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Chen K, Zhu L, Li J, Zhang Y, Yu Y, Wang X, Wei W, Huang K, Xu W. High-content tailoring strategy to improve the multifunctionality of functional nucleic acids. Biosens Bioelectron 2024; 261:116494. [PMID: 38901394 DOI: 10.1016/j.bios.2024.116494] [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: 05/08/2024] [Revised: 05/30/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
Functional nucleic acids (FNAs) have attracted increasing attention in recent years due to their diverse physiological functions. The understanding of their conformational recognition mechanisms has advanced through nucleic acid tailoring strategies and sequence optimization. With the development of the FNA tailoring techniques, they have become a methodological guide for nucleic acid repurposing. Therefore, it is necessary to systematize the relationship between FNA tailoring strategies and the development of nucleic acid multifunctionality. This review systematically categorizes eight types of FNA multifunctionality, and introduces the traditional FNA tailoring strategy from five aspects, including deletion, substitution, splitting, fusion and elongation. Based on the current state of FNA modification, a new generation of FNA tailoring strategy, called the high-content tailoring strategy, was unprecedentedly proposed to improve FNA multifunctionality. In addition, the multiple applications of rational tailoring-driven FNA performance enhancement in various fields were comprehensively summarized. The limitations and potential of FNA tailoring and repurposing in the future are also explored in this review. In summary, this review introduces a novel tailoring theory, systematically summarizes eight FNA performance enhancements, and provides a systematic overview of tailoring applications across all categories of FNAs. The high-content tailoring strategy is expected to expand the application scenarios of FNAs in biosensing, biomedicine and materials science, thus promoting the synergistic development of various fields.
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Affiliation(s)
- Keren Chen
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jie Li
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yangzi Zhang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Yongxia Yu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Xiaofu Wang
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Wei Wei
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kunlun Huang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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2
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Lim J, Son SU, Ki J, Kim S, Lee J, Jang S, Seo SB, Jang H, Kang T, Jung J, Kim E, Lim EK. Dual structure-switching aptamer-mediated signal amplification cascade for SARS-CoV-2 detection. Biosens Bioelectron 2024; 259:116375. [PMID: 38749283 DOI: 10.1016/j.bios.2024.116375] [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: 03/06/2024] [Revised: 04/29/2024] [Accepted: 05/08/2024] [Indexed: 06/03/2024]
Abstract
Since the outbreak of the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) at the end of 2019, the spread of the virus has posed a significant threat to public health and the global economy. This work proposed a one-step, dual-structure-switching aptamer-mediated signal amplification cascade for rapid and sensitive detection of the SARS-CoV-2 nucleocapsid protein. This system consisted of two DNA aptamers with structure-switching functionality and fuel DNA, where a cascade of strand hybridization and displacement triggered fluorescence generation and signal amplification. This aptamer-based amplification cascade required neither an amplification stage using enzymes nor pre-processing steps such as washing, viral isolation, and gene extraction. The assay could distinguish SARS-CoV-2 from other respiratory viruses and detect up to 1.0 PFU/assay of SARS-CoV-2 within 30 min at room temperature. In 35 nasopharyngeal clinical samples, the assay accurately assessed 25 positive and 10 negative clinical swab samples, which were confirmed using quantitative polymerase chain reaction. The strategy reported herein can help detect newly emerging pathogens and biomarkers of various diseases in liquid samples. In addition, the developed detection system consisting of only DNA and fluorophores can be widely integrated into liquid biopsy platforms for disease diagnosis.
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Affiliation(s)
- Jaewoo Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Medical Device Development Center, Osong Medical Innovation Foundation, 123 Osongsaengmyeong-ro, Chungcheongbuk-do, 28160, Republic of Korea
| | - Seong Uk Son
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology 125 Gwahak-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Jisun Ki
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sunjoo Kim
- Department of Laboratory Medicine, Gyeongsang National University Changwon Hospital, Changwon, 51472, Republic of Korea
| | - Jina Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology 125 Gwahak-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Soojin Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology 125 Gwahak-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Seung Beom Seo
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Juyeon Jung
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology 125 Gwahak-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Eunjung Kim
- Department of Bioengineering & Nano-bioengineering, Research Center for Bio Materials and Process Development, Incheon National University, Incheon, 22012, Republic of Korea; Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea.
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology 125 Gwahak-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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3
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Gabrusenok PV, Ramazanov RR, Kasyanenko NA, Lantushenko AO, Sokolov PA. pH-dependent binding of ATP aptamer to the target and competition strands: Fluorescent melting curve fitting study. Biochim Biophys Acta Gen Subj 2024; 1868:130689. [PMID: 39134247 DOI: 10.1016/j.bbagen.2024.130689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/02/2024] [Accepted: 08/05/2024] [Indexed: 08/18/2024]
Abstract
The pH varies in different tissues and organelles and also changes during some diseases. In this regard, the application of molecular switches that use a competition-based aptamer switch design in biological systems requires studying the thermodynamics of such systems at different pH values. In this work, we studied the binding of the classical ATP aptamer to ATP and competition strands under different pH and ionic conditions using fluorescent melting curve analysis. We have developed an original approach to processing source data from a PCR thermal cycler. It is based on constructing a thermodynamic model of the melting profile and the subsequent fit of experimental curves within this model. We have shown that this approach enables us to narrow the temperature region under study to the width of the melting region without a significant loss in the quality of the result. This impressively expands the application area of this approach compared to frequently used techniques that require mandatory measurement of the signal outside the melting region. The results obtained by the method showed that the thermodynamic parameters of the ATP aptamer and its duplexes with competition strands change depending on pH. Therefore, molecular switches that use a competition strand to the ATP aptamer may have a pH-dependent sensitivity that has not been previously considered. This should be taken into account for future rational design of similar systems.
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Affiliation(s)
- P V Gabrusenok
- St. Petersburg University, 13B Universitetskaya Emb., St. Petersburg, 199034, Russia
| | - R R Ramazanov
- St. Petersburg University, 13B Universitetskaya Emb., St. Petersburg, 199034, Russia
| | - N A Kasyanenko
- St. Petersburg University, 13B Universitetskaya Emb., St. Petersburg, 199034, Russia
| | - A O Lantushenko
- Sevastopol State University, 33 Universitetskaya Street, Sevastopol, 299053, Russia
| | - P A Sokolov
- St. Petersburg University, 13B Universitetskaya Emb., St. Petersburg, 199034, Russia.
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4
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Ye C, Lukas H, Wang M, Lee Y, Gao W. Nucleic acid-based wearable and implantable electrochemical sensors. Chem Soc Rev 2024; 53:7960-7982. [PMID: 38985007 PMCID: PMC11308452 DOI: 10.1039/d4cs00001c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
The rapid advancements in nucleic acid-based electrochemical sensors for implantable and wearable applications have marked a significant leap forward in the domain of personal healthcare over the last decade. This technology promises to revolutionize personalized healthcare by facilitating the early diagnosis of diseases, monitoring of disease progression, and tailoring of individual treatment plans. This review navigates through the latest developments in this field, focusing on the strategies for nucleic acid sensing that enable real-time and continuous biomarker analysis directly in various biofluids, such as blood, interstitial fluid, sweat, and saliva. The review delves into various nucleic acid sensing strategies, emphasizing the innovative designs of biorecognition elements and signal transduction mechanisms that enable implantable and wearable applications. Special perspective is given to enhance nucleic acid-based sensor selectivity and sensitivity, which are crucial for the accurate detection of low-level biomarkers. The integration of such sensors into implantable and wearable platforms, including microneedle arrays and flexible electronic systems, actualizes their use in on-body devices for health monitoring. We also tackle the technical challenges encountered in the development of these sensors, such as ensuring long-term stability, managing the complexity of biofluid dynamics, and fulfilling the need for real-time, continuous, and reagentless detection. In conclusion, the review highlights the importance of these sensors in the future of medical engineering, offering insights into design considerations and future research directions to overcome existing limitations and fully realize the potential of nucleic acid-based electrochemical sensors for healthcare applications.
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Affiliation(s)
- Cui Ye
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA.
| | - Heather Lukas
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA.
| | - Minqiang Wang
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA.
| | - Yerim Lee
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA.
| | - Wei Gao
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA.
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5
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Pei S, Babity S, Sara Cordeiro A, Brambilla D. Integrating microneedles and sensing strategies for diagnostic and monitoring applications: The state of the art. Adv Drug Deliv Rev 2024; 210:115341. [PMID: 38797317 DOI: 10.1016/j.addr.2024.115341] [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: 02/17/2024] [Revised: 04/23/2024] [Accepted: 05/18/2024] [Indexed: 05/29/2024]
Abstract
Microneedles (MNs) offer minimally-invasive access to interstitial fluid (ISF) - a potent alternative to blood in terms of monitoring physiological analytes. This property is particularly advantageous for the painless detection and monitoring of drugs and biomolecules. However, the complexity of the skin environment, coupled with the inherent nature of the analytes being detected and the inherent physical properties of MNs, pose challenges when conducting physiological monitoring using this fluid. In this review, we discuss different sensing mechanisms and highlight advancements in monitoring different targets, with a particular focus on drug monitoring. We further list the current challenges facing the field and conclude by discussing aspects of MN design which serve to enhance their performance when monitoring different classes of analytes.
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Affiliation(s)
- Shihao Pei
- Faculté de pharmacie, Université de Montréal, 2940 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada
| | - Samuel Babity
- Faculté de pharmacie, Université de Montréal, 2940 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada
| | - Ana Sara Cordeiro
- Leicester Institute for Pharmaceutical Innovation, Leicester School of Pharmacy, De Montfort University, Leicester LE1 9BH, United Kingdom.
| | - Davide Brambilla
- Faculté de pharmacie, Université de Montréal, 2940 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada.
