51
|
Komarova N, Barkova D, Kuznetsov A. Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology. Int J Mol Sci 2020; 21:E8774. [PMID: 33233573 PMCID: PMC7699794 DOI: 10.3390/ijms21228774] [Citation(s) in RCA: 17] [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: 10/24/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HTS) meets this demand of SELEX. Analysis of the data obtained from sequencing of the libraries produced during and after aptamer isolation provides an informative basis for precise aptamer identification and for examining the structure and function of nucleic acid ligands. This review discusses the technical aspects and the potential of the integration of HTS with SELEX.
Collapse
Affiliation(s)
- Natalia Komarova
- Scientific-Manufacturing Complex Technological Centre, 1–7 Shokin Square, Zelenograd, 124498 Moscow, Russia; (D.B.); (A.K.)
| | | | | |
Collapse
|
52
|
Kubiczek D, Raber H, Bodenberger N, Oswald T, Sahan M, Mayer D, Wiese S, Stenger S, Weil T, Rosenau F. The Diversity of a Polyclonal FluCell-SELEX Library Outperforms Individual Aptamers as Emerging Diagnostic Tools for the Identification of Carbapenem Resistant Pseudomonas aeruginosa. Chemistry 2020; 26:14536-14545. [PMID: 32515842 PMCID: PMC7756519 DOI: 10.1002/chem.202000213] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Indexed: 11/06/2022]
Abstract
Textbook procedures require the use of individual aptamers enriched in SELEX libraries which are subsequently chemically synthesized after their biochemical characterization. Here we show that this reduction of the available sequence space of large libraries and thus the diversity of binding molecules reduces the labelling efficiency and fidelity of selected single aptamers towards different strains of the human pathogen Pseudomonas aeruginosa compared to a polyclonal aptamer library enriched by a whole-cell-SELEX involving fluorescent aptamers. The library outperformed single aptamers in reliable and specific targeting of different clinically relevant strains, allowed to inhibit virulence associated cellular functions and identification of bound cell surface targets by aptamer based affinity purification and mass spectrometry. The stunning ease of this FluCell-SELEX and the convincing performance of the P. aeruginosa specific library may pave the way towards generally new and efficient diagnostic techniques based on polyclonal aptamer libraries not only in clinical microbiology.
Collapse
Affiliation(s)
- Dennis Kubiczek
- Institute of pharmaceutical biotechnologyUlm University89081UlmGermany
| | - Heinz Raber
- Institute of pharmaceutical biotechnologyUlm University89081UlmGermany
| | | | - Thomas Oswald
- Institute of pharmaceutical biotechnologyUlm University89081UlmGermany
| | - Melis Sahan
- Institute of pharmaceutical biotechnologyUlm University89081UlmGermany
| | - Daniel Mayer
- Institute for Medical Microbiology and HygieneUniversity Hospital Ulm89081UlmGermany
| | | | - Steffen Stenger
- Institute for Medical Microbiology and HygieneUniversity Hospital Ulm89081UlmGermany
| | - Tanja Weil
- Department Synthesis of MacromoleculesMax-Planck-Institute for Polymer Research Mainz55128MainzGermany
| | - Frank Rosenau
- Institute of pharmaceutical biotechnologyUlm University89081UlmGermany
- Department Synthesis of MacromoleculesMax-Planck-Institute for Polymer Research Mainz55128MainzGermany
| |
Collapse
|
53
|
Taneja V, Goel M, Shankar U, Kumar A, Khilnani GC, Prasad HK, Prasad GBKS, Gupta UD, Sharma TK. An Aptamer Linked Immobilized Sorbent Assay (ALISA) to Detect Circulatory IFN-α, an Inflammatory Protein among Tuberculosis Patients. ACS COMBINATORIAL SCIENCE 2020; 22:656-666. [PMID: 33063508 DOI: 10.1021/acscombsci.0c00108] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Dysregulation of IFN-α is the basis for pathogenesis of autoimmune as well as infectious diseases. Identifying inflammatory signatures in peripheral blood of patients is an approach for monitoring active infection. Hence, estimation of type I IFNs as an inflammatory biomarker to scrutinize disease status after treatment is useful. Accordingly, an Aptamer Linked Immobilized Sorbent Assay (ALISA) for the detection of IFN-α in serum samples was developed. Sixteen aptamers were screened for their ability to bind IFN-α. Aptamer IFNα-3 exhibited specificity for IFN-α with no cross-reactivity with interferons β and γ and human serum albumin. The disassociation constant (Kd) was determined to be 3.96 ± 0.36 nM, and the limit of detection was ∼2 ng. The characterized IFNα-3 aptamer was used in ALISA to screen tuberculosis (TB) patients' sera. An elevated IFN-α level in sera derived from untreated TB patients (median = 0.31), compared to nontuberculous household contacts (median = 0.13) and healthy volunteers (median = 0.12), and further a decline in IFN-α level among treated patients (median = 0.13) were seen. The ALISA assay facilitates direct estimation of inflammatory protein(s) in circulation unlike mRNA estimation by real time PCR. Designing of aptamers similar to the IFNα-3 aptamer provides a novel approach to assess other inflammatory protein(s) in patients before, during, and after completion of treatment and would denote clinical improvement in successfully treated patients.
Collapse
Affiliation(s)
- Vibha Taneja
- National JALMA Institute of Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282001, India
- Department of Biochemistry, Jiwaji University, Gwalior, Madhya Pradesh 474011, India
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute, Incubator, NCR Biotech Science Cluster, Third Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, India
- Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Manish Goel
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Uma Shankar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Gopi C. Khilnani
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Hanumanthappa K. Prasad
- Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | | | - Umesh D. Gupta
- National JALMA Institute of Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282001, India
| | - Tarun K. Sharma
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute, Incubator, NCR Biotech Science Cluster, Third Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, India
| |
Collapse
|
54
|
Puzari U, Mukherjee AK. Recent developments in diagnostic tools and bioanalytical methods for analysis of snake venom: A critical review. Anal Chim Acta 2020; 1137:208-224. [DOI: 10.1016/j.aca.2020.07.054] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 01/19/2023]
|
55
|
Chatterjee B, Kalyani N, Anand A, Khan E, Das S, Bansal V, Kumar A, Sharma TK. GOLD SELEX: a novel SELEX approach for the development of high-affinity aptamers against small molecules without residual activity. Mikrochim Acta 2020; 187:618. [PMID: 33074441 DOI: 10.1007/s00604-020-04577-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022]
Abstract
GOLD SELEX, a novel SELEX approach has been developed that obviates the need for target immobilization for aptamer development. The approach purely relies on the affinity of the aptamers towards its target, to get detached from the gold nanoparticle (GNP) surface (weak attraction) after binding with its target. Thus, only the completely detached aptamers are selected for the next round of SELEX. This, in-process, also addresses the issue of residual binding and thus improves the sensitivity of the developed aptamers. As a proof of concept for establishing the utility of the approach for small molecules, we have developed aptamers against dichlorvos (DV), a pesticide in just 8 rounds. Using these aptamer candidates, we have developed an aptamer-NanoZyme (GNP having peroxidase mimic activity) based colorimetric assay. The developed aptamer displayed high affinity (Kd in sub micromolar range) and selectivity for DV. The developed assay could detect as low as 15 μM DV. The best-performing aptamer was also able to work in real samples like river water and commercial apple juice. The GOLD SELEX approach developed in this study, we believe, can act as a template for future SELEX strategy development and can replace the conventional SELEX strategy.
Collapse
Affiliation(s)
- Bandhan Chatterjee
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, 121001, India
| | - Neeti Kalyani
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, 121001, India
| | - Anjali Anand
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, 121001, India
| | - Eshan Khan
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Soonjyoti Das
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, 121001, India
| | - Vipul Bansal
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Lab (NBRL), School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria, 3001, Australia
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Tarun Kumar Sharma
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, 121001, India.
| |
Collapse
|
56
|
Jain S, Kaur J, Prasad S, Roy I. Nucleic acid therapeutics: a focus on the development of aptamers. Expert Opin Drug Discov 2020; 16:255-274. [PMID: 32990095 DOI: 10.1080/17460441.2021.1829587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Aptamers provide exciting opportunities for the development of specific and targeted therapeutic approaches. AREAS COVERED In this review, the authors discuss different therapeutic options available with nucleic acids, including aptamers, focussing on similarities and differences between them. The authors concentrate on case studies with specific aptamers, which exemplify their distinct advantages. The reasons for failure, wherever available, are deliberated upon. Attempts to accelerate the in vitro selection process have been discussed. Challenges with aptamers in terms of their specificity and targeted delivery and strategies to overcome these are described. Examples of precise regulation of systemic half-life of aptamers using antidotes are discussed. EXPERT OPINION Despite their nontoxic nature, a variety of reasons limit the therapeutic potential of aptamers in the clinic. The analysis of adverse effects observed with the pegnivacogin/anivamersen pair has highlighted the need to screen for preexisting PEG antibodies in any clinical trial involving pegylated molecules. Surprisingly, and promisingly, the ability of nucleic acid therapeutics to breach the blood brain barrier seems achievable. The recognition of specific motifs, e.g. G-quadruplex in thrombin-binding aptamers, or a 'nucleation' zone while designing aptamer-antidote pairs, is likely to accelerate the discovery of therapeutically efficacious molecules.
Collapse
Affiliation(s)
- Swati Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Jaskirat Kaur
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Shivcharan Prasad
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| |
Collapse
|
57
|
Yi J, Xiao W, Li G, Wu P, He Y, Chen C, He Y, Ding P, Kai T. The research of aptamer biosensor technologies for detection of microorganism. Appl Microbiol Biotechnol 2020; 104:9877-9890. [PMID: 33047168 DOI: 10.1007/s00253-020-10940-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/27/2020] [Accepted: 10/01/2020] [Indexed: 12/21/2022]
Abstract
The activities and transmissions of microorganisms are closely related to human, and all kinds of diseases caused by pathogenic microorganisms have attracted attention in the world and brought many challenges to human health and public health. The traditional microbial detection technologies have characteristics of longer detection cycle and complicated processes, therefore, which can no longer meet the detection requirements in the field of public health. At present, it is the focus to develop and design a novel, rapid, and simple microbial detection method in the field of public health. Herein, this article summarized the development of aptamer biosensor technologies for detection of microorganism in the aspect of bacteria, viruses, and toxins in detail, including optical aptamer sensors such as fluorometry and colorimetry, electrochemical aptamer sensors, and other technologies combined with aptamer. KEY POINTS: • Aptamer biosensor is a good platform for microbial detection. • Aptamer biosensors include optical sensors and electrochemical sensors. • Aptamer sensors have been widely used in the detection of bacteria, viruses, and other microorganisms.
