreated. This underscores the pressing clinical need for rapid and accurate detection of this harmful bacteria. In this study, we report the screening and discovery of a novel biomarker for S. pneumoniae detection. We used S. pneumoniae nucleases as biomarker and we have identified a specific oligonucleotide that works as substrate. This biomarker relies on a specific nuclease activity found on the bacterial membrane, forming the basis for the development of both fluorescence and electrochemical biosensors. We observed an exceptionally high sensitivity in the performance of the electrochemical biosensor, detecting as low as 102 CFU mL-1, whereas the fluorescence sensor demonstrated comparatively lower efficiency, with a detection limit of 106 CFU mL-1. Moreover, the specificity studies have demonstrated the biosensors' remarkable capacity to identify S. pneumoniae from other pathogenic bacteria. Significantly, both biosensors have demonstrated the ability to identify S. pneumoniae cultured from clinical samples, providing compelling evidence of the potential clinical utility of this innovative detection system.
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Affiliation(s)
- Garazi Goikoetxea
- Nucleic Acids Technologies Laboratory (NAT-Lab), Linköping University, 58185, Sweden.
- Department of Cellular Biology and Histology, Faculty of Medicine and Odontology, University of Basque Country (UPV/EHU), 48940, Spain
- SOMAprobes SL. Donostia, 20009, Spain
| | - Khadija-Tul Kubra Akhtar
- Nucleic Acids Technologies Laboratory (NAT-Lab), Linköping University, 58185, Sweden.
- Wallenberg Center for Molecular Medicine, Linköping University, 58185, Sweden
- Department of Physics, Chemistry and Biology, Linköping University, 58185, Sweden
| | - Alona Prysiazhniuk
- Nucleic Acids Technologies Laboratory (NAT-Lab), Linköping University, 58185, Sweden.
- Wallenberg Center for Molecular Medicine, Linköping University, 58185, Sweden
- Department of Physics, Chemistry and Biology, Linköping University, 58185, Sweden
- Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Baris A Borsa
- Nucleic Acids Technologies Laboratory (NAT-Lab), Linköping University, 58185, Sweden.
- Wallenberg Center for Molecular Medicine, Linköping University, 58185, Sweden
- Department of Physics, Chemistry and Biology, Linköping University, 58185, Sweden
| | | | - Murat Kavruk
- Department of Medical Biology, School of Medicine, Istanbul Aydin University, Istanbul, Turkey
| | - Veli C Ozalp
- Department of Medical Biology, Atilim University, 06830, Ankara, Turkey
| | - Frank J Hernandez
- Nucleic Acids Technologies Laboratory (NAT-Lab), Linköping University, 58185, Sweden.
- Wallenberg Center for Molecular Medicine, Linköping University, 58185, Sweden
- Department of Physics, Chemistry and Biology, Linköping University, 58185, Sweden
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Borsa BA, Hernandez LI, Jiménez T, Tellapragada C, Giske CG, Hernandez FJ. Therapeutic-oligonucleotides activated by nucleases (TOUCAN): A nanocarrier system for the specific delivery of clinical nucleoside analogues. J Control Release 2023; 361:260-269. [PMID: 37541593 DOI: 10.1016/j.jconrel.2023.07.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023]
Abstract
Nucleoside analogues have been in clinical use since 1960s and they are still used as the first therapeutic option for several cancers and viral infections, due to their high therapeutic efficacy. However, their wide clinical acceptance has been limited due to their high toxicity and severe side effects to patients. Herein, we report on a nanocarrier system that delivers nucleosides analogues in a target-specific manner, making nucleoside-based therapeutics safer and with the possibility to be used in other human conditions. This system, named, Therapeutic OligonUCleotides Activated by Nucleases" (TOUCAN) combines: i) the recognition power of oligonucleotides as substrates, ii) the use of nucleases as enzymatic biomarkers and iii) the clinical efficacy of nucleoside analogues, in a single approach. As a proof-of-concept, we report on a TOUCAN that is activated by a specific nuclease produced by bacteria and releases a therapeutic nucleoside, floxuridine. We demonstrate, for the first time, that, by incorporating a therapeutic nucleoside analogue into oligonucleotide probes, we can specifically inhibit bacterial growth in cultures. In this study, Staphylococcus aureus was selected as the targeted bacteria and the TOUCAN strategy successfully inhibited its growth with minimal inhibitory concentration (MIC) values ranging from 0.62 to 40 mg/L across all tested strains. Moreover, our results indicate that the intravenous administration of TOUCANs at a dose of 20 mg/kg over a 24-h period is a highly effective method for treating bacterial infections in a mouse model of pyomyositis. Importantly, no signs of toxicity were observed in our in vitro and in vivo studies. This work can significantly impact the current management of bacterial infections, laying the grounds for the development of a different class of antibiotics. Furthermore, it can provide a safer delivery platform for clinical nucleoside therapeutics in any human conditions, such as cancer and viral infection, where specific nuclease activity has been reported.