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6
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Kim J, Yoo H, Woo S, Oh SS. Aptasensor-encapsulating semi-permeable proteinosomes for direct target detection in non-treated biofluids. Biosens Bioelectron 2024; 251:116062. [PMID: 38350238 DOI: 10.1016/j.bios.2024.116062] [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: 10/30/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/15/2024]
Abstract
Detecting biomarkers in biofluids directly without sample treatments makes molecular diagnostics faster and more efficient. Aptasensors, the nucleic acid-based molecular biosensors, can detect a wide range of target molecules, but their susceptibility to degradation and aggregation by nucleases and charged proteins, respectively, limits their direct use in clinical samples. In this work, we demonstrate that when aptasensors are encapsulated in proteinosomes, the protein-based liposome mimics, clinically important small molecules can be sensitively and selectively detected in non-treated specimens, such as 100 % unpurified serum. As serum albumin is used to form the membrane, the nanomeshed proteinosomes become semi-permeable and antifouling, which enables exclusive admission of small molecules while blocking unwanted large proteins. Consequently, the enclosed aptasensors can maintain close-to-optimal performance for target binding, and nucleolytic degradation and electrostatic aggregation are effectively suppressed. Three different structure-switching aptamers specific for estradiol, dopamine, and cocaine, respectively, are demonstrated to fully conserve their high affinities and specificities inside the microcapsules. The shielding effect of proteinosomes is indeed exceptional; the enclosed DNA aptasensors remain completely intact over 18 h in serum and even in an extremely concentrated DNase solution (1 mg/ml, ∼300,000× the serum level). Moreover, the proteinosome-mediated compartmentalization enables independent operation of multiple aptasensors in the same mixture. Hence, simultaneous real-time sensing of two different targets is demonstrated with different operation modes, 'recording' target appearance and 'reporting' target concentration changes. This work is the first demonstration of small-molecule-specific aptasensors operating with optimal performance in serum environments and will find promising applications in molecular diagnostics.
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Affiliation(s)
- Jinmin Kim
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, South Korea
| | - Hyebin Yoo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, South Korea
| | - Sungwook Woo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, South Korea.
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, South Korea; Institute for Convergence Research and Education in Advanced Technology (I-CREATE), Yonsei University, Incheon, 21983, South Korea.
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7
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Patoine K, Ta K, Gilbert A, Percuoco M, Gerdon AE. Equilibrium interactions of biomimetic DNA aptamers produce intrafibrillar calcium phosphate mineralization of collagen. Acta Biomater 2024; 179:234-242. [PMID: 38554888 DOI: 10.1016/j.actbio.2024.03.018] [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: 11/10/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/02/2024]
Abstract
Native and biomimetic DNA structures have been demonstrated to impact materials synthesis under a variety of conditions but have only just begun to be explored in this role compared to other biopolymers such as peptides, proteins, polysaccharides, and glycopolymers. One selected DNA aptamer has been explored in calcium phosphate and calcium carbonate mineralization, demonstrating sequence-dependent control of kinetics, morphology, and crystallinity. This aptamer is here applied to a biologically-relevant bone model system that uses collagen hydrogels. In the presence of the aptamer, intrafibrillar collagen mineralization is observed compared to negative controls and a positive control using well-studied poly-aspartic acid. The mechanism of interaction is explored through affinity measurements, kinetics of calcium uptake, and kinetics of aptamer uptake into the forming mineral. There is a marked difference observed between the selected aptamer containing a G-quadruplex secondary structure compared to a control sequence with no G-quadruplex. It is hypothesized that the equilibrium interaction of the aptamer with calcium-phosphate precursors and with the collagen itself leads to slow kinetic mineral formation and a morphology appropriate to bone. This points to new uses for DNA aptamers in biologically-relevant mineralization systems and the possibility of future biomedical applications. STATEMENT OF SIGNIFICANCE: Collagen is the protein structural component that mineralizes with calcium phosphate to form durable bone. Crystalline calcium phosphate must be infused throughout the collagen fiber structure to produce a strong material. This process is assisted by soluble proteins that interact with both calcium phosphate precursors and the collagen protein and has been proposed to follow a polymer-induce liquid precursor (PILP) model. Further understanding of this model and control of the process through synthetic, biomimetic molecules could have significant advantages in biomedical, restorative procedures. For the first time, synthetic DNA aptamers with specific secondary structures are here shown to influence and direct collagen mineralization. The mechanism of this process has been studied to demonstrate an important equilibrium between the DNA aptamer, calcium phosphate precursors, and collagen.
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Affiliation(s)
- Kassidy Patoine
- Department of Chemistry & Physics, Emmanuel College, 400 Fenway, Boston, MA 02115, United States
| | - Kristy Ta
- Department of Chemistry & Physics, Emmanuel College, 400 Fenway, Boston, MA 02115, United States
| | - Amanda Gilbert
- Department of Chemistry & Physics, Emmanuel College, 400 Fenway, Boston, MA 02115, United States
| | - Marielle Percuoco
- Department of Chemistry & Physics, Emmanuel College, 400 Fenway, Boston, MA 02115, United States
| | - Aren E Gerdon
- Department of Chemistry & Physics, Emmanuel College, 400 Fenway, Boston, MA 02115, United States.
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8
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Wolfe M, Cramer A, Webb S, Goorskey E, Chushak Y, Mirau P, Arroyo-Currás N, Chávez JL. Rational Approach to Optimizing Conformation-Switching Aptamers for Biosensing Applications. ACS Sens 2024; 9:717-725. [PMID: 38270529 PMCID: PMC10897929 DOI: 10.1021/acssensors.3c02004] [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: 09/22/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 01/26/2024]
Abstract
The utilization of structure-switching aptamers (SSAs) has enabled the development of novel sensing platforms for the sensitive and continuous detection of molecules. De novo development of SSAs, however, is complex and laborious. Here we describe a rational approach to SSA optimization that simultaneously improves aptamer binding affinity and introduces target-dependent conformation-switching for compatibility with real-world biosensor applications. Key structural features identified from NMR and computational modeling were used to optimize conformational switching in the presence of target, while large-scale, microarray-based mutation analysis was used to map regions of the aptamer permissive to mutation and identify combinations of mutations with stronger binding affinity. Optimizations were carried out in a relevant biofluid to ensure a seamless transition of the aptamer to a biosensing platform. Initial proof-of-concept for this approach is demonstrated with a cortisol binding aptamer but can easily be translated to other relevant aptamers. Cortisol is a hormone correlated with the stress response that has been associated with various medical conditions and is present at quantifiable levels in accessible biofluids. The ability to continuously track levels of stress in real-time via cortisol monitoring, which can be enabled by the aptamers reported here, is crucial for assessing human health and performance.
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Affiliation(s)
- Monica Wolfe
- 711th
Human Performance Wing, Air Force Research Laboratory, WPAFB, Ohio 45433, United States
- UES,
Inc., Dayton, Ohio 45433, United States
| | - Alyssa Cramer
- 711th
Human Performance Wing, Air Force Research Laboratory, WPAFB, Ohio 45433, United States
- UES,
Inc., Dayton, Ohio 45433, United States
| | - Sean Webb
- 711th
Human Performance Wing, Air Force Research Laboratory, WPAFB, Ohio 45433, United States
- UES,
Inc., Dayton, Ohio 45433, United States
| | - Eva Goorskey
- 711th
Human Performance Wing, Air Force Research Laboratory, WPAFB, Ohio 45433, United States
| | - Yaroslav Chushak
- 711th
Human Performance Wing, Air Force Research Laboratory, WPAFB, Ohio 45433, United States
- Henry
M. Jackson Foundation for the Advancement of Military Medicine, WPAFB, Ohio 45433, United States
| | - Peter Mirau
- Materials
and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Ohio 45433, United States
| | - Netzahualcóyotl Arroyo-Currás
- Department
of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Jorge L. Chávez
- 711th
Human Performance Wing, Air Force Research Laboratory, WPAFB, Ohio 45433, United States
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9
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Shi L, Jin Y, Liu J. Intramolecular aptamer switches. Analyst 2024; 149:745-750. [PMID: 38193253 DOI: 10.1039/d3an02022c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Aptamer switches as effective biosensing tools have become a focal point of research in engineered aptasensors. Intramolecular aptamer switches are more versatile, affordable, and simpler than classical "open-close" and strand displacement-based aptamer switches. Recently, many new aptamers with an overall hairpin structure have been reported. In this study, intramolecular aptamer switches were developed by adding new base pairs to the end of aptamers. The additional nucleotides can pair with the internal domains of the aptamer, causing a change in its conformation from the original secondary structure without a target. When a target binds to an aptamer, a marked change in the structure of the aptamer is expected. As models for testing this intramolecular aptamer switch idea, aptamers of oxytetracycline (OTC), 17β-estradiol (E2), and adenosine were employed. When the additional base pairs are too long, binding the target to the aptamer becomes more challenging. This research offers valuable insights into the development of intramolecular aptamer switches and their potential applications in biosensor design.
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Affiliation(s)
- Lu Shi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
| | - Yan Jin
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
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10
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Chamorro A, Rossetti M, Bagheri N, Porchetta A. Rationally Designed DNA-Based Scaffolds and Switching Probes for Protein Sensing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:71-106. [PMID: 38273204 DOI: 10.1007/10_2023_235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
The detection of a protein analyte and use of this type of information for disease diagnosis and physiological monitoring requires methods with high sensitivity and specificity that have to be also easy to use, rapid and, ideally, single step. In the last 10 years, a number of DNA-based sensing methods and sensors have been developed in order to achieve quantitative readout of protein biomarkers. Inspired by the speed, specificity, and versatility of naturally occurring chemosensors based on structure-switching biomolecules, significant efforts have been done to reproduce these mechanisms into the fabrication of artificial biosensors for protein detection. As an alternative, in scaffold DNA biosensors, different recognition elements (e.g., peptides, proteins, small molecules, and antibodies) can be conjugated to the DNA scaffold with high accuracy and precision in order to specifically interact with the target protein with high affinity and specificity. They have several advantages and potential, especially because the transduction signal can be drastically enhanced. Our aim here is to provide an overview of the best examples of structure switching-based and scaffold DNA sensors, as well as to introduce the reader to the rational design of innovative sensing mechanisms and strategies based on programmable functional DNA systems for protein detection.