Collapse
Affiliation(s)
- Jiecan Yi
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China.,School of Public Health, Changsha Medical University, Changsha, 410219, Hunan, China
| | - Wen Xiao
- Hunan Institute of Food Quality Supervision Inspection and Research, Changsha, 410000, Hunan, China
| | - Guiyin Li
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541014, Guangxi, China
| | - Pian Wu
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China
| | - Yayuan He
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China
| | - Cuimei Chen
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China
| | - Yafei He
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China
| | - Ping Ding
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China.
| | - Tianhan Kai
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410078, Hunan, China.
| |
Collapse
|
58
|
Bagheri Hashkavayi A, Cha BS, Lee ES, Kim S, Park KS. Advances in Exosome Analysis Methods with an Emphasis on Electrochemistry. Anal Chem 2020; 92:12733-12740. [PMID: 32902258 DOI: 10.1021/acs.analchem.0c02745] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Exosomes, small extracellular vesicles, are released by various cell types. They are found in bodily fluids, including blood, urine, serum, and saliva, and play essential roles in intercellular communication. Exosomes contain various biomarkers, such as nucleic acids and proteins, that reflect the status of their parent cells. Since they influence tumorigenesis and metastasis in cancer patients, exosomes are excellent noninvasive potential indicators for early cancer detection. Aptamers with specific binding properties have distinct advantages over antibodies, making them effective versatile bioreceptors for the detection of exosome biomarkers. Here, we review various aptamer-based exosome detection approaches based on signaling methods, such as fluorescence, colorimetry, and chemiluminescence, focusing on electrochemical strategies that are easier, cost-effective, and more sensitive than others. Further, we discuss the clinical applications of electrochemical exosome analysis strategies as well as future research directions in this field.
Collapse
Affiliation(s)
- Ayemeh Bagheri Hashkavayi
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Byung Seok Cha
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Eun Sung Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Seokjoon Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| |
Collapse
|
59
|
Pérez-Cejuela HM, Herrero-Martínez JM, Simó-Alfonso EF. Recent Advances in Affinity MOF-Based Sorbents with Sample Preparation Purposes. Molecules 2020; 25:E4216. [PMID: 32938010 PMCID: PMC7571043 DOI: 10.3390/molecules25184216] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/01/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023] Open
Abstract
This review summarizes the recent advances concerning metal-organic frameworks (MOFs) modified with several biomolecules (e.g., amino acids, nucleobases, proteins, antibodies, aptamers, etc.) as ligands to prepare affinity-based sorbents for application in the sample preparation field. The preparation and incorporation strategies of these MOF-based affinity materials were described. Additionally, the different types of ligands that can be employed for the synthesis of these biocomposites and their application as sorbents for the selective extraction of molecules and clean-up of complex real samples is reported. The most important features of the developed biocomposites will be discussed throughout the text in different sections, and several examples will be also commented on in detail.
Collapse
Affiliation(s)
| | | | - Ernesto F. Simó-Alfonso
- Department of Analytical Chemistry, University of Valencia, C/Dr. Moliner, 50, 46100 Burjassot, Valencia, Spain; (H.M.P.-C.); (J.M.H.-M.)
| |
Collapse
|
60
|
Hassan EM, Dixon BR, Sattar SA, Stalker A, Örmeci B, DeRosa MC. Highly sensitive magnetic-microparticle-based aptasensor for Cryptosporidium parvum oocyst detection in river water and wastewater: Effect of truncation on aptamer affinity. Talanta 2020; 222:121618. [PMID: 33167272 DOI: 10.1016/j.talanta.2020.121618] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/15/2020] [Accepted: 08/31/2020] [Indexed: 12/22/2022]
Abstract
Many methods have been reported to detect Cryptosporidium parvum (C. parvum) oocysts in the water environment using monoclonal antibodies. Herein, we report the use of DNA aptamers as an alternative ligand. We present the highly sensitive detection of C. parvum oocysts in wastewater samples based on aptamer-conjugated magnetic beads. A previously selected DNA aptamer (R4-6) that binds to C. parvum oocysts with high affinity and selectivity was rationally truncated into two minimer aptamers (Min_Crypto1 and Min_Crypto2), and conjugated to micro-magnetic beads. In flow cytometry tests with phosphate buffer, river water, and wastewater samples, both the minimers showed improved affinity and specificity toward C. parvum oocysts than the parent R4-6. Moreover, Min_Crypto2 showed higher affinity to its target than the parent aptamer when testing in wastewater, indicating superior binding properties in a complex matrix. Using a fluorescence microplate-based assay, and when incubated with different numbers of oocysts, Min_Crypto2 showed a limit of detection as low as 5 C. parvum oocysts in 300 μL of wastewater. Results described here indicate that Min_Crypto2 has superior specificity and sensitivity for the detection of C. parvum oocysts, and has a strong potential to be used successfully in a sensor.
Collapse
Affiliation(s)
- Eman M Hassan
- Department of Civil and Environmental Engineering, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, Canada; Metrology Research Centre, National Research Council Canada, Ottawa, ON, K1A 0R6, Canada
| | - Brent R Dixon
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, K1A 0K9, Canada
| | - Syed A Sattar
- CREM Co Labs, Units 1-2, 3403 American Drive, Mississauga, ON, L4V 1T4, Canada; Emeritus of Microbiology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Andrew Stalker
- Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, K1A 0K9, Canada
| | - Banu Örmeci
- Department of Civil and Environmental Engineering, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, Canada.
| | - Maria C DeRosa
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, Canada.
| |
Collapse
|
61
|
Fairén AG, Gómez-Elvira J, Briones C, Prieto-Ballesteros O, Rodríguez-Manfredi JA, López Heredero R, Belenguer T, Moral AG, Moreno-Paz M, Parro V. The Complex Molecules Detector (CMOLD): A Fluidic-Based Instrument Suite to Search for (Bio)chemical Complexity on Mars and Icy Moons. ASTROBIOLOGY 2020; 20:1076-1096. [PMID: 32856927 PMCID: PMC7116096 DOI: 10.1089/ast.2019.2167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
Organic chemistry is ubiquitous in the Solar System, and both Mars and a number of icy satellites of the outer Solar System show substantial promise for having hosted or hosting life. Here, we propose a novel astrobiologically focused instrument suite that could be included as scientific payload in future missions to Mars or the icy moons: the Complex Molecules Detector, or CMOLD. CMOLD is devoted to determining different levels of prebiotic/biotic chemical and structural targets following a chemically general approach (i.e., valid for both terrestrial and nonterrestrial life), as well as their compatibility with terrestrial life. CMOLD is based on a microfluidic block that distributes a liquid suspension sample to three instruments by using complementary technologies: (1) novel microscopic techniques for identifying ultrastructures and cell-like morphologies, (2) Raman spectroscopy for detecting universal intramolecular complexity that leads to biochemical functionality, and (3) bioaffinity-based systems (including antibodies and aptamers as capture probes) for finding life-related and nonlife-related molecular structures. We highlight our current developments to make this type of instruments flight-ready for upcoming Mars missions: the Raman spectrometer included in the science payload of the ESAs Rosalind Franklin rover (Raman Laser Spectrometer instrument) to be launched in 2022, and the biomarker detector that was included as payload in the NASA Icebreaker lander mission proposal (SOLID instrument). CMOLD is a robust solution that builds on the combination of three complementary, existing techniques to cover a wide spectrum of targets in the search for (bio)chemical complexity in the Solar System.
Collapse
Affiliation(s)
- Alberto G. Fairén
- Centro de Astrobiología (CSIC-INTA), Madrid, Spain
- Department of Astronomy, Cornell University, Ithaca New York, USA
| | - Javier Gómez-Elvira
- Payload & Space Science Department, Instituto Nacional de Técnica Aeroespacial (INTA), Madrid, Spain
| | | | | | | | - Raquel López Heredero
- Payload & Space Science Department, Instituto Nacional de Técnica Aeroespacial (INTA), Madrid, Spain
| | - Tomás Belenguer
- Payload & Space Science Department, Instituto Nacional de Técnica Aeroespacial (INTA), Madrid, Spain
| | - Andoni G. Moral
- Payload & Space Science Department, Instituto Nacional de Técnica Aeroespacial (INTA), Madrid, Spain
| | | | - Víctor Parro
- Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| |
Collapse
|
62
|
Tao X, Wang X, Liu B, Liu J. Conjugation of antibodies and aptamers on nanozymes for developing biosensors. Biosens Bioelectron 2020; 168:112537. [PMID: 32882473 DOI: 10.1016/j.bios.2020.112537] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/11/2020] [Accepted: 08/21/2020] [Indexed: 02/06/2023]
Abstract
Nanozymes are engineered nanomaterials with enzyme-like activities. Over the past decade, impressive progresses on nanozymes in biosensing have been made due to their unique advantages of high stability, low cost, and easy modification compared to natural enzymes. For many biosensors, it is critical to conjugate nanozymes to affinity ligands such as antibodies and aptamers. Since different nanomaterials have different surface properties, conjugation methods need to be compatible with these properties. In addition, the effect of biomolecules on nanozyme activity needs to be considered. In this review, we first categorized nanozyme-based biosensors into four parts, respectively describing noncovalent and covalent modifications with antibodies and aptamers. Meanwhile, recent advances in antibody and aptamer labeled nanozyme biosensors are summarized, and the methods of their conjugation are further illustrated. Finally, conclusions and future perspectives for the development and application of nanozyme bioconjugates are discussed.
Collapse
Affiliation(s)
- Xiaoqi Tao
- College of Food Science, Southwest University, Chongqing, 400715, China; Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
| | - Xin Wang
- College of Food Science, Southwest University, Chongqing, 400715, China
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
| |
Collapse
|
63
|
Davydova AS, Timoshenko VV, Lomzov AA, Pyshnyi DV, Venyaminova AG, Vorobyeva MA. G-quadruplex 2'-F-modified RNA aptamers targeting hemoglobin: Structure studies and colorimetric assays. Anal Biochem 2020; 611:113886. [PMID: 32795455 DOI: 10.1016/j.ab.2020.113886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 10/23/2022]
Abstract
Biosensors that rely on aptamers as analyte-recognizing elements (also known as aptasensors) are gaining in popularity during recent years for analytical and biomedical applications. Among them, colorimetric ELISA-like systems seem very promising for biomarker detection in medical diagnostics. For their development, one should thoroughly consider the characteristics of the aptamers, with a particular focus on the secondary structure. In this study, we performed an in-depth structural study of previously selected hemoglobin-binding 2'-F-RNA aptamers using CD spectroscopy, enzymatic probing, and specific fluorophore binding. Only a combination of different assays allowed us to prove G-quadruplex formation for anti-hemoglobin 2'-F-RNA aptamers. We also demonstrated a possible application of these 2'-F-RNA aptamers for microplate colorimetric detection of human hemoglobin in both direct and sandwich formats.