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Affiliation(s)
- Baris A Borsa
- Wallenberg Center for Molecular Medicine (WCMM), Linköping, Sweden; Department of Physics, Chemistry and Biology (IFM), Linköping University, Sweden; Nucleic Acid Technologies Laboratory (NAT-Lab), Linköping, Sweden
| | - Luiza I Hernandez
- Department of Clinical and Experimental Medicine (IKE), Linköping University, Sweden; SOMAprobes, Science and Technology Park of Gipuzkoa, Donostia-San Sebastian, Spain
| | - Tania Jiménez
- SOMAprobes, Science and Technology Park of Gipuzkoa, Donostia-San Sebastian, Spain
| | - Chaitanya Tellapragada
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Frank J Hernandez
- Wallenberg Center for Molecular Medicine (WCMM), Linköping, Sweden; Department of Physics, Chemistry and Biology (IFM), Linköping University, Sweden; Nucleic Acid Technologies Laboratory (NAT-Lab), Linköping, Sweden.
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Dursun AD, Borsa BA, Bayramoglu G, Arica MY, Ozalp VC. Surface plasmon resonance aptasensor for Brucella detection in milk. Talanta 2021; 239:123074. [PMID: 34809985 DOI: 10.1016/j.talanta.2021.123074] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/31/2021] [Accepted: 11/15/2021] [Indexed: 01/03/2023]
Abstract
A Surface Plasmon Resonance (SPR) aptasensor was developed for the detection of Brucella melitensis (B. melitensis) in milk samples. Brucellosis is a bacterial zoonotic disease with global distribution caused mostly by contaminated milk or their products. Aptamers recognizing B. melitensis were selected following a whole bacteria-SELEX procedure. Two aptamers were chosen for high affinity and high specificity. The high affinity aptamer (B70 aptamer) was immobilized on the surface of magnetic silica core-shell nanoparticles for initial purification of the target bacteria cells from milk matrix. Another aptamer, highly specific for B. melitensis cells (B46 aptamer), was used to prepare SPR sensor chips for sensitive determination of Brucella in eluted samples from magnetic purification since direct injection of milk samples to SPR sensor chips is known for a high background unspecific signal. Thus, we integrated a quick and efficient magnetic isolation step for subsequent instant detection of B. melitensis contamination in one ml of milk sample by SPR with a LOD value as low as 27 ± 11 cells.
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Affiliation(s)
- Ali D Dursun
- Department of Physiology, School of Medicine, Atilim University, 06830, Ankara, Turkey; Vocational School of Health Services, Atilim University, 06830, Ankara, Turkey
| | - Baris A Borsa
- Linköping University, Molecular Physics and Nanoscience (MOLYT), Nucleic Acids Technology Lab (Nat-Lab), Linköping, Sweden
| | - Gulay Bayramoglu
- Biochemical Processing and Biomaterial Research Laboratory, Gazi University, 06500, Teknikokullar, Ankara, Turkey; Department of Chemistry, Faculty of Sciences, Gazi University, 06500, Teknikokullar, Ankara, Turkey
| | - M Yakup Arica
- Biochemical Processing and Biomaterial Research Laboratory, Gazi University, 06500, Teknikokullar, Ankara, Turkey
| | - Veli C Ozalp
- Department of Biology, Medical School, Atilim University, 06830, Ankara, Turkey.
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Borsa BA, Sudagidan M, Aldag ME, Baris II, Acar EE, Acuner C, Kavruk M, Ozalp VC. Antibiotic administration in targeted nanoparticles protects the faecal microbiota of mice. RSC Med Chem 2021; 12:380-383. [PMID: 34046621 PMCID: PMC8130601 DOI: 10.1039/d0md00347f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/13/2020] [Indexed: 12/17/2022] Open
Abstract
Antibiotic therapy comes with disturbances on human microbiota, resulting in changes of bacterial communities and thus leading to well-established health problems. In this study, we demonstrated that targeted teicoplanin administration maintains the faecal microbiota composition undisturbed in a mouse model while reaching therapeutic improvements for S. aureus infection.