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Affiliation(s)
| | - Marianna Rossetti
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
| | - Neda Bagheri
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
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11
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Hariri AA, Cartwright AP, Dory C, Gidi Y, Yee S, Thompson IAP, Fu KX, Yang K, Wu D, Maganzini N, Feagin T, Young BE, Afshar BH, Eisenstein M, Digonnet MJF, Vuckovic J, Soh HT. Modular Aptamer Switches for the Continuous Optical Detection of Small-Molecule Analytes in Complex Media. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2304410. [PMID: 37975267 DOI: 10.1002/adma.202304410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Aptamers are a promising class of affinity reagents because signal transduction mechanisms can be built into the reagent, so that they can directly produce a physically measurable output signal upon target binding. However, endowing the signal transduction functionality into an aptamer remains a trial-and-error process that can compromise its affinity or specificity and typically requires knowledge of the ligand binding domain or its structure. In this work, a design architecture that can convert an existing aptamer into a "reversible aptamer switch" whose kinetic and thermodynamic properties can be tuned without a priori knowledge of the ligand binding domain or its structure is described. Finally, by combining these aptamer switches with evanescent-field-based optical detection hardware that minimizes sample autofluorescence, this study demonstrates the first optical biosensor system that can continuously measure multiple biomarkers (dopamine and cortisol) in complex samples (artificial cerebrospinal fluid and undiluted plasma) with second and subsecond-scale time responses at physiologically relevant concentration ranges.
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Affiliation(s)
- Amani A Hariri
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Alyssa P Cartwright
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Constantin Dory
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Yasser Gidi
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Steven Yee
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Ian A P Thompson
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Kaiyu X Fu
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Kiyoul Yang
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Diana Wu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Nicolò Maganzini
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Trevor Feagin
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Brian E Young
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Behrad Habib Afshar
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | | | - Michel J F Digonnet
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Jelena Vuckovic
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - H Tom Soh
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
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12
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Zhang T, Liu J, Zhang L, Irfan M, Su X. Recent advances in aptamer-based biosensors for potassium detection. Analyst 2023; 148:5340-5354. [PMID: 37750217 DOI: 10.1039/d3an01053h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Maintaining a stable level of potassium is crucial for proper bodily function because even a slight imbalance can result in serious disorders like hyperkalemia and hypokalemia. Therefore, detecting and monitoring potassium ion (K+) levels are of utmost importance. Various biosensors have been developed for rapid K+ detection, with aptamer-based biosensors garnering significant attention due to their high sensitivity and specificity. This review focuses on aptamer-based biosensors for K+ detection, providing an overview of their signal generation strategies, including electrochemical, field-effect transistor, nanopore, colorimetric, and fluorescent systems. The analytical performance of these biosensors is evaluated comprehensively. In addition, factors that affect their efficiency, such as their physicochemical properties, regeneration for reusability, and linkers/spacers, are listed. Lastly, this review examines the major challenges faced by aptamer-based biosensors in K+ detection and discusses potential future developments.
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Affiliation(s)
- Tengfang Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Jiajia Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Muhammad Irfan
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China.
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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13
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Stuber A, Douaki A, Hengsteler J, Buckingham D, Momotenko D, Garoli D, Nakatsuka N. Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores. ACS NANO 2023; 17:19168-19179. [PMID: 37721359 PMCID: PMC10569099 DOI: 10.1021/acsnano.3c05377] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Aptamers that undergo conformational changes upon small-molecule recognition have been shown to gate the ionic flux through nanopores by rearranging the charge density within the aptamer-occluded orifice. However, mechanistic insight into such systems where biomolecular interactions are confined in nanoscale spaces is limited. To understand the fundamental mechanisms that facilitate the detection of small-molecule analytes inside structure-switching aptamer-modified nanopores, we correlated experimental observations to theoretical models. We developed a dopamine aptamer-functionalized nanopore sensor with femtomolar detection limits and compared the sensing behavior with that of a serotonin sensor fabricated with the same methodology. When these two neurotransmitters with comparable mass and equal charge were detected, the sensors showed an opposite electronic behavior. This distinctive phenomenon was extensively studied using complementary experimental techniques such as quartz crystal microbalance with dissipation monitoring, in combination with theoretical assessment by the finite element method and molecular dynamic simulations. Taken together, our studies demonstrate that the sensing behavior of aptamer-modified nanopores in detecting specific small-molecule analytes correlates with the structure-switching mechanisms of individual aptamers. We believe that such investigations not only improve our understanding of the complex interactions occurring in confined nanoscale environments but will also drive further innovations in biomimetic nanopore technologies.
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Affiliation(s)
- Annina Stuber
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Ali Douaki
- Instituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Julian Hengsteler
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Denis Buckingham
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Dmitry Momotenko
- Department
of Chemistry, Carl von Ossietzky University
of Oldenburg, Oldenburg D-26129, Germany
| | - Denis Garoli
- Instituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Nako Nakatsuka
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
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14
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Yu M, He T, Wang Q, Cui C. Unraveling the Possibilities: Recent Progress in DNA Biosensing. BIOSENSORS 2023; 13:889. [PMID: 37754122 PMCID: PMC10526863 DOI: 10.3390/bios13090889] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/29/2023] [Accepted: 09/09/2023] [Indexed: 09/28/2023]
Abstract
Due to the advantages of its numerous modification sites, predictable structure, high thermal stability, and excellent biocompatibility, DNA is the ideal choice as a key component of biosensors. DNA biosensors offer significant advantages over existing bioanalytical techniques, addressing limitations in sensitivity, selectivity, and limit of detection. Consequently, they have attracted significant attention from researchers worldwide. Here, we exemplify four foundational categories of functional nucleic acids: aptamers, DNAzymes, i-motifs, and G-quadruplexes, from the perspective of the structure-driven functionality in constructing DNA biosensors. Furthermore, we provide a concise overview of the design and detection mechanisms employed in these DNA biosensors. Noteworthy advantages of DNA as a sensor component, including its programmable structure, reaction predictility, exceptional specificity, excellent sensitivity, and thermal stability, are highlighted. These characteristics contribute to the efficacy and reliability of DNA biosensors. Despite their great potential, challenges remain for the successful application of DNA biosensors, spanning storage and detection conditions, as well as associated costs. To overcome these limitations, we propose potential strategies that can be implemented to solve these issues. By offering these insights, we aim to inspire subsequent researchers in related fields.
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Affiliation(s)
| | | | | | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China; (M.Y.)
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15
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Wang Y, Liu Y, Wang LL, Zhang QL, Xu L. Integrating Ligands into Nucleic Acid Systems. Chembiochem 2023; 24:e202300292. [PMID: 37401635 DOI: 10.1002/cbic.202300292] [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: 04/11/2023] [Revised: 06/12/2023] [Accepted: 07/04/2023] [Indexed: 07/05/2023]
Abstract
Signal transduction from non-nucleic acid ligands (small molecules and proteins) to structural changes of nucleic acids plays a crucial role in both biomedical analysis and cellular regulations. However, how to bridge between these two types of molecules without compromising the expandable complexity and programmability of the nucleic acid nanomachines is a critical challenge. Compared with the previously most widely applied transduction strategies, we review the latest advances of a kinetically controlled approach for ligand-oligonucleotide transduction in this Concept article. This new design works through an intrinsic conformational alteration of the nucleic acid aptamer upon the ligand binding as a governing factor for nucleic acid strand displacement reactions. The functionalities and applications of this transduction system as a ligand converter on biosensing and DNA computation are described and discussed. Furthermore, we propose some potential scenarios for utilization of this ligand transduction design to regulate gene expression through synthetic RNA switches in the cellular contexts. Finally, future perspectives regarding this ligand-oligonucleotide transduction platform are also discussed.
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Affiliation(s)
- Yang Wang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging National-Regional Key Technology Engineering Laboratory for Medical Ultrasound School of Biomedical Engineering, School of Medicine, Shenzhen, 518060, China
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yan Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Liang-Liang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qiu-Long Zhang
- School of Pharmacy and Medical Technology, Putian University, Putian, 351100, Fujian, China
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
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16
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Ogorek AN, Zhou X, Martell JD. Switchable DNA Catalysts for Proximity Labeling at Sites of Protein-Protein Interactions. J Am Chem Soc 2023; 145:16913-16923. [PMID: 37463457 DOI: 10.1021/jacs.3c05578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Proximity labeling (PL) has emerged as a powerful approach to elucidate proteomes within a defined radius around a protein of interest (POI). In PL, a catalyst is attached to the POI and tags nearby endogenous proteins, which are then isolated by affinity purification and identified by mass spectrometry. Although existing PL methods have yielded numerous biological insights, proteomes with greater spatial resolution could be obtained if PL catalysts could be activated at more specific subcellular locations, such as sites where both the POI and a chemical stimulus are present or sites of protein-protein interactions (PPIs). Here, we report DNA-based switchable PL catalysts that are attached to a POI and become activated only when a secondary molecular trigger is present. The DNA catalysts consist of a photocatalyst and a spectral quencher tethered to a DNA oligomer. They are catalytically inactive by default but undergo a conformational change in response to a specific molecular trigger, thus activating PL. We designed a system in which the DNA catalyst becomes activated on living mammalian cells specifically at sites of Her2-Her3 heterodimers and c-Met homodimers, PPIs known to increase the invasion and growth of certain cancers. While this study employs a Ru(bpy)3-type complex for tagging proteins with biotin phenol, the switchable DNA catalyst design is compatible with diverse synthetic PL photocatalysts. Furthermore, the switchable DNA PL catalysts can be constructed from conformation-switching DNA aptamers that respond to small molecules, ions, and proteins, opening future opportunities for PL in highly specific subcellular locations.