Collapse
Affiliation(s)
- Anna S Davydova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.
| | | | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Mariya A Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| |
Collapse
|
64
|
Calzada V. Aptamers in Diagnostic and Molecular Imaging Applications. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 174:141-160. [PMID: 31848635 DOI: 10.1007/10_2019_115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The origin of the term diagnostic comes from the Greek word gnosis, meaning "to know." In medicine, a diagnostic can predict the pathology risk, disease status, treatment, and prognosis, even following therapy. An early and correct diagnosis is necessary for an efficient treatment. Moreover, it is possible to predict if and why a therapy will be successful or fail, enabling the timely application of alternative therapeutic strategies. Available diagnostics are due to the advances in biotechnology; however, more sensitive, low-cost, and noninvasive methodologies are still a challenge. Knowledge about molecular characteristics provide personalized information, which is the goal of future medicine. Today, multiple diagnostic techniques have emerged, with which it is possible to distinguish molecular patterns.In this way, aptamers are the perfect tools to recognize molecular targets and can be easily modified to confer additional functions. Their versatile characteristics and low cost make aptamers ideal for diagnostic applications.This chapter is a review of aptamer-based diagnostics in biomedicine, with a special focus on probe design and molecular imaging. Graphical Abstract.
Collapse
Affiliation(s)
- Victoria Calzada
- Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
| |
Collapse
|
65
|
Díaz-Amaya S, Zhao M, Allebach JP, Chiu GTC, Stanciu LA. Ionic Strength Influences on Biofunctional Au-Decorated Microparticles for Enhanced Performance in Multiplexed Colorimetric Sensors. ACS APPLIED MATERIALS & INTERFACES 2020; 12:32397-32409. [PMID: 32645268 DOI: 10.1021/acsami.0c07636] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The rising development of biosensors offers a great potential for health, food, and environmental monitoring. However, in many colorimetric platforms, there is a performance limitation stemming from the tendency of traditional Au nanoparticles toward nonspecific aggregation in response to changing ionic strength (salt concentration). This work puts forward a new type of colorimetric aptamer-functionalized labeling of microparticles, which allows to leverage an increase in ionic strength as a positive driver of enhanced detection performance of analytical targets. The resulting device is a cost-effective, instrument-free, portable, and reliable aptasensor that serves as basis for the fabrication of universal paper-based colorimetric platforms with the capability of multiplex, multireplicates and provides quantitative colorimetric detection. A controlled fabrication process was demonstrated by keeping 90% of the signal obtained from the as-fabricated devices (n = 40) within ± 1 standard deviation (SD) (relative SD = 5.69%) and following a mesokurtic normal-like distribution (p = 0.385). We propose for the first time a salt-induced aggregation mechanism for highly stable multilayered label particles (ssDNA-PEI-Au-PS) as the basis of the detection scheme. The use of DNA aptamers as capture biomolecules and PEI as an encapsulating agent allows for a sensitive and highly specific colorimetric response. As a proof of concept, multiplexed detection of mercury (Hg2+) and arsenic (As3+) was demonstrated. In addition, we introduced a robust image analysis algorithm for testing zone segmentation and color signal quantification that allowed for analytical detection, reaching a limit of detection of 1 ppm for both targeted analytes, with enough evidence (p > 0.05) to prove the high specificity of the fabricated device versus a pool of possible interferent ions.
Collapse
Affiliation(s)
- Susana Díaz-Amaya
- Department of Materials Engineering, Purdue University. West Lafayette, Indiana 47907, United States
- Birck Nanotechnology Center, Purdue University. West Lafayette, Indiana 47907, United States
| | - Min Zhao
- School of Electrical and Computer Engineering, Purdue University. West Lafayette, Indiana 47907, United States
| | - Jan P Allebach
- School of Electrical and Computer Engineering, Purdue University. West Lafayette, Indiana 47907, United States
| | - George T-C Chiu
- School of Electrical and Computer Engineering, Purdue University. West Lafayette, Indiana 47907, United States
- School of Mechanical Engineering, Purdue University. West Lafayette, Indiana 47907, United States
| | - Lia A Stanciu
- Department of Materials Engineering, Purdue University. West Lafayette, Indiana 47907, United States
- Birck Nanotechnology Center, Purdue University. West Lafayette, Indiana 47907, United States
| |
Collapse
|
66
|
Smith MH, Fologea D. Kinetic Exclusion Assay of Biomolecules by Aptamer Capture. SENSORS (BASEL, SWITZERLAND) 2020; 20:E3442. [PMID: 32570818 PMCID: PMC7348807 DOI: 10.3390/s20123442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 11/23/2022]
Abstract
DNA aptamers are short nucleotide oligomers selected to bind a target ligand with affinity and specificity rivaling that of antibodies. These remarkable features recommend aptamers as candidates for analytical and therapeutic applications that traditionally use antibodies as biorecognition elements. Numerous traditional and emerging analytical techniques have been proposed and successfully implemented to utilize aptamers for sensing purposes. In this work, we exploited the analytical capabilities offered by the kinetic exclusion assay technology to measure the affinity of fluorescent aptamers for their thrombin target and quantify the concentration of analyte in solution. Standard binding curves constructed by using equilibrated mixtures of aptamers titrated with thrombin were fitted with a 1:1 binding model and provided an effective Kd of the binding in the sub-nanomolar range. However, our experimental results suggest that this simple model does not satisfactorily describe the binding process; therefore, the possibility that the aptamer is composed of a mixture of two or more distinct Kd populations is discussed. The same standard curves, together with a four-parameter logistic equation, were used to determine "unknown" concentrations of thrombin in mock samples. The ability to identify and characterize complex binding stoichiometry, together with the determination of target analyte concentrations in the pM-nM range, supports the adoption of this technology for kinetics, equilibrium, and analytical purposes by employing aptamers as biorecognition elements.
Collapse
Affiliation(s)
- Mark H. Smith
- Department of Physics, Boise State University, 1910 University Drive, Boise, ID 83725, USA;
- Biomolecular Sciences Graduate Programs, Boise State University, 1910 University Drive, Boise, ID 83725, USA
| | - Daniel Fologea
- Department of Physics, Boise State University, 1910 University Drive, Boise, ID 83725, USA;
- Biomolecular Sciences Graduate Programs, Boise State University, 1910 University Drive, Boise, ID 83725, USA
| |
Collapse
|
67
|
Svigelj R, Dossi N, Pizzolato S, Toniolo R, Miranda-Castro R, de-Los-Santos-Álvarez N, Lobo-Castañón MJ. Truncated aptamers as selective receptors in a gluten sensor supporting direct measurement in a deep eutectic solvent. Biosens Bioelectron 2020; 165:112339. [PMID: 32729482 DOI: 10.1016/j.bios.2020.112339] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022]
Abstract
Enzyme-linked immunosorbent assays are currently the most popular methods to quantify gluten in foods. Unfortunately, the antibodies used as specific receptors in such methods are not compatible with the usual solvents for the extraction of gluten proteins. In consequence, commercial tests require a high dilution of the sample after the extraction, increasing the limit of quantification and decreasing convenience. In this work, we have rationally truncated an aptamer capable of recognizing gliadin in a deep eutectic solvent (DES). The truncated aptamer is a 19-nucleotides-long DNA that minimizes self-hybridization, allowing the development of an electrochemical sandwich-based sensor for the quantification of gluten in the DES ethaline. The sensor incorporates two identical biotin-labeled truncated aptamers, one of which is immobilized on a carbon screen-printed electrode and the other reports the binding of gliadin after incubation in streptavidin-peroxidase. This sensor can detect gliadin in DES, with a dynamic range between 1 and 100 μg/L and an intra-assay coefficient of variation of 11%. This analytical performance allows the quantification of 20 μg of gluten/kg of food when 1 g of food is extracted with 10 mL of ethaline. We demonstrate the ability of this method to achieve the measurement of gluten in food samples, after the extraction with pure ethaline. The assay is useful for the analysis of residual gluten levels in foods, thus facilitating the evaluation of any potential health risk associated with the consumption of such food by people with celiac disease or other gluten-related disorders.
Collapse
Affiliation(s)
- Rossella Svigelj
- Department of Agrifood, Environmental and Animal Science, University of Udine, Italy
| | - Nicolo Dossi
- Department of Agrifood, Environmental and Animal Science, University of Udine, Italy
| | - Stefania Pizzolato
- Department of Agrifood, Environmental and Animal Science, University of Udine, Italy
| | - Rosanna Toniolo
- Department of Agrifood, Environmental and Animal Science, University of Udine, Italy.
| | - Rebeca Miranda-Castro
- Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, Av. de Roma, 33011, Oviedo, Spain
| | - Noemí de-Los-Santos-Álvarez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, Av. de Roma, 33011, Oviedo, Spain
| | - María Jesús Lobo-Castañón
- Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, Av. de Roma, 33011, Oviedo, Spain.
| |
Collapse
|
68
|
Díaz-Fernández A, Lorenzo-Gómez R, Miranda-Castro R, de-Los-Santos-Álvarez N, Lobo-Castañón MJ. Electrochemical aptasensors for cancer diagnosis in biological fluids - A review. Anal Chim Acta 2020; 1124:1-19. [PMID: 32534661 DOI: 10.1016/j.aca.2020.04.022] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022]
Abstract
The tunability of SELEX procedure is an essential feature to supply bioaffinity receptors (aptamers) almost on demand for analytical and therapeutic purposes. This longstanding ambition is, however, not straightforward. Non-invasive cancer diagnosis, so called liquid biopsy, requires collection of body fluids with minimal or no sample pretreatment. In those raw matrices, aptamers must recognize minute amounts of biomarkers that are not unique entities but large sets of variants evolving with the disease stage. The susceptibility of aptasensors to assay conditions has driven the selection of aptamers to natural environments to ensure their optimum performance in clinical samples. We present herein a compilation of the SELEX procedures in natural milieus. By revising the electrochemical aptasensors applied to clinical samples for cancer diagnosis and tracing back to the original SELEX we analyze whether aptamers raised using these SELEX strategies are being incorporated to the diagnostic devices and how aptasensors are finding their way to a market dominated by antibody-based assays.
Collapse
Affiliation(s)
- Ana Díaz-Fernández
- Dpto. Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, Avenida de Roma, 33011, Oviedo, Spain.
| | - Ramón Lorenzo-Gómez
- Dpto. Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, Avenida de Roma, 33011, Oviedo, Spain.
| | - Rebeca Miranda-Castro
- Dpto. Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, Avenida de Roma, 33011, Oviedo, Spain.
| | - Noemí de-Los-Santos-Álvarez
- Dpto. Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, Avenida de Roma, 33011, Oviedo, Spain.
| | - María Jesús Lobo-Castañón
- Dpto. Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, Avenida de Roma, 33011, Oviedo, Spain.
| |
Collapse
|
69
|
DNA-based nanobiosensors for monitoring of water quality. Int J Hyg Environ Health 2020; 226:113485. [DOI: 10.1016/j.ijheh.2020.113485] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/28/2020] [Accepted: 02/10/2020] [Indexed: 12/20/2022]
|
70
|
Hassan EM, DeRosa MC. Recent advances in cancer early detection and diagnosis: Role of nucleic acid based aptasensors. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115806] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
71
|
Das R, Chaterjee B, Kapil A, Sharma TK. Aptamer-NanoZyme mediated sensing platform for the rapid detection of Escherichia coli in fruit juice. SENSING AND BIO-SENSING RESEARCH 2020. [DOI: 10.1016/j.sbsr.2019.100313] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
72
|
Reid R, Chatterjee B, Das SJ, Ghosh S, Sharma TK. Application of aptamers as molecular recognition elements in lateral flow assays. Anal Biochem 2020; 593:113574. [PMID: 31911046 DOI: 10.1016/j.ab.2020.113574] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/02/2020] [Accepted: 01/02/2020] [Indexed: 02/07/2023]
Abstract
Owing to their ease in operation and fast turnaround time, lateral flow assays (LFAs) are increasingly being used as point-of-care diagnostic tests for variety of analytes. In a majority of these LFAs, antibodies are used as a molecular recognition element. Antibodies have a number of limitations such as high batch-to-batch variation, poor stability, long development time, difficulty in functionalization and need for ethical approval and cold chain. All these factors pose a great challenge to scale up the antibody-based tests. In recent years, the advent of aptamer technology has made a paradigm shift in the point-of-care diagnostics owing to the various advantages of aptamers over antibodies that favour their adaptability on a variety of sensing platforms including the lateral flow. In this review, we have highlighted the advantages of aptamers over antibodies, suitability of aptamers for lateral flow platforms, different types of aptamer-based LFAs and various labels for aptamer-based LFAs. We have also provided a summary of the applications of aptamer technology in LFAs for analytical applications.