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Affiliation(s)
- Baris A Borsa
- Nucleic Acid Technologies Lab, Department of Physics, Chemistry and Biology (IFM), Linköping University SE-58183 Linköping Sweden
| | - Mert Sudagidan
- Kit-Argem Research Centre, Konya Food and Agriculture University Meram 42080 Konya Turkey
| | - Mehmet E Aldag
- Department of Medical Microbiology, Corlu State Hospital Tekirdag Turkey
| | - Isik I Baris
- Department of Pathology, Cakmak Erdem Hospital Istanbul Turkey
| | - Elif E Acar
- Kit-Argem Research Centre, Konya Food and Agriculture University Meram 42080 Konya Turkey
| | - Cagatay Acuner
- Department of Medical Microbiology, Medical School, Yeditepe University Istanbul Turkey
| | - Murat Kavruk
- Test and Calibration Center, Turkish Standards Institution (TSE) 41400, Gebze Kocaeli Turkey
| | - Veli C Ozalp
- Department of Medical Biology, Medical School, Atilim University Incek 06830 Ankara Turkey
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Ucak S, Sudagidan M, Borsa BA, Mansuroglu B, Ozalp VC. Inhibitory effects of aptamer targeted teicoplanin encapsulated PLGA nanoparticles for Staphylococcus aureus strains. World J Microbiol Biotechnol 2020; 36:69. [PMID: 32333113 DOI: 10.1007/s11274-020-02845-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/17/2020] [Indexed: 12/13/2022]
Abstract
Emergence of resistance to traditional antibiotic treatments necessitates alternative delivery systems. Teicoplanin is a glycopeptide antibiotic used in the treatments of serious infections caused by Gram-positive bacteria, including Methicillin Resistant Staphylococcus aureus (MRSA). One strategy to keep up with antibiotic resistance development is to limit dose and amount during treatments. Targeted delivery systems of antibiotics have been suggested as a mechanism to slow-down the evolution of resistance and to increase efficiency of the antimicrobials on already resistant pathogens. In this study, we report teicoplanin delivery nanoparticles of Poly Lactic-co-Glycolic Acid (PLGA), which are functionalized with S. aureus specific aptamers. A 32-fold decrease in minimum inhibitory concentration (MIC) values of teicoplanin for S. aureus was demonstrated for susceptible strains and about 64-fold decline in MIC value was achieved for moderately resistant clinical isolates of MRSA upon teicoplanin treatment with aptamer-PLGA nanoparticles. Although teicoplanin delivery in PLGA nanoparticles without targeting demonstrated eightfold decrease in MIC of susceptible strains of S. aureus and S. epidermidis and twofold in MIC of resistant strains, the aptamer targeting specifically decreased MIC for S. aureus, but not for S. epidermidis. Therefore, aptamer-targeted PLGA delivery of antibiotic can be an attractive alternative to combat with some of the multi-drug resistant bacterial pathogens.
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Affiliation(s)
- Samet Ucak
- Department of Molecular Biology and Genetics, Yildiz Technical University, Istanbul, Turkey.,School of Medicine, Altinbas University, Istanbul, Turkey
| | - Mert Sudagidan
- Kit-Argem Research Center, Konya Food and Agriculture University, 42080, Konya, Turkey
| | - Baris A Borsa
- Department of Chemistry, Physics and Biology (IFM), Linköping University, Linköping, Sweden
| | - Banu Mansuroglu
- Department of Molecular Biology and Genetics, Yildiz Technical University, Istanbul, Turkey
| | - Veli C Ozalp
- Medical School, Department of Medical Biology, Atilim University, 06830, Ankara, Turkey.