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Affiliation(s)
- Ashley N Ogorek
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Xu Zhou
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D Martell
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53726, United States
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17
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Yoshikawa AM, Rangel AE, Zheng L, Wan L, Hein LA, Hariri AA, Eisenstein M, Soh HT. A massively parallel screening platform for converting aptamers into molecular switches. Nat Commun 2023; 14:2336. [PMID: 37095144 PMCID: PMC10126150 DOI: 10.1038/s41467-023-38105-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/14/2023] [Indexed: 04/26/2023] Open
Abstract
Aptamer-based molecular switches that undergo a binding-induced conformational change have proven valuable for a wide range of applications, such as imaging metabolites in cells, targeted drug delivery, and real-time detection of biomolecules. Since conventional aptamer selection methods do not typically produce aptamers with inherent structure-switching functionality, the aptamers must be converted to molecular switches in a post-selection process. Efforts to engineer such aptamer switches often use rational design approaches based on in silico secondary structure predictions. Unfortunately, existing software cannot accurately model three-dimensional oligonucleotide structures or non-canonical base-pairing, limiting the ability to identify appropriate sequence elements for targeted modification. Here, we describe a massively parallel screening-based strategy that enables the conversion of virtually any aptamer into a molecular switch without requiring any prior knowledge of aptamer structure. Using this approach, we generate multiple switches from a previously published ATP aptamer as well as a newly-selected boronic acid base-modified aptamer for glucose, which respectively undergo signal-on and signal-off switching upon binding their molecular targets with second-scale kinetics. Notably, our glucose-responsive switch achieves ~30-fold greater sensitivity than a previously-reported natural DNA-based switch. We believe our approach could offer a generalizable strategy for producing target-specific switches from a wide range of aptamers.
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Affiliation(s)
- Alex M Yoshikawa
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | | | - Liwei Zheng
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Leighton Wan
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Linus A Hein
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Amani A Hariri
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Michael Eisenstein
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - H Tom Soh
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA.
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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18
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Parolo C, Idili A, Heikenfeld J, Plaxco KW. Conformational-switch biosensors as novel tools to support continuous, real-time molecular monitoring in lab-on-a-chip devices. LAB ON A CHIP 2023; 23:1339-1348. [PMID: 36655710 PMCID: PMC10799767 DOI: 10.1039/d2lc00716a] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Recent years have seen continued expansion of the functionality of lab on a chip (LOC) devices. Indeed LOCs now provide scientists and developers with useful and versatile platforms across a myriad of chemical and biological applications. The field still fails, however, to integrate an often important element of bench-top analytics: real-time molecular measurements that can be used to "guide" a chemical response. Here we describe the analytical techniques that could provide LOCs with such real-time molecular monitoring capabilities. It appears to us that, among the approaches that are general (i.e., that are independent of the reactive or optical properties of their targets), sensing strategies relying on binding-induced conformational change of bioreceptors are most likely to succeed in such applications.
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Affiliation(s)
- Claudio Parolo
- Barcelona Institute for Global Health, Hospital Clínic Universitat de Barcelona, 08036, Barcelona, Spain
| | - Andrea Idili
- Department of Chemical Science and Technologies, University of Rome, Tor Vergata, 00133 Rome, Italy
| | - Jason Heikenfeld
- Novel Devices Laboratory, University of Cincinnati, Cincinnati, Ohio, USA
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA.
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California, USA
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19
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Soni R, Krishna AM, More SH, Sharma A. Reversible Modulation of Aptamer-Ligand Binding in RNA Light-Up Aptamers Containing G-Quadruplex Using Chemical Stimuli. Chembiochem 2023; 24:e202200574. [PMID: 36352557 DOI: 10.1002/cbic.202200574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/07/2022] [Indexed: 11/11/2022]
Abstract
Regulating a system in equilibrium transiently to out-of-equilibrium by using certain stimuli is the strategy used by natural biomolecules to function. Herein, we showed that the interaction of synthetic RNA aptamers, having a G-quadruplex core structure, with their corresponding ligands could be regulated from their equilibrium state to non-equilibrium state in a reversible manner using simple chemical stimuli (Ag+ and cysteine). The approach would be useful for designing aptamer regulators that work in a dynamic nucleic acid network, where a strict control on aptamer-ligand interaction is needed. In addition, to the best of our knowledge, this is the first report which shows that RNA G-quadruplexes can be disrupted by the addition of silver ions. This would be useful not only in designing RNA-based sensors or regulators but would also be useful for understanding the role of metal ions in RNA folding and catalysis.
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Affiliation(s)
- Rashi Soni
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - A Murali Krishna
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Shahaji H More
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Ashwani Sharma
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India.,Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
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20
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Mohsen MG, Midy MK, Balaji A, Breaker R. Exploiting natural riboswitches for aptamer engineering and validation. Nucleic Acids Res 2023; 51:966-981. [PMID: 36617976 PMCID: PMC9881172 DOI: 10.1093/nar/gkac1218] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/04/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023] Open
Abstract
Over the past three decades, researchers have found that some engineered aptamers can be made to work well in test tubes but that these same aptamers might fail to function in cells. To help address this problem, we developed the 'Graftamer' approach, an experimental platform that exploits the architecture of a natural riboswitch to enhance in vitro aptamer selection and accelerate in vivo testing. Starting with combinatorial RNA pools that contain structural features of a guanine riboswitch aptamer interspersed with regions of random sequence, we performed multiplexed in vitro selection with a collection of small molecules. This effort yielded aptamers for quinine, guanine, and caffeine that appear to maintain structural features of the natural guanine riboswitch aptamer. Quinine and caffeine aptamers were each grafted onto a natural guanine riboswitch expression platform and reporter gene expression was monitored to determine that these aptamers function in cells. Additionally, we determined the secondary structure features and survival mechanism of a class of RNA sequences that evade the intended selection strategy, providing insight into improving this approach for future efforts. These results demonstrate that the Graftamer strategy described herein represents a convenient and straightforward approach to develop aptamers and validate their in vivo function.
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Affiliation(s)
- Michael G Mohsen
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA,Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA
| | - Matthew K Midy
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Aparaajita Balaji
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Ronald R Breaker
- To whom correspondence should be addressed. Tel: +1 203 432 9389; Fax: +1 203 432 6161;
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21
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Zhang QL, Wang Y, Wang LL, Xie F, Wu RY, Ma XY, Li H, Liu Y, Yao S, Xu L. Programming Non-Nucleic Acid Molecules into Computational Nucleic Acid Systems. Angew Chem Int Ed Engl 2023; 62:e202214698. [PMID: 36373715 DOI: 10.1002/anie.202214698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Indexed: 11/16/2022]
Abstract
Nucleic acid (NA) computation has been widely developed in the past years to solve kinds of logic and mathematic issues in both information technologies and biomedical analysis. However, the difficulty to integrate non-NA molecules limits its power as a universal platform for molecular computation. Here, we report a versatile prototype of hybridized computation integrated with both nucleic acids and non-NA molecules. Employing the conformationally controlled ligand converters, we demonstrate that non-NA molecules, including both small molecules and proteins, can be computed as nucleic acid strands to construct the circuitry with increased complexity and scalability, and can be even programmed to solve arithmetical calculations within the computational nucleic acid system. This study opens a new door for molecular computation in which all-NA circuits can be expanded with integration of various ligands, and meanwhile, ligands can be precisely programmed by the nuclei acid computation.
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Affiliation(s)
- Qiu-Long Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Liang-Liang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Fan Xie
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ruo-Yue Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xu-Yang Ma
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Han Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yan Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Shunchun Yao
- School of Electric Power Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
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22
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Zhang J, Lu Y, Gao W, Yang P, Cheng N, Jin Y, Chen J. Structure-switching locked hairpin triggered rolling circle amplification for ochratoxin A (OTA) detection by ICP-MS. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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23
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Onaş AM, Dascălu C, Raicopol MD, Pilan L. Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets. BIOSENSORS 2022; 12:816. [PMID: 36290952 PMCID: PMC9599214 DOI: 10.3390/bios12100816] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Nucleic-acid aptamers consisting in single-stranded DNA oligonucleotides emerged as very promising biorecognition elements for electrochemical biosensors applied in various fields such as medicine, environmental, and food safety. Despite their outstanding features, such as high-binding affinity for a broad range of targets, high stability, low cost and ease of modification, numerous challenges had to be overcome from the aptamer selection process on the design of functioning biosensing devices. Moreover, in the case of small molecules such as metabolites, toxins, drugs, etc., obtaining efficient binding aptamer sequences proved a challenging task given their small molecular surface and limited interactions between their functional groups and aptamer sequences. Thus, establishing consistent evaluation standards for aptamer affinity is crucial for the success of these aptamers in biosensing applications. In this context, this article will give an overview on the thermodynamic and structural aspects of the aptamer-target interaction, its specificity and selectivity, and will also highlight the current methods employed for determining the aptamer-binding affinity and the structural characterization of the aptamer-target complex. The critical aspects regarding the generation of aptamer-modified electrodes suitable for electrochemical sensing, such as appropriate bioreceptor immobilization strategy and experimental conditions which facilitate a convenient anchoring and stability of the aptamer, are also discussed. The review also summarizes some effective small molecule aptasensing platforms from the recent literature.
