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Zheng H, Munusamy S, Arora P, Jahani R, Guan X. A highly sensitive nanopore platform for measuring RNase A activity. Talanta 2024; 276:126276. [PMID: 38796995 PMCID: PMC11187776 DOI: 10.1016/j.talanta.2024.126276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/11/2024] [Accepted: 05/16/2024] [Indexed: 05/29/2024]
Abstract
Ribonuclease A (RNase A) plays significant roles in several physiological and pathological conditions and can be used as a valuable diagnostic biomarker for human diseases such as myocardial infarction and cancer. Hence, it is of great importance to develop a rapid and cost-effective method for the highly sensitive detection of RNase A. The significance of RNase A assay is further enhanced by the growing attention from the biotechnology and pharmaceutical industries to develop RNA-based vaccines and drugs in large part as a result of the successful development of mRNA vaccines in the COVID-19 pandemic. Herein, we report a label-free method for the detection of RNase A by monitoring its proteolytic cleavage of an RNA substrate in a nanopore. The method is ultra-sensitive with the limit of detection reaching as low as 30 fg per milliliter. Furthermore, sensor selectivity and the effects of temperature, incubation time, metal ion, salt concentration on sensor sensitivity were also investigated.
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Affiliation(s)
- Haiyan Zheng
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
| | | | - Pearl Arora
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Rana Jahani
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
| | - Xiyun Guan
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
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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] [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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Ali AA, Al-Othman A, Al-Sayah MH. Multifunctional stimuli-responsive hybrid nanogels for cancer therapy: Current status and challenges. J Control Release 2022; 351:476-503. [PMID: 36170926 DOI: 10.1016/j.jconrel.2022.09.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/18/2022]
Abstract
With cancer research shifting focus to achieving multifunctionality in cancer treatment strategies, hybrid nanogels are making a rapid rise to the spotlight as novel, multifunctional, stimuli-responsive, and biocompatible cancer therapeutic strategies. They can possess cancer cell-specific cytotoxic effects themselves, carry drugs or enzymes that can produce cytotoxic effects, improve imaging modalities, and target tumor cells over normal cells. Hybrid nanogels bring together a wide range of desirable properties for cancer treatment such as stimuli-responsiveness, efficient loading and protection of molecules such as drugs or enzymes, and effective crossing of cellular barriers among other properties. Despite their promising abilities, hybrid nanogels are still far from being used in the clinic, and their available data remains relatively limited. However, many studies can be done to facilitate this clinical transition. This review is critically summarizing and analyzing the recent information and progress on the use of hybrid nanogels particularly inorganic nanoparticle-based and organic nanoparticle-based hybrid nanogels in the field of oncology and future directions to aid in transferring those results to the clinic. This work concludes that the future of hybrid nanogels is greatly impacted by therapeutic and non-therapeutic factors. Therapeutic factors include the lack of hemocompatibility studies, acute and chronic toxicological studies, and information on agglomeration capability and extent, tumor heterogeneity, interaction with proteins in physiological fluids, endocytosis-exocytosis, and toxicity of the nanogels' breakdown products. Non-therapeutic factors include the lack of clear regulatory guidelines and standardized assays, limitations of animal models, and difficulties associated with good manufacture practices (GMP).
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Affiliation(s)
- Amaal Abdulraqeb Ali
- Biomedical Engineering Graduate Program, American University of Sharjah, Sharjah, P.O. Box 26666, United Arab Emirates
| | - Amani Al-Othman
- Department of Chemical Engineering, American University of Sharjah, Sharjah, P.O. Box 26666, United Arab Emirates.
| | - Mohammad H Al-Sayah
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, Sharjah, P.O. Box 26666, United Arab Emirates
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Balian A, Hernandez FJ. Nucleases as molecular targets for cancer diagnosis. Biomark Res 2021; 9:86. [PMID: 34809722 PMCID: PMC8607607 DOI: 10.1186/s40364-021-00342-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/03/2021] [Indexed: 11/17/2022] Open
Abstract
Early cancer diagnosis is a crucial element to improved treatment options and survival. Great research efforts have been made in the search for better performing cancer diagnostic biomarkers. However, the quest continues as novel biomarkers with high accuracy for an early diagnosis remain an unmet clinical need. Nucleases, which are enzymes capable of cleaving nucleic acids, have been long considered as potential cancer biomarkers. The implications of nucleases are key for biological functions, their presence in different cellular counterparts and catalytic activity led the enthusiasm towards investigating the role of nucleases as promising cancer biomarkers. However, the most essential feature of these proteins, which is their enzymatic activity, has not been fully exploited. This review discusses nucleases interrogated as cancer biomarkers, providing a glimpse of their physiological roles. Moreover, it highlights the potential of harnessing the enzymatic activity of cancer-associated nucleases as a novel diagnostic biomarker using nucleic acid probes as substrates.
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Affiliation(s)
- Alien Balian
- Department of Physics, Chemistry and Biology, Linköping University, 58185, Linköping, Sweden
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
| | - Frank J Hernandez
- Department of Physics, Chemistry and Biology, Linköping University, 58185, Linköping, Sweden.