Collapse
Affiliation(s)
- Ruth Reid
- Centre for Biological Engineering, Loughborough University, UK
| | - Bandhan Chatterjee
- Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Soon Jyoti Das
- Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Sourav Ghosh
- Centre for Biological Engineering, Loughborough University, UK.
| | - Tarun Kumar Sharma
- Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India.
| |
Collapse
|
73
|
Davydova A, Krasitskaya V, Vorobjev P, Timoshenko V, Tupikin A, Kabilov M, Frank L, Venyaminova A, Vorobyeva M. Reporter-recruiting bifunctional aptasensor for bioluminescent analytical assays. RSC Adv 2020; 10:32393-32399. [PMID: 35516485 PMCID: PMC9056652 DOI: 10.1039/d0ra05117a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/21/2020] [Indexed: 12/26/2022] Open
Abstract
A novel structure-switching bioluminescent 2′-F-RNA aptasensor consists of analyte-binding and obelin-recruiting modules, joined into a bi-specific aptamer construct.
Collapse
Affiliation(s)
- Anna Davydova
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| | - Vasilisa Krasitskaya
- Institute of Biophysics SB RAS
- Federal Research Center “Krasnoyarsk Science Center SB RAS”
- Krasnoyarsk 660036
- Russia
| | - Pavel Vorobjev
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
- Novosibirsk State University
- 630090 Novosibirsk
| | - Valentina Timoshenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| | - Alexey Tupikin
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| | - Marsel Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| | - Ludmila Frank
- Institute of Biophysics SB RAS
- Federal Research Center “Krasnoyarsk Science Center SB RAS”
- Krasnoyarsk 660036
- Russia
- Siberian Federal University
| | - Alya Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| | - Mariya Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| |
Collapse
|
74
|
Wan Y, Zhao J, He J, Lou X. Nano-Affi: a solution-phase, label-free, colorimetric aptamer affinity assay based on binding-inhibited aggregation of gold nanoparticles. Analyst 2020; 145:4276-4282. [DOI: 10.1039/d0an00827c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The ideal way to assess aptamer affinity is when both aptamer and target are in a native state, without the unpredictable interference associated with labelling and surface immobilization.
Collapse
Affiliation(s)
- Yuan Wan
- Department of Chemistry
- Capital Normal University
- Beijing
- China
| | - Jiaxing Zhao
- Department of Chemistry
- Capital Normal University
- Beijing
- China
| | - Junlin He
- State Key Laboratory of Toxicology and Medical Countermeasures
- Beijing Institute of Pharmacology and Toxicology
- Beijing
- China
| | - Xinhui Lou
- Department of Chemistry
- Capital Normal University
- Beijing
- China
| |
Collapse
|
75
|
Tomita S, Sugai H, Mimura M, Ishihara S, Shiraki K, Kurita R. Optical Fingerprints of Proteases and Their Inhibited Complexes Provided by Differential Cross-Reactivity of Fluorophore-Labeled Single-Stranded DNA. ACS APPLIED MATERIALS & INTERFACES 2019; 11:47428-47436. [PMID: 31747245 DOI: 10.1021/acsami.9b17829] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The detection of proteases and their complexes with inhibitor proteins is of great importance for diagnosis and medical-treatment applications. In this study, we report a fingerprint-based sensor using an array of single-stranded DNAs (ssDNAs) labeled with environment-responsive 3'-carboxytetramethylrhodamine (TAMRA) for the identification of proteases. Four TAMRA-modified ssDNAs with different sequences solubilized in two different buffer solutions were incorporated in an array that was capable of generating fluorescent fingerprints unique to the proteases through diverse cross-reactive interactions, allowing the discrimination of (i) 8 proteases and (ii) 12 different mixtures of trypsin and its inhibitor protein (α1-antitrypsin) by multivariate analysis. Constructing an array with TAMRA-modified DNA aptamers that bind to different sites of human thrombin provides fluorescence fingerprints that reflect a reduction of the exposed surface area of thrombin upon complexation with antithrombin III, even in the presence of human serum. We finally demonstrate the potential of hybridization with complementary DNAs as an effective means to easily double the fingerprint information for proteases. Our approach based on the cross-reactive capability of ssDNAs enables high-throughput fingerprint-based sensing that can be flexibly designed and easily constructed, not only for the identification of a variety of proteins including proteases but also for the evaluation of their complexation ability.
Collapse
Affiliation(s)
- Shunsuke Tomita
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology , 1-1-1 Higashi , Tsukuba , Ibaraki 305-8566 , Japan
- DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), DBT-AIST International Center for Translational & Environmental Research (DAICENTER) , National Institute of Advanced Industrial Science and Technology , 1-1-1 Higashi , Tsukuba , Ibaraki 305-8566 , Japan
| | - Hiroka Sugai
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology , 1-1-1 Higashi , Tsukuba , Ibaraki 305-8566 , Japan
| | - Masahiro Mimura
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology , 1-1-1 Higashi , Tsukuba , Ibaraki 305-8566 , Japan
- Faculty of Pure and Applied Sciences , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8573 , Japan
| | - Sayaka Ishihara
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology , 1-1-1 Higashi , Tsukuba , Ibaraki 305-8566 , Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8573 , Japan
| | - Ryoji Kurita
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology , 1-1-1 Higashi , Tsukuba , Ibaraki 305-8566 , Japan
- DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), DBT-AIST International Center for Translational & Environmental Research (DAICENTER) , National Institute of Advanced Industrial Science and Technology , 1-1-1 Higashi , Tsukuba , Ibaraki 305-8566 , Japan
- Faculty of Pure and Applied Sciences , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8573 , Japan
| |
Collapse
|
76
|
Jauset-Rubio M, Botero ML, Skouridou V, Aktas GB, Svobodova M, Bashammakh AS, El-Shahawi MS, Alyoubi AO, O’Sullivan CK. One-Pot SELEX: Identification of Specific Aptamers against Diverse Steroid Targets in One Selection. ACS OMEGA 2019; 4:20188-20196. [PMID: 31815219 PMCID: PMC6893951 DOI: 10.1021/acsomega.9b02412] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/01/2019] [Indexed: 05/10/2023]
Abstract
Aptamers are well-established biorecognition molecules used in a wide variety of applications for the detection of their respective targets. However, individual SELEX processes typically performed for the identification of aptamers for each target can be quite time-consuming, labor-intensive, and costly. An alternative strategy is proposed herein for the simultaneous identification of different aptamers binding distinct but structurally similar targets in one single selection. This one-pot SELEX approach, using the steroids estradiol, progesterone, and testosterone as model targets, was achieved by combining the benefits of counter-SELEX with the power of next-generation sequencing and bioinformatics analysis. The pools from the last stage of the selection were compared in order to discover sequences with preferential abundance in only one of the pools. This led to the identification of aptamer candidates with potential specificity to a single steroid target. Binding studies demonstrated the high affinity of each selected aptamer for its respective target, and low nanomolar range dissociation constants calculated were similar to those previously reported for steroid-binding aptamers selected using traditional SELEX approaches. Finally, the selected aptamers were exploited in microtiter plate assays, achieving nanomolar limits of detection, while the specificity of these aptamers was also demonstrated. Overall, the one-pot SELEX strategy led to the discovery of aptamers for three different steroid targets in one single selection without compromising their affinity or specificity, demonstrating the power of this approach of aptamer discovery for the simultaneous selection of aptamers against multiple targets.
Collapse
Affiliation(s)
- Miriam Jauset-Rubio
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans
26, 43007 Tarragona, Spain
| | - Mary Luz Botero
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans
26, 43007 Tarragona, Spain
| | - Vasso Skouridou
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans
26, 43007 Tarragona, Spain
- E-mail: . Phone: +34977558576 (V.S.)
| | - Gülsen Betül Aktas
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans
26, 43007 Tarragona, Spain
| | - Marketa Svobodova
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans
26, 43007 Tarragona, Spain
| | - Abdulaziz S. Bashammakh
- Department
of Chemistry, Faculty of Science, King Abdulaziz
University, P.O. Box 80203, 21589 Jeddah, Saudi Arabia
| | - Mohammad S. El-Shahawi
- Department
of Chemistry, Faculty of Science, King Abdulaziz
University, P.O. Box 80203, 21589 Jeddah, Saudi Arabia
| | - Abdulrahman O. Alyoubi
- Department
of Chemistry, Faculty of Science, King Abdulaziz
University, P.O. Box 80203, 21589 Jeddah, Saudi Arabia
| | - Ciara K. O’Sullivan
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans
26, 43007 Tarragona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
- E-mail: . Phone: +34977559651 (C.K.O.)
| |
Collapse
|
77
|
Yi J, Wu P, Li G, Xiao W, Li L, He Y, He Y, Ding P, Chen C. A composite prepared from carboxymethyl chitosan and aptamer-modified gold nanoparticles for the colorimetric determination of Salmonella typhimurium. Mikrochim Acta 2019; 186:711. [PMID: 31650251 DOI: 10.1007/s00604-019-3827-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 09/14/2019] [Indexed: 11/27/2022]
Abstract
An aptamer-based assay is described for the determination of Salmonella typhimurium (S. typh). Carboxymethyl chitosan was loaded with amino-modified aptamer against S. typh, and then adsorbed on gold nanoparticles by electrostatic interaction to form a composite that acts as the molecular recognition element. In the presence of S. typh, it will be bound by the aptamer, and this changes the structure of the recognition element. On addition of salt solution, the gold nanoparticles agglomerate so that the color of the solution changes from red to blue. S. typh can be detected via measurement of the absorbance at 550 nm. Absorbance increases linearly with the logarithm of the S. typh concentration in the range from 100 to 109 cfu·mL-1. The limit of detection is 16 cfu·mL-1. The specificity and practicability of the assay were evaluated. The recoveries of S. typh from spiked milk samples are between 92.4 and 97.2%. The analytical results are basically consistent with those of a plate counting method. Graphical abstract Schematic representation of the colorimetric assay for Salmonella typhimuium (S. typh) using carboxymethyl chitosan (CMCS)-aptamer (Apt)-gold nanoparticles (AuNPs) composites.