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Affiliation(s)
- Andra Mihaela Onaş
- Advanced Polymer Materials Group, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
| | - Constanţa Dascălu
- Faculty of Applied Sciences, University ‘Politehnica’ of Bucharest, 313 Splaiul Independenţei, District 6, 060042 Bucharest, Romania
| | - Matei D. Raicopol
- Faculty of Chemical Engineering and Biotechnologies, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
| | - Luisa Pilan
- Faculty of Chemical Engineering and Biotechnologies, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
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24
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Yue F, Liu M, Bai M, Hu M, Li F, Guo Y, Vrublevsky I, Sun X. Novel Electrochemical Aptasensor Based on Ordered Mesoporous Carbon/2D Ti3C2 MXene as Nanocarrier for Simultaneous Detection of Aminoglycoside Antibiotics in Milk. BIOSENSORS 2022; 12:bios12080626. [PMID: 36005022 PMCID: PMC9405622 DOI: 10.3390/bios12080626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022]
Abstract
Herein, a novel electrochemical aptasensor using a broad-spectrum aptamer as a biorecognition element was constructed based on a screen-printed carbon electrode (SPCE) for simultaneous detection of aminoglycoside antibiotics (AAs). The ordered mesoporous carbon (OMC) was firstly modified on 2D Ti3C2 MXene. The addition of OMC not only effectively improved the stability of the aptasensor, but also prevented the stacking of Ti3C2 sheets, which formed a good current passage for signal amplification. The prepared OMC@Ti3C2 MXene functioned as a nanocarrier to accommodate considerable aptamers. In the presence of AAs, the transport of electron charge on SPCE surface was influenced by the bio-chemical reactions of the aptamer and AAs, generating a significant decline in the differential pulse voltammetry (DPV) signals. The proposed aptasensor presented a wide linear range and the detection limit was 3.51 nM. Moreover, the aptasensor, with satisfactory stability, reproducibility and specificity, was successfully employed to detect the multi-residuals of AAs in milk. This work provided a novel strategy for monitoring AAs in milk.
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Affiliation(s)
- Fengling Yue
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
| | - Mengyue Liu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
| | - Mengyuan Bai
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
| | - Mengjiao Hu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
| | - Falan Li
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, Zibo 255049, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, Zibo 255049, China
| | - Yemin Guo
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, Zibo 255049, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, Zibo 255049, China
| | - Igor Vrublevsky
- Department of Information Security, Belarusian State University of Informatics and Radioelectronics, 220013 Minsk, Belarus
| | - Xia Sun
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255049, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, Zibo 255049, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, Zibo 255049, China
- Correspondence: ; Tel.: +86-0533-2786558
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Victorious A, Zhang Z, Chang D, Maclachlan R, Pandey R, Xia J, Gu J, Hoare T, Soleymani L, Li Y. A DNA Barcode‐Based Aptasensor Enables Rapid Testing of Porcine Epidemic Diarrhea Viruses in Swine Saliva Using Electrochemical Readout. Angew Chem Int Ed Engl 2022; 61:e202204252. [DOI: 10.1002/anie.202204252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Amanda Victorious
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
| | - Zijie Zhang
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | | | - Richa Pandey
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
| | - Jianrun Xia
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Todd Hoare
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
- Department of Chemical Engineering McMaster University Canada
| | - Leyla Soleymani
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
- Department of Engineering Physics McMaster University Canada
- Michael G. DeGroote Institute for Infectious Disease Research McMaster University Canada
| | - Yingfu Li
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
- Michael G. DeGroote Institute for Infectious Disease Research McMaster University Canada
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26
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Sykes KS, White RJ. Effects of Nucleic Acid Structural Heterogeneity on the Electrochemistry of Tethered Redox Molecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7322-7330. [PMID: 35639972 PMCID: PMC10150402 DOI: 10.1021/acs.langmuir.2c00840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The cation condensation-induced collapse of electrode-bound nucleic acids and the resulting change in the electrochemical signal is a useful tool to predict the structure and redox probe location of heterogeneous structures of surface-tethered DNA probes─a common architecture employed in the development of electrochemical sensors. In this paper, we measure the faradaic current of an appended redox molecule at the 3' position of the nucleic acid using cyclic voltammetry before and after nucleic acid collapse for various nucleic acid architectures and heterogeneous mixtures on the same electrode surface. The voltammetric peak current change with collapse correlates with the proximity of the redox molecules from the surface. For stem-loop probes, the terminal methylene blue is initially held closer to the surface, such that inducing collapse, by reducing the dielectric permittivity of the interrogation solution, results in a ∼30% increase in current. However, when incorporating pseudoknot probes that hold methylene blue further away from the electrode surface, the current change is much larger (∼120%), indicating a larger conformation change. Upon a 50:50 ratio of the two, we observe a change in current that relates to the ratiometric distribution of the probe used to make the surfaces. Additionally, using cyclic voltammetry, we find that the change between diffusion-limited and diffusion-independent peak currents is dependent upon the distinct structural characteristics of DNA probes on the surface (stem-loop or pseudoknot), as well as the ratios of different DNA probes on the surface. Thus, we demonstrate that the heterogeneous nature of DNA probes governs the corresponding electrochemical signals, which can lead to a better understanding on how to predict the structures of functional nucleic acids on electrode surfaces and how this affects surface-to-surface variability and electrochemical response.
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Affiliation(s)
- Kiana S. Sykes
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
| | - Ryan J. White
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
- Department of Electrical and Computer Engineering, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
- Corresponding Author:
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27
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Victorious A, Zhang Z, Chang D, Malachlan R, Pandey R, Xia J, Gu J, Hoare T, Soleymani L, Li Y. A DNA Barcode‐Based Aptasensor Enables Rapid Testing of Porcine Epidemic Diarrhea Viruses in Swine Saliva Using Electrochemical Readout. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Zijie Zhang
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Dingran Chang
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | | | | | - Jianrun Xia
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Jimmy Gu
- McMurry University Biochemistry and Biomedical Sciences CANADA
| | - Todd Hoare
- McMurry University Chemical Engineering CANADA
| | - Leyla Soleymani
- McMastser University Engineering Physics 1280 Main Street W. L8S 4M1 Hamilton CANADA
| | - Yingfu Li
- McMaster University Biochemistry and Biomedical Sciences CANADA
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28
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Sester C, McCone JA, Sen A, Vorster I, Harvey JE, Hodgkiss JM. Unravelling the binding mode of a methamphetamine aptamer: a spectroscopic and calorimetric investigation. Biophys J 2022; 121:2193-2205. [PMID: 35474264 DOI: 10.1016/j.bpj.2022.04.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/10/2022] [Accepted: 04/22/2022] [Indexed: 11/25/2022] Open
Abstract
Nucleic acid aptamers are bio-molecular recognition agents that bind to their targets with high specificity and affinity, and hold promise in a range of biosensor and therapeutic applications. In the case of small molecule targets, their small size and limited number of functional groups constitute challenges for their detection by aptamer-based biosensors because bio-recognition events may both be weak and produce poorly transduced signals. The binding affinity is principally used to characterize aptamer-ligand interactions; however a structural understanding of bio-recognition is arguably more valuable in order to design a strong response in biosensor applications. Using a combination of nuclear magnetic resonance, circular dichroism, and isothermal titration calorimetry, we propose a binding model for a new methamphetamine aptamer and determine the main interactions driving complex formation. These measurements reveal only modest structural changes to the aptamer upon binding and are consistent with a conformational selection binding model. The aptamer-methamphetamine complex formation was observed to be entropically driven, apparently involving hydrophobic and electrostatic interactions. Taken together, our results exemplify a means of elucidating small molecule-aptamer binding interactions, which may be decisive in the development of aptasensors and therapeutics, and may contribute to a deeper understanding of interactions driving aptamer selection.
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Affiliation(s)
- Clement Sester
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington PO Box 600, Wellington 6040, New Zealand; School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington 6040, New Zealand
| | - Jordan Aj McCone
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Anindita Sen
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington PO Box 600, Wellington 6040, New Zealand; School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington 6040, New Zealand
| | - Ian Vorster
- School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington 6040, New Zealand
| | - Joanne E Harvey
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Justin M Hodgkiss
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington PO Box 600, Wellington 6040, New Zealand; School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington 6040, New Zealand.
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29
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Paper based microfluidic platform for single-step detection of mesenchymal stromal cells secreted VEGF. Anal Chim Acta 2022; 1199:339588. [DOI: 10.1016/j.aca.2022.339588] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/26/2022] [Accepted: 02/07/2022] [Indexed: 12/11/2022]
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30
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Xu J, Xiang J, Chen J, Wan T, Deng H, Li D. High sensitivity detection of tumor cells in biological samples using a multivalent aptamer strand displacement strategy. Analyst 2022; 147:634-644. [PMID: 35040831 DOI: 10.1039/d1an01949j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Monitoring the cell surface-expressed nucleolin facilitates early cancer diagnosis. Herein, we developed a multivalent aptamer displacement strand duplex strategy on cell membranes using a multi-receptor co-recognition design for improving the sensitivity and specificity of cancer cell recognition with an ultra-low background. The AS1411 aptamer labeled with the FAM fluorophore can be quenched using a partial complementary sequence modified with a BHQ1 tag which is partially hybridized with the AS1411 aptamer to create a receptor-activating aptamer. The multi-AS1411 activable probe based on the strand displacement strategy was constructed using multiple copies of the structure-switching AS1411 aptamer (bearing a short poly-A tail) linked together using the poly-T long chain (as a scaffold) which was synthesized by Terminal Deoxynucleotidyl Transferase (TDT)-mediated extension. We demonstrated the promising efficacy and sensitivity of our method in recognizing tumor cells in both cell mixtures and clinical cytology specimens. Due to its simple and fast operation with excellent cell recognition sensitivity and accuracy, it is expected to achieve the detection of low abundance target cells. Our approach will have broad application in clinical rapid detection and personalized medicine.