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden.
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Machado I, Goikoetxea G, Alday E, Jiménez T, Arias-Moreno X, Hernandez FJ, Hernandez LI. Ultra-Sensitive and Specific Detection of S. aureus Bacterial Cultures Using an Oligonucleotide Probe Integrated in a Lateral Flow-Based Device. Diagnostics (Basel) 2021; 11:diagnostics11112022. [PMID: 34829369 PMCID: PMC8619029 DOI: 10.3390/diagnostics11112022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/25/2022] Open
Abstract
The identification of pathogens causing infectious diseases is still based on laborious and time-consuming techniques. Therefore, there is an urgent need for the development of novel methods and devices that can considerably reduce detection times, allowing the health professionals to administer the right treatment at the right time. Lateral flow-based systems provide fast, cheap and easy to use alternatives for diagnosis. Herein, we report on a lateral flow approach for specifically detecting S. aureus bacteria within 6 h.
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Affiliation(s)
- Isabel Machado
- SOMAprobes S.L., Mikeletegi Pasealekua, 83, 20009 Donostia, Spain; (I.M.); (G.G.); (E.A.); (T.J.); (X.A.-M.)
| | - Garazi Goikoetxea
- SOMAprobes S.L., Mikeletegi Pasealekua, 83, 20009 Donostia, Spain; (I.M.); (G.G.); (E.A.); (T.J.); (X.A.-M.)
- Department of Cellular Biology and Histology, Faculty of Medicine and Odontology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Enara Alday
- SOMAprobes S.L., Mikeletegi Pasealekua, 83, 20009 Donostia, Spain; (I.M.); (G.G.); (E.A.); (T.J.); (X.A.-M.)
| | - Tania Jiménez
- SOMAprobes S.L., Mikeletegi Pasealekua, 83, 20009 Donostia, Spain; (I.M.); (G.G.); (E.A.); (T.J.); (X.A.-M.)
| | - Xabier Arias-Moreno
- SOMAprobes S.L., Mikeletegi Pasealekua, 83, 20009 Donostia, Spain; (I.M.); (G.G.); (E.A.); (T.J.); (X.A.-M.)
| | - Frank J. Hernandez
- Department of Physics, Chemistry and Biology, Linköping University, 58185 Linköping, Sweden;
- Wallenberg Centre for Molecular Medicine, Linköping University, 58185 Linköping, Sweden
| | - Luiza I. Hernandez
- SOMAprobes S.L., Mikeletegi Pasealekua, 83, 20009 Donostia, Spain; (I.M.); (G.G.); (E.A.); (T.J.); (X.A.-M.)
- Correspondence:
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Jiménez T, Botero J, Otaegui D, Calvo J, Hernandez FJ, San Sebastian E. Rational Design and Experimental Analysis of Short-Oligonucleotide Substrate Specificity for Targeting Bacterial Nucleases. J Med Chem 2021; 64:12855-12864. [PMID: 34460263 PMCID: PMC8436206 DOI: 10.1021/acs.jmedchem.1c00884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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An undecamer oligonucleotide probe
based on a pair of deoxythymidines
flanked by several modified nucleotides is a specific and highly efficient
biosensor for micrococcal nuclease (MNase), an endonuclease produced
by Staphylococcus aureus. Herein, the
interaction mode and cleavage process on such oligonucleotide probes
are identified and described for the first time. Also, we designed
truncated pentamer probes as the minimum-length substrates required
for specific and efficient biosensing. By means of computational (virtual
docking) and experimental (ultra-performance liquid chromatography–mass
spectrometry and matrix-assisted laser desorption ionization time-of-flight)
techniques, we perform a sequence/structure–activity relationship
analysis, propose a catalytically active substrate–enzyme complex,
and elucidate a novel two-step phosphodiester bond hydrolysis mechanism,
identifying the cleavage sites and detecting and quantifying the resulting
probe fragments. Our results unravel a picture of both the enzyme–biosensor
complex and a two-step cleavage/biosensing mechanism, key to the rational
oligonucleotide design process.
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Affiliation(s)
- Tania Jiménez
- Somaprobes S.L, Mikeletegi Pasealekua, 83, 20009 Donostia, Gipuzkoa, Spain
| | - Juliana Botero
- Somaprobes S.L, Mikeletegi Pasealekua, 83, 20009 Donostia, Gipuzkoa, Spain.,Applied Chemistry Department, University of the Basque Country (UPV/EHU), 20018 San Sebastián, Spain
| | - Dorleta Otaegui
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), San Sebastian 20014, Spain
| | - Javier Calvo
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), San Sebastian 20014, Spain
| | - Frank J Hernandez
- Wallenberg Center for Molecular Medicine (WCMM), 58185 Linköping, Sweden.,Department of Physics, Chemistry and Biology, Linköping University, 58185 Linköping, Sweden
| | - Eider San Sebastian
- Applied Chemistry Department, University of the Basque Country (UPV/EHU), 20018 San Sebastián, Spain
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