Collapse
Affiliation(s)
- Jiecan Yi
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China
| | - Pian Wu
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China
| | - Guiyin Li
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541014, Guangxi, China
| | - Wen Xiao
- Hunan Institute of Food Quality Supervision Inspection and Research, Changsha, 410000, Hunan, China
| | - Lei Li
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Yayuan He
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China
| | - Yafei He
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China
| | - Ping Ding
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China.
| | - Cuimei Chen
- School of Public Health, Xiangnan University, Chenzhou, 423000, Hunan, China.
| |
Collapse
|
78
|
Dhiman A, Kumar C, Mishra SK, Sikri K, Datta I, Sharma P, Singh TP, Haldar S, Sharma N, Bansal A, Ahmad Y, Kumar A, Sharma TK, Tyagi JS. Theranostic Application of a Novel G-Quadruplex-Forming DNA Aptamer Targeting Malate Synthase of Mycobacterium tuberculosis. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:661-672. [PMID: 31704587 PMCID: PMC6849348 DOI: 10.1016/j.omtn.2019.09.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/29/2019] [Accepted: 09/27/2019] [Indexed: 12/28/2022]
Abstract
The successful management of tuberculosis (TB) requires efficient diagnosis and treatment. Further, the increasing prevalence of drug-resistant TB highlights the urgent need to develop novel inhibitors against both drug-susceptible and drug-resistant forms of disease. Malate synthase (MS), an enzyme of the glyoxylate pathway, plays a vital role in mycobacterial persistence, and therefore it is considered as an attractive target for novel anti-TB drug development. Recent studies have also ascribed an adhesin function to MS and established it as a potent diagnostic biomarker. In this study, a panel of Mycobacterium tuberculosis (Mtb) MS-specific single-stranded DNA aptamers was identified by Systematic Evolution of Ligands by EXponential enrichment (SELEX). The best-performing G-quadruplex-forming 44-mer aptamer, MS10, was optimized post-SELEX to generate an 11-mer aptamer, MS10-Trunc. This aptamer was characterized by various biochemical, biophysical, and in silico techniques. Its theranostic activity toward Mtb was established using enzyme inhibition, host cell binding, and invasion assays. MS10-Trunc aptamer exhibited high affinity for MS (equilibrium dissociation constant [KD] ∼19 pM) and displayed robust inhibition of MS enzyme activity with IC50 of 251.1 nM and inhibitor constant (Ki) of 230 nM. This aptamer blocked mycobacterial entry into host cells by binding to surface-associated MS. In addition, we have also demonstrated its application in the detection of tuberculous meningitis (TBM) in patients with sensitivity and specificity each of >97%.
Collapse
Affiliation(s)
- Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India; Faculty of Pharmacy, Uttarakhand Technical University, Dehradun 248007, Uttarakhand, India
| | - Chanchal Kumar
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Kriti Sikri
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ishara Datta
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sagarika Haldar
- Department of Experimental Medicine and Biotechnology, PGIMER, Sector 12, Chandigarh 160012, India; Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Neera Sharma
- Department of Biochemistry, Dr. Ram Manohar Lohia Hospital, New Delhi 110001, India
| | - Anjali Bansal
- Department of Pediatrics, Dr. Ram Manohar Lohia Hospital, New Delhi 110001, India
| | - Yusra Ahmad
- Faculty of Pharmacy, Uttarakhand Technical University, Dehradun 248007, Uttarakhand, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Tarun Kumar Sharma
- Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India.
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India; Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India.
| |
Collapse
|
79
|
Nielson CM, Jacobs JM, Orwoll ES. Proteomic studies of bone and skeletal health outcomes. Bone 2019; 126:18-26. [PMID: 30954730 PMCID: PMC7302501 DOI: 10.1016/j.bone.2019.03.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/12/2022]
Abstract
Proteins are an essential part of essentially all biological processes, and there is enormous variation in protein forms and concentrations that is not reflected in DNA or RNA. Recently there have been rapid advances in the ability to measure protein sequence, modification and concentration, particularly with methods based in mass spectrometry. Global measures of proteins in tissues or in the circulation provide a broad assessment of the proteome that can be extremely useful for discovery, and targeted proteomic measures can yield specific and sensitive assessments of specific peptides and proteins. While most proteomic measures are directed at the detection of consensus peptide sequences, mass spectrometry based proteomic methods also allow a detailed examination of the peptide sequence differences that result from genetic variants and that may have important effects on protein function. In evaluating proteomic data, a number of analytical considerations are important, including an understanding of missing data, the challenge of multiple testing and replication, and the use of rapidly evolving methods in systems biology. While proteomics has not yet had a major impact in skeletal research, interesting recent research has used these approaches in the study of bone cell biology and the discovery of biomarkers of skeletal disorders. Proteomics can be expected to have an increasing influence in the study of bone biology and pathophysiology.
Collapse
Affiliation(s)
| | - Jon M Jacobs
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | |
Collapse
|
80
|
Kurseev SA, Solovjev AM, Neumann MM, Medvedko AV, Sakharov IY. Chemiluminescent and Colorimetric Aptamer-Based Assays of Human α-Thrombin. ANAL LETT 2019. [DOI: 10.1080/00032719.2019.1640718] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Sergei A. Kurseev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Anton M. Solovjev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Marina M. Neumann
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | | | - Ivan Yu. Sakharov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
81
|
Díaz-Amaya S, Zhao M, Lin LK, Ostos C, Allebach JP, Chiu GTC, Deering AJ, Stanciu LA. Inkjet Printed Nanopatterned Aptamer-Based Sensors for Improved Optical Detection of Foodborne Pathogens. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805342. [PMID: 31033156 DOI: 10.1002/smll.201805342] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/15/2019] [Indexed: 06/09/2023]
Abstract
The increasing incidence of infectious outbreaks from contaminated food and water supply continues imposing a global burden for food safety, creating a market demand for on-site, disposable, easy-to-use, and cost-efficient devices. Despite of the rapid growth of biosensors field and the generation of breakthrough technologies, more than 80% of the platforms developed at lab-scale never will get to meet the market. This work aims to provide a cost-efficient, reliable, and repeatable approach for the detection of foodborne pathogens in real samples. For the first time an optimized inkjet printing platform is proposed taking advantage of a carefully controlled nanopatterning of novel carboxyl-functionalized aptameric ink on a nitrocellulose substrate for the highly efficient detection of E. coli O157:H7 (25 colony forming units (CFU) mL-1 in pure culture and 233 CFU mL-1 in ground beef) demonstrating the ability to control the variation within ±1 SD for at least 75% of the data collected even at very low concentrations. From the best of the knowledge this work reports the lowest limit of detection of the state of the art for paper-based optical detection of E. coli O157:H7, with enough evidence (p > 0.05) to prove its high specificity at genus, species, strain, and serotype level.
Collapse
Affiliation(s)
- Susana Díaz-Amaya
- Department of Materials Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Min Zhao
- School of Electrical and Computer Engineering, Purdue University West Lafayette, IN, 47907, USA
| | - Li-Kai Lin
- Department of Materials Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Carlos Ostos
- Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Medellín, 050010, Colombia
| | - Jan P Allebach
- School of Electrical and Computer Engineering, Purdue University West Lafayette, IN, 47907, USA
| | - George T-C Chiu
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Amanda J Deering
- Department of Food Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Lia A Stanciu
- Department of Materials Engineering, Purdue University, West Lafayette, IN, 47907, USA
| |
Collapse
|
82
|
Zheng Y, Zhao Y, Di Y, He L, Liao S, Li D, Liu X. In vitro selection of DNA aptamers for the development of chemiluminescence aptasensor for neuron-specific enolase (NSE) detection. RSC Adv 2019; 9:15513-15520. [PMID: 35514829 PMCID: PMC9064317 DOI: 10.1039/c9ra00785g] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/09/2019] [Indexed: 12/02/2022] Open
Abstract
Neuron-specific enolase (NSE) is one of the most commonly used serum tumor biomarker in clinical practice for small cell lung cancer screening, early diagnosis, evaluation of therapeutic efficacy and prognosis. In this study, we obtained DNA aptamers with great affinity and selectivity to NSE via subtractive SELEX approach. After 10 rounds, three candidate aptamers were successfully selected and identified. Their affinities were measured by surface plasmon resonance. Apt-5 aptamer with high binding affinity and good specificity were obtained, which had the dissociation constant (K D) values of 12.26 nM. In addition, electrophoretic mobility shift assay (EMSA) experiment also further indicated that the Apt-5 had a highly specific affinity to NSE without binding to HSA. The circular dichroism (CD) analysis revealed that the three aptamers formed stable B-form, stem-loop conformations. The selected aptamers were used to construct a chemiluminescence (CL) aptasensor biosensing platform to detect NSE from actual serum samples. Experimental results confirmed that the CL immunosensing platform had good sensitivity with detection limits of 1-100 ng mL-1. The results demonstrated that our obtained the Apt-5 aptsensor was highly specific in the detection of NSE in serum samples. The detection limit was 0.1 ng mL-1, which was lower than the 0.25 ng mL-1 limit of the ELISA used at the hospital. Moreover, the aptasensor can contribute to better detection of small cell lung cancer (SCLC).
Collapse
Affiliation(s)
- Yue Zheng
- The First Hospital of Qinhuangdao Affiliated to Hebei Medical University Qinhuangdao 066000 China +86-0335-590-8121
| | - Yunwang Zhao
- The First Hospital of Qinhuangdao Affiliated to Hebei Medical University Qinhuangdao 066000 China +86-0335-590-8121
| | - Ya Di
- The First Hospital of Qinhuangdao Affiliated to Hebei Medical University Qinhuangdao 066000 China +86-0335-590-8121
| | - Lei He
- College of Environment & Chemical Engineering, Yanshan University Qinhuangdao 066004 China
| | - Shiqi Liao
- College of Life Sciences, Lanzhou University Lanzhou 730000 China
| | - Dongdong Li
- College of Life Sciences, Lanzhou University Lanzhou 730000 China
| | - Xiaofei Liu
- Key Laboratory of Polymer Material of Gansu Province, Institute of Polymer, Northwest Normal University Lanzhou 730070 China
| |
Collapse
|
83
|
Moreno M, Fernández-Algar M, Fernández-Chamorro J, Ramajo J, Martínez-Salas E, Briones C. A Combined ELONA-(RT)qPCR Approach for Characterizing DNA and RNA Aptamers Selected against PCBP-2. Molecules 2019; 24:molecules24071213. [PMID: 30925703 PMCID: PMC6480920 DOI: 10.3390/molecules24071213] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/24/2019] [Accepted: 03/26/2019] [Indexed: 11/21/2022] Open
Abstract
Improvements in Systematic Evolution of Ligands by EXponential enrichment (SELEX) technology and DNA sequencing methods have led to the identification of a large number of active nucleic acid molecules after any aptamer selection experiment. As a result, the search for the fittest aptamers has become a laborious and time-consuming task. Herein, we present an optimized approach for the label-free characterization of DNA and RNA aptamers in parallel. The developed method consists in an Enzyme-Linked OligoNucleotide Assay (ELONA) coupled to either real-time quantitative PCR (qPCR, for DNA aptamers) or reverse transcription qPCR (RTqPCR, for RNA aptamers), which allows the detection of aptamer-target interactions in the high femtomolar range. We have applied this methodology to the affinity analysis of DNA and RNA aptamers selected against the poly(C)-binding protein 2 (PCBP-2). In addition, we have used ELONA-(RT)qPCR to quantify the dissociation constant (Kd) and maximum binding capacity (Bmax) of 16 high affinity DNA and RNA aptamers. The Kd values of the high affinity DNA aptamers were compared to those derived from colorimetric ELONA performed in parallel. Additionally, Electrophoretic Mobility Shift Assays (EMSA) were used to confirm the binding of representative PCBP-2-specific RNA aptamers in solution. We propose this ELONA-(RT)qPCR approach as a general strategy for aptamer characterization, with a broad applicability in biotechnology and biomedicine.