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Affiliation(s)
- Jieru Xu
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Jiahui Xiang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Jialing Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Tao Wan
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Hongli Deng
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Dairong Li
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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31
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Huang PJJ, Liu J. Selection of Aptamers for Sensing Caffeine and Discrimination of Its Three Single Demethylated Analogues. Anal Chem 2022; 94:3142-3149. [PMID: 35143165 DOI: 10.1021/acs.analchem.1c04349] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With the growing consumption of caffeine-containing beverages, detection of caffeine has become an important biomedical, bioanalytical, and environmental topic. We herein isolated four high-quality aptamers for caffeine with dissociation constants ranging from 2.2 to 14.6 μM as characterized using isothermal titration calorimetry. Different binding patterns were obtained for the three single demethylated analogues: theobromine, theophylline, and paraxanthine, highlighting the effect of the molecular symmetry of the arrangement of the three methyl groups in caffeine. A structure-switching fluorescent sensor was designed showing a detection limit of 1.2 μM caffeine, which reflected the labeled caffeine concentration within 6.1% difference for eight commercial beverages. In 20% human serum, a detection limit of 4.0 μM caffeine was achieved. With the four aptamer sensors forming an array, caffeine and the three analogues were well separated from nine other closely related molecules.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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32
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Wang R, Cao Y, Qu H, Wang Y, Zheng L. Label-free detection of Cu(II) in fish using a graphene field-effect transistor gated by structure-switching aptamer probes. Talanta 2022; 237:122965. [PMID: 34736690 DOI: 10.1016/j.talanta.2021.122965] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/25/2022]
Abstract
Copper sulfate is a widely used agent to control insects, bacteria and algae for fishery. However, excess amount of copper ions in water accumulate in aquatic products through the ecological cycle system, highly threatening food safety and public health. Therefore, it is urgent to develop a rapid and efficient method for the determination of copper content in aquatic products. In this study, we developed a label-free biosensor for Cu(II) based on a graphene field-effect transistor gated by structure-switching aptamer probes (SSA-GFET) against Cu(II) we obtained before. The detection mechanism of the biosensor is attributed to the surface charge shift and the potential change of the gate electrode upon the specific binding of Cu(II). The SSA-GFET biosensor has a low detection limit of 10 nM and a linear range of 10 nM to 3 μM to Cu(II). In addition to the excellent selectivity to Cu(II), the biosensor also showes the advantage of high recovery rate for detection of Cu(II) in real fish samples. Because of the detection characteristics of label-free SSA-GFET, it has great advantages in the field of food safety and environmental detection.
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Affiliation(s)
- Rongrong Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yong Cao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Hao Qu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China; Engineering Research Center of Bioprocess, Ministry of Education, Hefei University of Technology, Hefei, 230009, China.
| | - Yanbo Wang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang Gongshang University, Hangzhou, 310035, China
| | - Lei Zheng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China; Intelligent Interconnected Systems Laboratory of Anhui Province, Hefei University of Technology, Hefei, 230009, China.
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33
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Dillen A, Lammertyn J. Paving the way towards continuous biosensing by implementing affinity-based nanoswitches on state-dependent readout platforms. Analyst 2022; 147:1006-1023. [DOI: 10.1039/d1an02308j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combining affinity-based nanoswitches with state-dependent readout platforms allows for continuous biosensing and acquisition of real-time information about biochemical processes occurring in the environment of interest.
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Affiliation(s)
- Annelies Dillen
- KU Leuven, Department of Biosystems – Biosensors Group, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
| | - Jeroen Lammertyn
- KU Leuven, Department of Biosystems – Biosensors Group, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
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34
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Xie M, Zhao F, Zhang Y, Xiong Y, Han S. Recent advances in aptamer-based optical and electrochemical biosensors for detection of pesticides and veterinary drugs. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108399] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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35
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Lv Z, Wang Q, Yang M. Multivalent Duplexed-Aptamer Networks Regulated a CRISPR-Cas12a System for Circulating Tumor Cell Detection. Anal Chem 2021; 93:12921-12929. [PMID: 34533940 DOI: 10.1021/acs.analchem.1c02228] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although circulating tumor cells (CTCs) have great potential to act as the mini-invasive liquid biopsy cancer biomarker, a rapid and sensitive CTC detection method remains lacking. CRISPR-Cas12a has recently emerged as a promising tool in biosensing applications with the characteristic of fast detection, easy operation, and high sensitivity. Herein, we reported a CRISPR-Cas12a-based CTC detection sensor that is regulated by the multivalent duplexed-aptamer networks (MDANs). MDANs were synthesized on a magnetic bead surface by rolling circle amplification (RCA), which contain multiple duplexed-aptamer units that allow structure switching induced by cell-binding events. The presence of target cells can trigger the release of free "activator DNA" from the MDANs structure to activate the downstream CRISPR-Cas12a for signal amplification. Furthermore, the 3D DNA network formed by RCA products also provided significantly higher sensitivity than the monovalent aptamer. As a proof-of-concept study, we chose the most widely used sgc8 aptamer that specifically recognizes CCRF-CEM cells to validate the proposed approach. The MDANs-Cas12a system could afford a simple and fast CTC detection workflow with a detection limit of 26 cells mL-1. We also demonstrated that the MDANs-Cas12a could directly detect the CTCs in human blood samples, indicating a great potential of the MDANs-Cas12a in clinical CTC-based liquid biopsy.
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Affiliation(s)
- Zhengxian Lv
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering and State Key Lab of Marine Environmental Science, Xiamen University, Xiamen 361005, China
| | - Qiuquan Wang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering and State Key Lab of Marine Environmental Science, Xiamen University, Xiamen 361005, China
| | - Minghui Yang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
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36
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Sanford AA, Rangel AE, Feagin TA, Lowery RG, Argueta-Gonzalez HS, Heemstra JM. RE-SELEX: restriction enzyme-based evolution of structure-switching aptamer biosensors. Chem Sci 2021; 12:11692-11702. [PMID: 34659704 PMCID: PMC8442683 DOI: 10.1039/d1sc02715h] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/23/2021] [Indexed: 11/21/2022] Open
Abstract
Aptamers are widely employed as recognition elements in small molecule biosensors due to their ability to recognize small molecule targets with high affinity and selectivity. Structure-switching aptamers are particularly promising for biosensing applications because target-induced conformational change can be directly linked to a functional output. However, traditional evolution methods do not select for the significant conformational change needed to create structure-switching biosensors. Modified selection methods have been described to select for structure-switching architectures, but these remain limited by the need for immobilization. Herein we describe the first homogenous, structure-switching aptamer selection that directly reports on biosensor capacity for the target. We exploit the activity of restriction enzymes to isolate aptamer candidates that undergo target-induced displacement of a short complementary strand. As an initial demonstration of the utility of this approach, we performed selection against kanamycin A. Four enriched candidate sequences were successfully characterized as structure-switching biosensors for detection of kanamycin A. Optimization of biosensor conditions afforded facile detection of kanamycin A (90 μM to 10 mM) with high selectivity over three other aminoglycosides. This research demonstrates a general method to directly select for structure-switching biosensors and can be applied to a broad range of small-molecule targets.
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Affiliation(s)
- Aimee A Sanford
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
| | - Alexandra E Rangel
- Department of Chemistry, Center for Cell and Genome Science, University of Utah Salt Lake City Utah 84112 USA
| | - Trevor A Feagin
- Department of Chemistry, Center for Cell and Genome Science, University of Utah Salt Lake City Utah 84112 USA
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37
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Regan B, O'Kennedy R, Collins D. Advances in point-of-care testing for cardiovascular diseases. Adv Clin Chem 2021; 104:1-70. [PMID: 34462053 DOI: 10.1016/bs.acc.2020.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Point-of-care testing (POCT) is a specific format of diagnostic testing that is conducted without accompanying infrastructure or sophisticated instrumentation. Traditionally, such rapid sample-to-answer assays provide inferior analytical performances to their laboratory counterparts when measuring cardiac biomarkers. Hence, their potentially broad applicability is somewhat bound by their inability to detect clinically relevant concentrations of cardiac troponin (cTn) in the early stages of myocardial injury. However, the continuous refinement of biorecognition elements, the optimization of detection techniques, and the fabrication of tailored fluid handling systems to manage the sensing process has stimulated the production of commercial assays that can support accelerated diagnostic pathways. This review will present the latest commercial POC assays and examine their impact on clinical decision-making. The individual elements that constitute POC assays will be explored, with an emphasis on aspects that contribute to economically feasible and highly sensitive assays. Furthermore, the prospect of POCT imparting a greater influence on early interventions for medium to high-risk individuals and the potential to re-shape the paradigm of cardiovascular risk assessments will be discussed.
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Affiliation(s)
- Brian Regan
- School of Biotechnology, Dublin City University, Dublin, Ireland.
| | - Richard O'Kennedy
- School of Biotechnology, Dublin City University, Dublin, Ireland; Research Complex, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - David Collins
- School of Biotechnology, Dublin City University, Dublin, Ireland
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38
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Zhang QL, Wang LL, Liu Y, Lin J, Xu L. A kinetically controlled platform for ligand-oligonucleotide transduction. Nat Commun 2021; 12:4654. [PMID: 34341342 PMCID: PMC8329073 DOI: 10.1038/s41467-021-24962-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 07/16/2021] [Indexed: 12/15/2022] Open
Abstract
Ligand-oligonucleotide transduction provides the critical pathway to integrate non-nucleic acid molecules into nucleic acid circuits and nanomachines for a variety of strand-displacement related applications. Herein, a general platform is constructed to convert the signals of ligands into desired oligonucleotides through a precise kinetic control. In this design, the ligand-aptamer binding sequence with an engineered duplex stem is introduced between the toehold and displacement domains of the invading strand to regulate the strand-displacement reaction. Employing this platform, we achieve efficient transduction of both small molecules and proteins orthogonally, and more importantly, establish logical and cascading operations between different ligands for versatile transduction. Besides, this platform is capable of being directly coupled with the signal amplification systems to further enhance the transduction performance. This kinetically controlled platform presents unique features with designing simplicity and flexibility, expandable complexity and system compatibility, which may pave a broad road towards nucleic acid-based developments of sophisticated transduction networks.