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Balian A, Garcia Gonzalez J, Bastida N, Akhtar KTK, Borsa BA, Hernandez FJ. Kinetic Screening of Nuclease Activity using Nucleic Acid Probes. J Vis Exp 2019. [PMID: 31736483 DOI: 10.3791/60005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Nucleases are a class of enzymes that break down nucleic acids by catalyzing the hydrolysis of the phosphodiester bonds that link the ribose sugars. Nucleases display a variety of vital physiological roles in prokaryotic and eukaryotic organisms, ranging from maintaining genome stability to providing protection against pathogens. Altered nuclease activity has been associated with several pathological conditions including bacterial infections and cancer. To this end, nuclease activity has shown great potential to be exploited as a specific biomarker. However, a robust and reproducible screening method based on this activity remains highly desirable. Herein, we introduce a method that enables screening for nuclease activity using nucleic acid probes as substrates, with the scope of differentiating between pathological and healthy conditions. This method offers the possibility of designing new probe libraries, with increasing specificity, in an iterative manner. Thus, multiple rounds of screening are necessary to refine the probes' design with enhanced features, taking advantage of the availability of chemically modified nucleic acids. The considerable potential of the proposed technology lies in its flexibility, high reproducibility, and versatility for the screening of nuclease activity associated with disease conditions. It is expected that this technology will allow the development of promising diagnostic tools with a great potential in the clinic.
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Affiliation(s)
- Alien Balian
- Department of Physics, Chemistry and Biology, Linköping University; Wallenberg Centre for Molecular Medicine (WCMM); Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University
| | - Javier Garcia Gonzalez
- Department of Physics, Chemistry and Biology, Linköping University; Wallenberg Centre for Molecular Medicine (WCMM); Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University
| | - Nora Bastida
- Department of Physics, Chemistry and Biology, Linköping University; Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University
| | - Khadija-Tul Kubra Akhtar
- Department of Physics, Chemistry and Biology, Linköping University; Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University
| | - Baris A Borsa
- Department of Physics, Chemistry and Biology, Linköping University; Wallenberg Centre for Molecular Medicine (WCMM); Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University
| | - Frank J Hernandez
- Department of Physics, Chemistry and Biology, Linköping University; Wallenberg Centre for Molecular Medicine (WCMM); Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University;
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Borsa BA, Tuna BG, Hernandez FJ, Hernandez LI, Bayramoglu G, Arica MY, Ozalp VC. Staphylococcus aureus detection in blood samples by silica nanoparticle-oligonucleotides conjugates. Biosens Bioelectron 2016; 86:27-32. [DOI: 10.1016/j.bios.2016.06.023] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/27/2016] [Accepted: 06/09/2016] [Indexed: 01/01/2023]
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Kavruk M, Celikbicak O, Ozalp VC, Borsa BA, Hernandez FJ, Bayramoglu G, Salih B, Arica MY. Antibiotic loaded nanocapsules functionalized with aptamer gates for targeted destruction of pathogens. Chem Commun (Camb) 2016; 51:8492-5. [PMID: 25891472 DOI: 10.1039/c5cc01869b] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this study, we designed aptamer-gated nanocapsules for the specific targeting of cargo to bacteria with controlled release of antibiotics based on aptamer-receptor interactions. Aptamer-gates caused a specific decrease in minimum inhibitory concentration (MIC) values of vancomycin for Staphylococcus aureus when mesoporous silica nanoparticles (MSNs) were used for bacteria-targeted delivery.
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Affiliation(s)
- M Kavruk
- Department of Biotechnology, Middle East Technical University, Turkey
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Hernandez FJ, Hernandez LI, Kavruk M, Arıca YM, Bayramoğlu G, Borsa BA, Öktem HA, Schäfer T, Özalp VC. NanoKeepers: stimuli responsive nanocapsules for programmed specific targeting and drug delivery. Chem Commun (Camb) 2015; 50:9489-92. [PMID: 25008577 DOI: 10.1039/c4cc04248d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bacterial resistance is a high priority clinical issue worldwide. Thus, an effective system that rapidly provides specific treatment for bacterial infections using controlled dose release remains an unmet clinical need. Herein, we report on the NanoKeepers approach for the specific targeting of S. aureus with controlled release of antibiotics based on nuclease activity.
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Affiliation(s)
- Frank J Hernandez
- POLYMAT, University of Basque Country UPV/EHU, Avda. Tolosa 72, 20018 Donostia-San Sebastián, Spain.
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Ozgun G, Borsa BA. A rare but diagnostic fungal microorganism in cervical Pap smears. INDIAN J PATHOL MICR 2013; 55:606-7. [PMID: 23455828 DOI: 10.4103/0377-4929.107854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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