Collapse
Affiliation(s)
- Miguel Moreno
- Laboratory of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, 28850 Madrid, Spain.
| | - María Fernández-Algar
- Laboratory of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, 28850 Madrid, Spain.
| | | | - Jorge Ramajo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049 Madrid, Spain.
| | | | - Carlos Briones
- Laboratory of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, 28850 Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain.
| |
Collapse
|
84
|
Das R, Dhiman A, Mishra SK, Haldar S, Sharma N, Bansal A, Ahmad Y, Kumar A, Tyagi JS, Sharma TK. Structural switching electrochemical DNA aptasensor for the rapid diagnosis of tuberculous meningitis. Int J Nanomedicine 2019; 14:2103-2113. [PMID: 30988611 PMCID: PMC6440448 DOI: 10.2147/ijn.s189127] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background Tuberculous meningitis (TBM) is the most devastating manifestation of extra-pulmonary tuberculosis. About 33% of TBM patients die due to very late diagnosis of the disease. Conventional diagnostic methods based on signs and symptoms, cerebrospinal fluid (CSF) smear microscopy or liquid culture suffer from either poor sensitivity or long turnaround time (up to 8 weeks). Therefore, in order to manage the disease efficiently, there is an urgent and unmet need for a rapid and reliable diagnostic test. Methods In the current study, to address the diagnostic challenge of TBM, a highly rapid and sensitive structural switching electrochemical aptasensor was developed by combining the electrochemical property of methylene blue (MB) with the molecular recognition ability of a ssDNA aptamer. To demonstrate the clinical diagnostic utility of the developed aptasensor, a blinded study was performed on 81 archived CSF specimens using differential pulse voltammetry. Results The electrochemical aptasensor developed in the current study can detect as low as 10 pg HspX in CSF background and yields a highly discriminatory response (P<0.0001) for TBM and not-TBM categories with ~95% sensitivity and ~97.5% specificity and has the ability to deliver sample-to-answer in ≤30 minutes. Conclusion In summary, we demonstrate a new aptamer-based electrochemical biosensing strategy by exploiting the target-induced structural switching of H63 SL-2 M6 aptamer and electroactivity of aptamer-tagged MB for the detection of HspX in CSF samples for the diagnosis of TBM. Further, the clinical utility of this sensor could be extended for the diagnosis of other forms of tuberculosis in the near future.
Collapse
Affiliation(s)
- Ritu Das
- AptaBharat Innovation Pvt. Ltd., Faridabad, India,
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi, India, .,Faculty of Pharmacy, Uttarakhand Technical University (UTU), Dehradun, India
| | - Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, India
| | - Sagarika Haldar
- Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, India, , .,Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | | | | | - Yusra Ahmad
- Faculty of Pharmacy, Uttarakhand Technical University (UTU), Dehradun, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, India
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi, India, .,Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, India, ,
| | - Tarun Kumar Sharma
- AptaBharat Innovation Pvt. Ltd., Faridabad, India, .,Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, India, ,
| |
Collapse
|
85
|
Development and characterization of novel 2'-F-RNA aptamers specific to human total and glycated hemoglobins. Anal Biochem 2019; 570:43-50. [PMID: 30742800 DOI: 10.1016/j.ab.2019.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 02/07/2023]
Abstract
Aptamers are short DNA and RNA fragments which bind their molecular targets with affinity and specificity comparable to those of antibodies. Here, we describe the selection of novel 2'-F-RNA aptamers against total human hemoglobin or its glycated form HbA1c. After SELEX and high-throughput sequencing of the enriched libraries, affinities and specificities of candidate aptamers and their truncated variants were examined by the solid-phase bioluminescent assay. As a result, we identified aptamers specific to both hemoglobins or only glycated HbA1c. The developed 2'-F-RNA aptamers have shown their applicability for detection of total and glycated hemoglobin in one sample.
Collapse
|
86
|
Özyurt C, Canbay ZÇ, Dinçkaya E, Evran S. A highly sensitive DNA aptamer-based fluorescence assay for sarcosine detection down to picomolar levels. Int J Biol Macromol 2019; 129:91-97. [PMID: 30738156 DOI: 10.1016/j.ijbiomac.2019.02.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/01/2019] [Accepted: 02/05/2019] [Indexed: 12/23/2022]
Abstract
Sarcosine is an amino acid derivative, which is considered as a key metabolite in various metabolic processes. Therefore, simple and sensitive detection methods are needed for further understanding its metabolic role and diagnostic value. In this study, we developed a novel method that meets the need for practical and sensitive detection in a complex medium mimicking urine conditions. For this aim, we selected sarcosine-specific DNA aptamers using graphene oxide-assisted systemic evolution of ligands by exponential enrichment (GO-SELEX). The candidate aptamers were labeled with 6-carboxyfluorescein (6-FAM) at their 5' ends. Two aptamers, namely 9S and 13S produced a significant fluorescence signal upon sarcosine binding. Both aptamers enabled a sensitive analysis with a detection limit of 0.5 pM. The linear detection ranged between 5 pM and 50 μM for 9S aptamer, while 13S aptamer enabled a wider linear detection range between 5 pM and 500 μM. The aptamer-based assay allowed rapid detection with no need for chemical derivatization of sarcosine and sophisticated instruments. Moreover, the aptamer-based assay was free of interference from urea and human serum albumin.
Collapse
Affiliation(s)
- Canan Özyurt
- Department of Biochemistry, Faculty of Science, Ege University, 35100 Bornova-İzmir, Turkey
| | - Zeynep Çelik Canbay
- Department of Biochemistry, Faculty of Science, Ege University, 35100 Bornova-İzmir, Turkey
| | - Erhan Dinçkaya
- Department of Biochemistry, Faculty of Science, Ege University, 35100 Bornova-İzmir, Turkey
| | - Serap Evran
- Department of Biochemistry, Faculty of Science, Ege University, 35100 Bornova-İzmir, Turkey.
| |
Collapse
|
87
|
Aptamer-mediated colorimetric and electrochemical detection of Pseudomonas aeruginosa utilizing peroxidase-mimic activity of gold NanoZyme. Anal Bioanal Chem 2019; 411:1229-1238. [PMID: 30637436 DOI: 10.1007/s00216-018-1555-z] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/13/2018] [Accepted: 12/18/2018] [Indexed: 01/04/2023]
Abstract
Despite of various advancements in biosensing, a rapid, accurate, and on-site detection of a bacterial pathogen is a real challenge due to the lack of appropriate diagnostic platforms. To address this unmet need, we herein report an aptamer-mediated tunable NanoZyme sensor for the detection of Pseudomonas aeruginosa, an infectious bacterial pathogen. Our approach exploits the inherent peroxidase-like NanoZyme activity of gold nanoparticles (GNPs) in combination with high affinity and specificity of a Pseudomonas aeruginosa-specific aptamer (F23). The presence of aptamer inhibits the inherent peroxidase-like activity of GNPs by simple adsorption on to the surface of GNPs. However, in the presence of cognate target (P. aeruginosa), owing to the high affinity for P. aeruginosa, the aptamer leaves the GNP surface, allowing GNPs to resume their peroxidase-like activity, resulting in oxidation of 3,3',5,5'-tetramethylbenzidine (TMB). As TMB is an electrochemically active species, we have been able to translate the NanoZyme-based method into an ultrasensitive electrochemical assay using disposable carbon screen-printed electrode. This approach is highly sensitive and allows us to rapidly detect P. aeruginosa with a low-end detection limit of ~ 60 CFU/mL in water within 10 min. This generic aptamer-NanoZyme-based electrochemical sensing strategy may, in principle, be applicable for the detection of various other bacterial pathogens.
Collapse
|
88
|
Chatterjee B, Kalyani N, Das S, Anand A, Sharma TK. Nano-realm for point-of-care (POC) bacterial diagnostics. J Microbiol Methods 2019. [DOI: 10.1016/bs.mim.2019.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
89
|
Lavania S, Das R, Dhiman A, Myneedu VP, Verma A, Singh N, Sharma TK, Tyagi JS. Aptamer-Based TB Antigen Tests for the Rapid Diagnosis of Pulmonary Tuberculosis: Potential Utility in Screening for Tuberculosis. ACS Infect Dis 2018; 4:1718-1726. [PMID: 30350564 DOI: 10.1021/acsinfecdis.8b00201] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pulmonary tuberculosis is the most common manifestation of tuberculosis, and to this day, sputum smear microscopy remains the most widely used diagnostic test in resource-limited settings despite its suboptimal sensitivity. Here we report the development of two DNA aptamer-based diagnostic tests, namely aptamer linked immobilized sorbent assay (Aptamer ALISA) and electrochemical sensor (ECS), for the direct detection of a TB biomarker HspX in sputum. First we compared the performance of Aptamer ALISA with anti-HspX polyclonal antibody-based enzyme linked immunosorbent assay (Antibody ELISA) in a blinded study of 314 sputum specimens. Aptamer ALISA displayed a high sensitivity of 94.1% (95% CI 86.8-98%) as compared to 68.2% sensitivity (95% CI 57.2-77.9%) of Antibody ELISA ( p-value < 0.05) using culture as the reference standard without compromising test specificity of 100%. Out of nine smear-negative culture-positive samples, six were positive by Aptamer ALISA and only two were detected by Antibody ELISA. ALISA detected as positive 80 of 85 culture-positive TB as compared to 57 of 81 diagnosed as TB by X-ray ( p-value < 0.0001). These findings demonstrate the superiority of the aptamer-based test over smear microscopy, antibody-based ELISA, and chest X-ray for TB detection ( p-value < 0.0001 for all). Further, we have developed a ∼30 min point-of-care ECS test that discriminates between tuberculous and nontuberculous sputum with a sensitivity of ∼92.3% and specificity of 91.2%. The tests developed in the current study cost ∼$1-3/test and have potential utility in active case finding in high-risk groups and screening for pulmonary TB among presumptive TB subjects.