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Affiliation(s)
- Qiu-Long Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, China
| | - Liang-Liang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, China
| | - Yan Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, China
| | - Jiao Lin
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, China.
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39
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Nakatsuka N, Heard KJ, Faillétaz A, Momotenko D, Vörös J, Gage FH, Vadodaria KC. Sensing serotonin secreted from human serotonergic neurons using aptamer-modified nanopipettes. Mol Psychiatry 2021; 26:2753-2763. [PMID: 33767349 PMCID: PMC9997689 DOI: 10.1038/s41380-021-01066-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/17/2021] [Accepted: 03/11/2021] [Indexed: 02/01/2023]
Abstract
The serotonergic system in the human brain modulates several physiological processes, and altered serotonergic neurotransmission has been implicated in the neuropathology of several psychiatric disorders. The study of serotonergic neurotransmission in psychiatry has long been restricted to animal models, but advances in cell reprogramming technology have enabled the generation of serotonergic neurons from patient-induced pluripotent stem cells (iPSCs). While iPSC-derived human serotonergic neurons offer the possibility to study serotonin (5-HT) release and uptake, particularly by 5-HT-modulating drugs such as selective serotonin reuptake inhibitors (SSRIs), a major limitation is the inability to reliably quantify 5-HT secreted from neurons in vitro. Herein, we address this technical gap via a novel sensing technology that couples 5-HT-specific DNA aptamers into nanopores (glass nanopipettes) with orifices of ~10 nm to detect 5-HT in complex neuronal culture medium with higher selectivity, sensitivity, and stability than existing methods. The 5-HT aptamers undergo conformational rearrangement upon target capture and serve as gatekeepers of ionic flux through the nanopipette opening. We generated human serotonergic neurons in vitro and detected secreted 5-HT using aptamer-coated nanopipettes in a low nanomolar range, with the possibility of detecting significantly lower (picomolar) concentrations. Furthermore, as a proof of concept, we treated human serotonergic neurons in vitro with the SSRI citalopram and detected a significant increase in extracellular 5-HT using the aptamer-modified nanopipettes. We demonstrate the utility of such methods for 5-HT detection, raising the possibility of fast quantification of neurotransmitters secreted from patient-derived live neuronal cells.
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Affiliation(s)
- Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - Kelly J Heard
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Alix Faillétaz
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - Dmitry Momotenko
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Krishna C Vadodaria
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA.
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Dillen A, Vandezande W, Daems D, Lammertyn J. Unraveling the effect of the aptamer complementary element on the performance of duplexed aptamers: a thermodynamic study. Anal Bioanal Chem 2021; 413:4739-4750. [PMID: 34109445 DOI: 10.1007/s00216-021-03444-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022]
Abstract
Duplexed aptamers (DAs) are widespread aptasensor formats that simultaneously recognize and signal the concentration of target molecules. They are composed of an aptamer and aptamer complementary element (ACE) which consists of a short oligonucleotide that partially inhibits the aptamer sequence. Although the design principles to engineer DAs are straightforward, the tailored development of DAs for a particular target is currently based on trial and error due to limited knowledge of how the ACE sequence affects the final performance of DA biosensors. Therefore, we have established a thermodynamic model describing the influence of the ACE on the performance of DAs applied in equilibrium assays and demonstrated that this relationship can be described by the binding strength between the aptamer and ACE. To validate our theoretical findings, the model was applied to the 29-mer anti-thrombin aptamer as a case study, and an experimental relation between the aptamer-ACE binding strength and performance of DAs was established. The obtained results indicated that our proposed model could accurately describe the effect of the ACE sequence on the performance of the established DAs for thrombin detection, applied for equilibrium assays. Furthermore, to characterize the binding strength between the aptamer and ACEs evaluated in this work, a set of fitting equations was derived which enables thermodynamic characterization of DNA-based interactions through thermal denaturation experiments, thereby overcoming the limitations of current predictive software and chemical denaturation experiments. Altogether, this work encourages the development, characterization, and use of DAs in the field of biosensing.
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Affiliation(s)
- Annelies Dillen
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
| | - Wouter Vandezande
- Department of Microbial and Molecular Systems - Centre for Membrane Separations, Adsorption, Catalysis and Spectroscopy for Sustainable Solutions, KU Leuven, Celestijnenlaan 200F, Box 2454, 3001, Leuven, Belgium
| | - Devin Daems
- Department of Chemistry - AXES research group, University of Antwerp, Groenenborgerlaan 171, 2010, Antwerpen, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium.
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Chung S, Sicklick JK, Ray P, Hall DA. Development of a Soluble KIT Electrochemical Aptasensor for Cancer Theranostics. ACS Sens 2021; 6:1971-1979. [PMID: 34008963 PMCID: PMC8785434 DOI: 10.1021/acssensors.1c00535] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
An electrochemical sensor based on a conformation-changing aptamer is reported to detect soluble KIT, a cancer biomarker, in human serum. The sensor was fabricated with a ferrocene-labeled aptamer (Kd < 5 nM) conjugated to a gold electrode. Quantitative KIT detection was achieved using electrochemical impedance spectroscopy (EIS) and square-wave voltammetry (SWV). EIS was used to optimize experimental parameters such as the aptamer-to-spacer ratio, aptamer immobilization time, pH, and KIT incubation time, and the sensor surface was characterized using voltammetry. The assay specificity was demonstrated using interfering species and exhibited high specificity toward the target protein. The aptasensor showed a wide dynamic range, 10 pg/mL-100 ng/mL in buffer, with a 1.15 pg/mL limit of detection. The sensor also has a linear response to KIT spiked in human serum and successfully detected KIT in cancer-cell-conditioned media. The proposed aptasensor has applications as a continuous or intermittent approach for cancer therapy monitoring and diagnostics (theranostics).
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Affiliation(s)
- Saeromi Chung
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California 92093, United States
| | - Jason K Sicklick
- Department of Surgery, Division of Surgical Oncology, Moores Cancer Center, University of California San Diego Health, San Diego, California 92093, United States
| | - Partha Ray
- Department of Surgery, Division of Surgical Oncology, Moores Cancer Center, University of California San Diego Health, San Diego, California 92093, United States
| | - Drew A Hall
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California 92093, United States
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
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Smart Nucleic Acids as Future Therapeutics. Trends Biotechnol 2021; 39:1289-1307. [PMID: 33980422 DOI: 10.1016/j.tibtech.2021.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/23/2021] [Accepted: 03/29/2021] [Indexed: 11/23/2022]
Abstract
Nucleic acid therapeutics (NATs) hold promise in treating undruggable diseases and are recognized as the third major category of therapeutics in addition to small molecules and antibodies. Despite the milestones that NATs have made in clinical translation over the past decade, one important challenge pertains to increasing the specificity of this class of drugs. Activating NATs exclusively in disease-causing cells is highly desirable because it will safely broaden the application of NATs to a wider range of clinical indications. Smart NATs are triggered through a photo-uncaging reaction or a specific molecular input such as a transcript, protein, or small molecule, thus complementing the current strategy of targeting cells and tissues with receptor-specific ligands to enhance specificity. This review summarizes the programmable modalities that have been incorporated into NATs to build in responsive behaviors. We discuss the various inputs, transduction mechanisms, and output response functions that have been demonstrated to date.
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Zhang F, Liu J. Label‐Free Colorimetric Biosensors Based on Aptamers and Gold Nanoparticles: A Critical Review. ACTA ACUST UNITED AC 2020. [DOI: 10.1002/anse.202000023] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Fang Zhang
- College of Biological Science and Engineering Fuzhou University Fuzhou 350108 People's Republic of China
- Department of Chemistry Waterloo Institute for Nanotechnology University of Waterloo Waterloo N2 L 3G1 Ontario Canada
| | - Juewen Liu
- Department of Chemistry Waterloo Institute for Nanotechnology University of Waterloo Waterloo N2 L 3G1 Ontario Canada
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Rangel AE, Hariri AA, Eisenstein M, Soh HT. Engineering Aptamer Switches for Multifunctional Stimulus-Responsive Nanosystems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2003704. [PMID: 33165999 DOI: 10.1002/adma.202003704] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/19/2020] [Indexed: 05/15/2023]
Abstract
Although RNA and DNA are best known for their capacity to encode biological information, it has become increasingly clear over the past few decades that these biomolecules are also capable of performing other complex functions, such as molecular recognition (e.g., aptamers) and catalysis (e.g., ribozymes). Building on these foundations, researchers have begun to exploit the predictable base-pairing properties of RNA and DNA in order to utilize nucleic acids as functional materials that can undergo a molecular "switching" process, performing complex functions such as signaling or controlled payload release in response to external stimuli including light, pH, ligand-binding and other microenvironmental cues. Although this field is still in its infancy, these efforts offer exciting potential for the development of biologically based "smart materials". Herein, ongoing progress in the use of nucleic acids as an externally controllable switching material is reviewed. The diverse range of mechanisms that can trigger a stimulus response, and strategies for engineering those functionalities into nucleic acid materials are explored. Finally, recent progress is discussed in incorporating aptamer switches into more complex synthetic nucleic acid-based nanostructures and functionalized smart materials.
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Affiliation(s)
- Alexandra E Rangel
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Amani A Hariri
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Michael Eisenstein
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - H Tom Soh
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
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Gray MD, Deore PS, Chung AJ, Van Riesen AJ, Manderville RA, Prabhakar PS, Wetmore SD. Lighting Up the Thrombin-Binding Aptamer G-Quadruplex with an Internal Cyanine-Indole-Quinolinium Nucleobase Surrogate. Direct Fluorescent Intensity Readout for Thrombin Binding without Topology Switching. Bioconjug Chem 2020; 31:2596-2606. [PMID: 33156614 DOI: 10.1021/acs.bioconjchem.0c00530] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fluorescent nucleobases represent an important class of molecular reporters of nucleic acid interactions. In this work, the advantages of utilizing a noncanonical fluorescent nucleobase surrogate for monitoring thrombin binding by the 15-mer thrombin binding aptamer (TBA) is presented. TBA folds into an antiparallel G-quadruplex (GQ) with loop thymidine (T) residues interacting directly with the protein in the thrombin-TBA complex. In the free GQ, T3 is solvent-exposed and does not form canonical base-pairs within the antiparallel GQ motif. Upon thrombin binding, T3 interacts directly with a hydrophobic protein binding pocket. Replacing T3 with a cyanine-indole-quinolinium (4QI) hemicyanine dye tethered to an acyclic 1,2-propanediol linker is shown to have minimal impact on GQ stability and structure with the internal 4QI displaying a 40-fold increase in emission intensity at 586 nm (excitation 508 nm) compared to the free dye in solution. Molecular dynamics (MD) simulations demonstrate that the 4QI label π-stacks with T4 and T13 within the antiparallel GQ fold, which is supported by strong energy transfer (ET) fluorescence from the GQ (donor) to the 4QI label (acceptor). Thrombin binding to 4QI-TBA diminishes π-stacking interactions between 4QI and the GQ structure to cause a turn-off emission intensity response with an apparent dissociation constant (Kd) of 650 nM and a limit of detection (LoD) of 150 nM. These features highlight the utility of internal noncanonical fluorescent surrogates for monitoring protein binding by GQ-folding aptamers in the absence of DNA topology switching.
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Affiliation(s)
- Micaela D Gray
- Department of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Prashant S Deore
- Department of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Andrew J Chung
- Department of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Abigail J Van Riesen
- Department of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Richard A Manderville
- Department of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Preethi Seelam Prabhakar
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D Wetmore
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
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Ye T, Zhang Z, Lu J, Yuan M, Cao H, Yin F, Wu X, Xu F. Enzyme-powered cascade three-dimensional DNA machine for the ultrasensitive determination of kanamycin. NANOSCALE 2020; 12:20883-20889. [PMID: 33048076 DOI: 10.1039/d0nr05077f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
DNA walking machines have been widely used in rapid and sensitive detection. In this work, we develop a single enzyme-powered DNA cascade machine for the ultrasensitive determination of kanamycin. To construct the cascade manner, two types of single-legged three-dimensional DNA walking machine are employed to implement integrated target recognition, signal transduction and signal amplification. Upon adding kanamycin to trigger the upstream machine, the sequential enzymatic cleavage drives the autonomous movement of the walking strand and produces plenty of dye-labeled fragments with fluorescence recovery. Meanwhile, these fragments also serve as walking strands to activate the downstream machine for cascade signal amplification. Taking advantage of this cascade DNA machine, ultrasensitive determination can be accomplished in 60 min. Under the optimum conditions, this method was highly selective toward kanamycin with a detection limit of 28 fM. This cascade signal amplification shows great potential for the rapid screening of antibiotics in food.
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Affiliation(s)
- Tai Ye
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Zhiwei Zhang
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Jiaqi Lu
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Min Yuan
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Hui Cao
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Fengqin Yin
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Xiuxiu Wu
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Fei Xu
- Shanghai Engineering Research Center for Food Rapid Detection, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
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Coria‐Oriundo LL, Ceretti H, Roupioz Y, Battaglini F. Redox Polyelectrolyte Modified Gold Nanoparticles Enhance the Detection of Adenosine in an Electrochemical Split‐Aptamer Assay. ChemistrySelect 2020. [DOI: 10.1002/slct.202002488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lucy L. Coria‐Oriundo
- INQUIMAE (CONICET) Departamento de Química Inorgánica Analítica y Química Física Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Ciudad Universitaria, Pabellón 2 C1428EHA Buenos Aires Argentina
- Facultad de Ciencias Universidad Nacional de Ingeniería Av. Túpac Amaru 210 Lima 25, Perú
| | - Helena Ceretti
- Universidad Nacional de Gral. Sarmiento, J. M. Gutiérrez 1150 B1613GSX, Los Polvorines, Prov. de Buenos Aires Argentina
| | - Yoann Roupioz
- Univ. Grenoble Alpes CNRS CEA SyMMES 38000 Grenoble France
| | - Fernando Battaglini
- INQUIMAE (CONICET) Departamento de Química Inorgánica Analítica y Química Física Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Ciudad Universitaria, Pabellón 2 C1428EHA Buenos Aires Argentina
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48
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Zhang Y, Du X, Deng S, Li C, He Q, He G, Zhou M, Wang H, Deng R. Dual Triple Helix-Aptamer Probes for Mix-and-Read Detecting Antibiotics in Fish and Milk. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9524-9529. [PMID: 32786851 DOI: 10.1021/acs.jafc.0c03801] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Antibiotic abuse in agricultural products leads to serious food safety issues. To this end, we proposed a mix-and-read and enzyme-free amplified assay for antibiotics based on a dual triple helix-aptamer probe, potentially applicable for on-site monitoring of antibiotic residues. A dual triple helix-aptamer probe can leverage the response toward target molecules without enzyme-based amplification, rendering it sensitive and robust for profiling target molecules. The proposed assay allowed mix-and-read detection of chloramphenicol with a detection limit of 0.18 nM. Besides, it accommodated for specifically resolving chloramphenicol among other antibiotics. Chloramphenicol residual in aquatic products in fish and milk can be precisely determined. Thus, the aptamer probe deems to enrich the toolbox for managing antibiotic use.
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Affiliation(s)
- Yong Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Xiaosheng Du
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Sha Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Chenghui Li
- Analytical & Testing Center, Sichuan University, Chengdu 610064, China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Guiping He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Mi Zhou
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Haibo Wang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
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49
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Churcher ZR, Garaev D, Hunter HN, Johnson PE. Reduction in Dynamics of Base pair Opening upon Ligand Binding by the Cocaine-Binding Aptamer. Biophys J 2020; 119:1147-1156. [PMID: 32882188 DOI: 10.1016/j.bpj.2020.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/25/2022] Open
Abstract
We have used magnetization transfer NMR experiments to measure the exchange rate constant (kex) of the imino protons in the unbound, cocaine-bound, and quinine-bound forms of the cocaine-binding DNA aptamer. Both long-stem 1 (MN4) and short-stem 1 (MN19) variants were analyzed, corresponding to structures with a prefolded secondary structure and ligand-induced-folding versions of this aptamer, respectively. The kex values were measured as a function of temperature from 5 to 45°C to determine the thermodynamics of the base pair opening for MN4. We find that the base pairs close to the ligand-binding site become stronger upon ligand binding, whereas those located away from the binding site do not strengthen. With the buffer conditions used in this study, we observe imino 1H signals in MN19 not previously seen, which leads us to conclude that in the free form, both stem 2 and parts of stem 3 are formed and that the base pairs in stem 1 become structured or more rigid upon binding. This is consistent with the kex values for MN19 decreasing in both stem 1 and at the ligand-binding site. Based on the temperature dependence of the kex values, we find that MN19 is more dynamic than MN4 in the free and both ligand-bound forms. For MN4, ligand-binding results in the reduction of dynamics that are localized to the binding site. These results demonstrate that an aptamer in which the base pairs are preformed also experiences a reduction in dynamics with ligand binding.
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Affiliation(s)
- Zachary R Churcher
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada
| | - Devid Garaev
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada
| | - Howard N Hunter
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada
| | - Philip E Johnson
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada.
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50
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Lu Y, Yuan Z, Bai J, Lin Q, Deng R, Luo A, Chi Y, Deng S, He Q. Directly profiling intact Staphylococcus aureus in water and foods via enzymatic cleavage aptasensor. Anal Chim Acta 2020; 1132:28-35. [PMID: 32980108 DOI: 10.1016/j.aca.2020.07.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/22/2020] [Accepted: 07/22/2020] [Indexed: 11/16/2022]
Abstract
Staphylococcus aureus (S. aureus) causes serious food-borne diseases, and tools able to directly profile intact S. aureus would greatly facilitate food safety and public health. Herein, we proposed a biosensing platform for culture-independent and separation-free profiling S. aureus, thus allow us to directly detect intact S. aureus in complex samples. The binding protection effect of aptamer-cell complex was introduced to construct the aptasensor, and it allowed to eliminate the optimization of aptamer probe sequences. The proposed aptasensor, terms enzymatic cleavage aptasensor could achieve a sensitive (a detection limit of 64 CFU/mL) and broad-concentration quantification (dynamic range 102-107 CFU/mL) of S. aureus. Furthermore, it could specifically identify intact S. aureus in complex samples, and the quantifying of S. aureus was achieved in tap water, milk and porker with high precision. Therefore, enzymatic cleavage aptasensor could be a good candidate for on-site biosensing platform of S. aureus, as well as other pathogens by replacing the aptamer sequences.
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Affiliation(s)
- Yunhao Lu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Zilan Yuan
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Jinrong Bai
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Qi Lin
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China.
| | - Aimin Luo
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 10048, China.
| | - Yuanlong Chi
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Sha Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China.
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