Collapse
Affiliation(s)
- Surabhi Lavania
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
- School of Biotechnology, Gautam Buddha University, Yamuna Express-way, Greater Noida, Uttar Pradesh 201308, India
| | - Ritu Das
- AptaBharat Innovation Private Limited, Translational Health Science and Technology Institute Incubator, Faridabad, Haryana 121001, India
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
- Faculty of Pharmacy, Uttarakhand Technical University (UTU), Dehradun, Uttarakhand 248007, India
| | - Vithal Prasad Myneedu
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Mehrauli, New Delhi 110030, India
| | - Ajoy Verma
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Mehrauli, New Delhi 110030, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Yamuna Express-way, Greater Noida, Uttar Pradesh 201308, India
| | - Tarun Kumar Sharma
- AptaBharat Innovation Private Limited, Translational Health Science and Technology Institute Incubator, Faridabad, Haryana 121001, India
- Center for Bio-design and Diagnostics, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurugram Express-way, PO box # 04, Faridabad 121001, India
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
- Center for Bio-design and Diagnostics, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurugram Express-way, PO box # 04, Faridabad 121001, India
| |
Collapse
|
90
|
Dhiman A, Anand A, Malhotra A, Khan E, Santra V, Kumar A, Sharma TK. Rational truncation of aptamer for cross-species application to detect krait envenomation. Sci Rep 2018; 8:17795. [PMID: 30542057 PMCID: PMC6290766 DOI: 10.1038/s41598-018-35985-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 11/02/2018] [Indexed: 11/12/2022] Open
Abstract
In majority of snakebite cases, the snake responsible for the bite remains unidentified. The traditional snakebite diagnostics method relies upon clinical symptoms and blood coagulation assays that do not provide accurate diagnosis which is important for epidemiological as well as diagnostics point of view. On the other hand, high batch-to-batch variations in antibody performance limit its application for diagnostic assays. In recent years, nucleic acid aptamers have emerged as a strong chemical rival of antibodies due to several obvious advantages, including but not limited to in vitro generation, synthetic nature, ease of functionalization, high stability and adaptability to various diagnostic formats. In the current study, we have rationally truncated an aptamer developed for α-Toxin of Bungarus multicinctus and demonstrated its utility for the detection of venom of Bungarus caeruleus. The truncated aptamer α-Tox-T2 (26mer) is found to have greater affinity than its 40-mer parent counterpart α-Tox-FL. The truncated aptamers are characterized and compared with parent aptamer for their binding, selectivity, affinity, alteration in secondary structure and limit of detection. Altogether, our findings establish the cross-species application of a DNA aptamer generated for α-Toxin of Bungarus multicinctus (a snake found in Taiwan and China) for the reliable detection of venom of Bungarus caeruleus (a snake found in the Indian subcontinent).
Collapse
Affiliation(s)
- Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi, 110029, India.,Faculty of Pharmacy, Uttarakhand Technical University (UTU), Dehradun, 248007, Uttarakhand, India
| | - Anjali Anand
- Centre for Biodesign and Diagnostics, Translational Health Science and Technology Institute (THSTI), Faridabad, 121001, Haryana, India
| | - Anita Malhotra
- School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Eshan Khan
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Vishal Santra
- Simultala Conservationists (Foundation for Wildlife), Nalikul, Hooghly, 712407, West Bengal, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Tarun Kumar Sharma
- Centre for Biodesign and Diagnostics, Translational Health Science and Technology Institute (THSTI), Faridabad, 121001, Haryana, India.
| |
Collapse
|
91
|
Sun Y, Lu J. Chemiluminescence-based aptasensors for various target analytes. LUMINESCENCE 2018; 33:1298-1305. [PMID: 30378250 DOI: 10.1002/bio.3557] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/06/2018] [Accepted: 09/08/2018] [Indexed: 01/05/2023]
Abstract
Aptamers (DNA or RNA) have complex three-dimensional shapes that can bind to specific targets. Relative to antibodies, aptamers benefit from their low cost of production, easy chemical modification, high chemical stability, reproducibility, and low levels of immunogenicity and toxicity. However, the true value of aptamers lies in their simplicity by which these molecules can be engineered into sensors as bio-recognition elements in diagnostics, drug discovery and therapy, environmental monitoring and food quality testing, etc. Many different types of techniques, such as optical, electrochemical, radiochemical and piezoelectronic methods, have been applied for the design of aptamer-based methods, in which chemiluminescence (CL) detection techniques have become very popular in recent years. This review focuses on the recent advances in the development of aptamer-based CL sensors for different target detection. We highlight specific examples that showcase the use of aptamers in practical applications, and provide the challenges and opportunities in this promising field.
Collapse
Affiliation(s)
- Yue Sun
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, China
| | - Jianzhong Lu
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, China
| |
Collapse
|
92
|
Kumari P, Lavania S, Tyagi S, Dhiman A, Rath D, Anthwal D, Gupta RK, Sharma N, Gadpayle AK, Taneja RS, Sharma L, Ahmad Y, Sharma TK, Haldar S, Tyagi JS. A novel aptamer-based test for the rapid and accurate diagnosis of pleural tuberculosis. Anal Biochem 2018; 564-565:80-87. [PMID: 30352198 DOI: 10.1016/j.ab.2018.10.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/30/2022]
Abstract
Pleural tuberculosis (pTB) is diagnosed by using a composite reference standard (CRS) since microbiological methods are grossly inadequate and an accurate diagnostic test remains an unmet need. The present study aimed to evaluate the utility of Mycobacterium tuberculosis (Mtb) antigen and DNA-based tests for pTB diagnosis. Patients were classified as 'Definite TB', 'Probable TB' and 'Non-TB' disease according to the CRS. We assessed the performance of in-house antigen detection assays, namely antibody-based Enzyme-Linked ImmunoSorbent Assay (ELISA) and aptamer-based Aptamer-Linked Immobilized Sorbent Assay (ALISA), targeting Mtb HspX protein and DNA-based tests namely, Xpert MTB/RIF and in-house devR-qPCR. ROC curves were generated for the combined group of 'Definite TB' and 'Probable TB' vs. 'Non-TB' disease group and cut-off values were derived to provide specificity of ≥98%. The sensitivity of ALISA was ∼93% vs. ∼24% of ELISA (p-value ≤0.0001). devR-qPCR exhibited a sensitivity of 50% vs. ∼22% of Xpert (p-value ≤0.01). This novel aptamer-based ALISA test surpasses the sensitivity criterion and matches the specificity requirement spelt out in the 'Target product profile' for extrapulmonary tuberculosis samples by Unitaid (Sensitivity ≥80%, Specificity 98%). The superior performance of the aptamer-based ALISA test indicates its translational potential to bridge the existing gap in pTB diagnosis.
Collapse
Affiliation(s)
- Pooja Kumari
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Surabhi Lavania
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Shaifali Tyagi
- Center for Bio-design and Diagnostics, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, PO box #04, Faridabad, 121001, India
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India; Faculty of Pharmacy, Uttarakhand Technical University, Dehradun, Uttarakhand, India
| | - Deepak Rath
- Dr. Ram Manohar Lohia Hospital, New Delhi, 110001, India
| | - Divya Anthwal
- Center for Bio-design and Diagnostics, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, PO box #04, Faridabad, 121001, India
| | - Rakesh Kumar Gupta
- Center for Bio-design and Diagnostics, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, PO box #04, Faridabad, 121001, India
| | - Neera Sharma
- Dr. Ram Manohar Lohia Hospital, New Delhi, 110001, India
| | - A K Gadpayle
- Dr. Ram Manohar Lohia Hospital, New Delhi, 110001, India
| | - R S Taneja
- Dr. Ram Manohar Lohia Hospital, New Delhi, 110001, India
| | - Lokesh Sharma
- Dr. Ram Manohar Lohia Hospital, New Delhi, 110001, India
| | - Yusra Ahmad
- Faculty of Pharmacy, Uttarakhand Technical University, Dehradun, Uttarakhand, India
| | - Tarun Kumar Sharma
- Center for Bio-design and Diagnostics, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, PO box #04, Faridabad, 121001, India; AptaBharat Innovation Pvt. Ltd., Translational Health Science and Technology Institute Incubator, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, PO box #04, Faridabad, 121001, India.
| | - Sagarika Haldar
- Center for Bio-design and Diagnostics, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, PO box #04, Faridabad, 121001, India.
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India; Center for Bio-design and Diagnostics, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, PO box #04, Faridabad, 121001, India.
| |
Collapse
|
93
|
Zhou Y, Li W, Tseng Y, Zhang J, Liu J. Developing slow-off dickkopf-1 aptamers for early-diagnosis of hepatocellular carcinoma. Talanta 2018; 194:422-429. [PMID: 30609553 DOI: 10.1016/j.talanta.2018.10.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/25/2018] [Accepted: 10/03/2018] [Indexed: 01/10/2023]
Abstract
In this work, we obtained fast-off and slow-off aptamer recognizing dickkopf-1(DKK1), a promising biomarker for detection of early-stage hepatocellular carcinoma (HCC), with high affinity in a single SELEX procedure. The two types of aptamer possessed distinct characteristics confirmed via different validation methods. In comparison to fast-off aptamers, slow-off aptamers were proven more suitable for aptamer-based ELISA assay. Using slow dissociation SELEX, slow-off aptamers were selectively retained. Meanwhile, a mutant (34del) of slow-off D10 was estimated with picomolar affinity (371.9 pM). The mutant was further truncated into 39nt before pairing with an antibody in the aptamer-based ELISA. The aptamer-target-antibody construction showed similar performance as conventional ELISA with a detection limit of 62.5 pg/ml. Quantification in 60 sera samples with the construction was also correlated with conventional ELISA. The results demonstrated novel DKK1 aptamer could replace capture antibody for potential early HCC diagnosis.
Collapse
Affiliation(s)
- Yin Zhou
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Wenshuai Li
- Department of Digestive Diseases of Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200040, China
| | - Yujen Tseng
- Department of Digestive Diseases of Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200040, China
| | - Jun Zhang
- Department of Digestive Diseases of Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200040, China.
| | - Jie Liu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Digestive Diseases of Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200040, China.
| |
Collapse
|
94
|
Biniuri Y, Albada B, Willner I. Probing ATP/ATP-Aptamer or ATP-Aptamer Mutant Complexes by Microscale Thermophoresis and Molecular Dynamics Simulations: Discovery of an ATP-Aptamer Sequence of Superior Binding Properties. J Phys Chem B 2018; 122:9102-9109. [PMID: 30188731 DOI: 10.1021/acs.jpcb.8b06802] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microscale thermophoresis (MST) is used to follow the dissociation constants corresponding to ATTO 488-labeled adenosine triphosphate (ATP) and the ATP-aptamer or ATP-aptamer mutants that include two binding sites for the ATP ligand. A set of eight ATP-aptamer mutants, where the thymidine bases, within the reported ATP binding aptamer sites, are substituted with cytosine bases, are examined. The MST-derived dissociation constant of ATP to the reported aptamer is Kd = 31 ± 3 μM, whereas most of the aptamer mutants show lower affinity (higher Kd values) toward the ATP ligand. One aptamer mutant reveals, however, a higher affinity toward the ATP ligand, as compared to the reported ATP-aptamer. Molecular dynamics and docking simulations identify the structural features that control the affinities of binding of the ATP ligand to the two binding sites associated with the ATP-aptamer or the ATP-aptamer mutants. The simulated structures suggest that H-bonds between the ATP ligand and G9 and G11 bases, within one binding domain, and the π-π interactions between G6 and the ATP purine moiety and the pyrimidine ring, in the second binding domain, control the affinity of binding interactions between the ATP ligand and the ATP-aptamer or ATP-aptamer mutant. Very good correlation between the computed Kd values and the MST-derived Kd values is found. The ATP-aptamer mutant (consisting of A1→ G, T4 → C, T12 → C, A24 → G, and T27 → C mutations) reveals superior binding affinities toward the ATP ligands ( Kd = 15 ± 1 μM) as compared to the binding affinity of ATP to the reported aptamer. These features of the mutant are supported by molecular dynamics simulations.
Collapse
Affiliation(s)
- Yonatan Biniuri
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Bauke Albada
- Laboratory of Organic Chemistry , Wageningen University & Research , Stippeneng 4 , 6708 WE , The Netherlands
| | - Itamar Willner
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| |
Collapse
|
95
|
Kalra P, Mishra SK, Kaur S, Kumar A, Prasad HK, Sharma TK, Tyagi JS. G-Quadruplex-Forming DNA Aptamers Inhibit the DNA-Binding Function of HupB and Mycobacterium tuberculosis Entry into Host Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:99-109. [PMID: 30245472 PMCID: PMC6148841 DOI: 10.1016/j.omtn.2018.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 08/16/2018] [Accepted: 08/16/2018] [Indexed: 01/26/2023]
Abstract
The entry and survival of Mycobacterium tuberculosis (Mtb) within host cells is orchestrated partly by an essential histone-like protein HupB (Rv2986c). Despite being an essential drug target, the lack of structural information has impeded the development of inhibitors targeting the indispensable and multifunctional C-terminal domain (CTD) of HupB. To bypass the requirement for structural information in the classical drug discovery route, we generated a panel of DNA aptamers against HupB protein through systemic evolution of ligands by exponential (SELEX) enrichment. Two G-quadruplex-forming high-affinity aptamers (HupB-4T and HupB-13T) were identified, each of which bound two distinct sites on full-length HupB, with an estimated KD of ∼1.72 μM and ∼0.17 μM, respectively, for the high-affinity sites. While HupB-4T robustly inhibited DNA-binding activity of HupB in vitro, both the aptamers recognized surface-located HupB and significantly blocked Mtb entry into THP-1 monocytic cells (p < 0.0001). In summary, DNA aptamers generated in this study block DNA-binding activity of HupB, inhibit virulent Mtb infection in host cells, and demonstrate aptamers to be inhibitors of HupB functions. This study also illustrates the utility of SELEX in developing inhibitors against essential targets for whom structural information is not available.
Collapse
Affiliation(s)
- Priya Kalra
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, Delhi 110029, India
| | - Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Madhya Pradesh 453552, India
| | - Surinder Kaur
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, Delhi 110029, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Madhya Pradesh 453552, India
| | | | - Tarun Kumar Sharma
- Centre for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India.
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, Delhi 110029, India; Centre for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India.
| |
Collapse
|
96
|
Generation and application of DNA aptamers against HspX for accurate diagnosis of tuberculous meningitis. Tuberculosis (Edinb) 2018; 112:27-36. [PMID: 30205966 DOI: 10.1016/j.tube.2018.07.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/05/2018] [Accepted: 07/08/2018] [Indexed: 11/20/2022]
Abstract
Tuberculous meningitis (TBM) is the most severe manifestation of tuberculosis and its diagnosis remains a challenge even today due to the lack of an adequate test. HspX antigen of Mycobacterium tuberculosis was previously established as a reliable diagnostic biomarker for TBM in an ELISA test format using anti-HspX polyclonal antibodies. Towards overcoming the limitations of batch-to-batch variation and challenges of scalability in antibody generation, we utilized Systematic Evolution of Ligands by EXponential enrichment (SELEX) to develop high affinity DNA aptamers against HspX as an alternative diagnostic reagent. Post-SELEX optimization of the best-performing aptamer candidate, H63, established its derivative H63 SL-2 M6 to be superior to its parent. Aptamer H63 SL-2 M6 displayed a specific and high affinity interaction with HspX (Kd ∼9.0 × 10-8 M). In an Aptamer Linked Immobilized Sorbent Assay (ALISA), H63 SL-2 M6 significantly differentiated between cerebrospinal fluid specimens from TBM and non-TBM subjects (n = 87, ***p < 0.0001) with ∼100% sensitivity and ∼91% specificity. Notably, ALISA exhibited comparable performance with previously reported antibody-based ELISA and qPCR. Altogether, our findings establish the utility of HspX aptamer for the reliable diagnosis of TBM and pave the way for developing an aptamer-based point-of-care test for TBM.
Collapse
|
97
|
Li H, Jin H, Wan W, Wu C, Wei L. Cancer nanomedicine: mechanisms, obstacles and strategies. Nanomedicine (Lond) 2018; 13:1639-1656. [PMID: 30035660 DOI: 10.2217/nnm-2018-0007] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Targeting nanoparticles to cancers for improved therapeutic efficacy and decreased side effects remains a popular concept in the past decades. Although the enhanced permeability and retention effect serves as a key rationale for all the currently commercialized nanoformulations, it does not enable uniform delivery of nanoparticles to all tumorous regions in all patients with sufficient quantities. Also, the increase in overall survival is often modest. Many factors may influence the delivering process of nanoparticles, which must be taken into consideration for the promise of nanomedicine in patients to be realized. Herein, we review the mechanisms and influencing factors during the delivery of cancer therapeutics and summarize current strategies that have been developed for the fabrication of smart drug delivery systems.
Collapse
Affiliation(s)
- Huafei Li
- Department of Pathology, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, PR China
- Tumor Immunology & Gene Therapy Center, Third Affiliated Hospital of the Second Military Medical University, 225 Changhai Road, Shanghai, 200438, PR China
- International Joint Cancer Institute, Translational Medicine Institute, the Second Military Medical University, 800 Xiangyin Road, Shanghai, 200433, PR China
- School of Life Sciences, Shanghai University, 333 Nanchen Road, Shanghai, 200444, PR China
| | - Hai Jin
- Department of Thoracic Surgery/LaboratoryDiagnosis, First Affiliated Hospital of the Second Military Medical University,168 Changhai Road, Shanghai, 200438, PR China
| | - Wei Wan
- Department of Orthopedic Oncology, Spine Tumor Center, Second Affiliated Hospital of the Second Military Medical University, 415 Fengyang Road, Shanghai, 200003, PR China
| | - Cong Wu
- Department of Thoracic Surgery/LaboratoryDiagnosis, First Affiliated Hospital of the Second Military Medical University,168 Changhai Road, Shanghai, 200438, PR China
| | - Lixin Wei
- Tumor Immunology & Gene Therapy Center, Third Affiliated Hospital of the Second Military Medical University, 225 Changhai Road, Shanghai, 200438, PR China
| |
Collapse
|
98
|
Kaur H, Bruno JG, Kumar A, Sharma TK. Aptamers in the Therapeutics and Diagnostics Pipelines. Theranostics 2018; 8:4016-4032. [PMID: 30128033 PMCID: PMC6096388 DOI: 10.7150/thno.25958] [Citation(s) in RCA: 231] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/16/2018] [Indexed: 12/17/2022] Open
Abstract
Aptamers are short single-stranded DNA or RNA oligonucleotides that can selectively bind to small molecular ligands or protein targets with high affinity and specificity, by acquiring unique three-dimensional structures. Aptamers have the advantage of being highly specific, relatively small in size, non-immunogenic and can be easily stabilized by chemical modifications, thus allowing expansion of their diagnostic and therapeutic potential. Since the invention of aptamers in the early 1990s, great efforts have been made to make them clinically relevant for diseases like macular degeneration, cancer, thrombosis and inflammatory diseases. Furthermore, owing to the aforementioned advantages and unique adaptability of aptamers to point-of-care platforms, aptamer technology has created a stable niche in the field of in vitro diagnostics by enhancing the speed and accuracy of diagnoses. The aim of this review is to give an overview on aptamers, highlight the inherent therapeutic and diagnostic opportunities and challenges associated with them and present various aptamers that have reached therapeutic clinical trials, diagnostic markets or that have immediate translational potential for therapeutics and diagnostics applications.
Collapse
Affiliation(s)
| | - John G. Bruno
- Operational Technologies Corporation, 4100 NW Loop 410, Suite 100, San Antonio, Texas 78229, USA
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Tarun Kumar Sharma
- Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute (THSTI), Faridabad-121001, Haryana, India
| |
Collapse
|
99
|
Samokhvalov AV, Safenkova IV, Eremin SA, Zherdev AV, Dzantiev BB. Measurement of (Aptamer–Small Target) KD Using the Competition between Fluorescently Labeled and Unlabeled Targets and the Detection of Fluorescence Anisotropy. Anal Chem 2018; 90:9189-9198. [DOI: 10.1021/acs.analchem.8b01699] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Alexey V. Samokhvalov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Irina V. Safenkova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Sergei A. Eremin
- Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| |
Collapse
|
100
|
Kalra P, Dhiman A, Cho WC, Bruno JG, Sharma TK. Simple Methods and Rational Design for Enhancing Aptamer Sensitivity and Specificity. Front Mol Biosci 2018; 5:41. [PMID: 29868605 PMCID: PMC5966647 DOI: 10.3389/fmolb.2018.00041] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/13/2018] [Indexed: 12/27/2022] Open
Abstract
Aptamers are structured nucleic acid molecules that can bind to their targets with high affinity and specificity. However, conventional SELEX (Systematic Evolution of Ligands by EXponential enrichment) methods may not necessarily produce aptamers of desired affinity and specificity. Thus, to address these questions, this perspective is intended to suggest some approaches and tips along with novel selection methods to enhance evolution of aptamers. This perspective covers latest novel innovations as well as a broad range of well-established approaches to improve the individual binding parameters (aptamer affinity, avidity, specificity and/or selectivity) of aptamers during and/or post-SELEX. The advantages and limitations of individual aptamer selection methods and post-SELEX optimizations, along with rational approaches to overcome these limitations are elucidated in each case. Further the impact of chosen selection milieus, linker-systems, aptamer cocktails and detection modules utilized in conjunction with target-specific aptamers, on the overall assay performance are discussed in detail, each with its own advantages and limitations. The simple variations suggested are easily available for facile implementation during and/or post-SELEX to develop ultrasensitive and specific assays. Finally, success studies of established aptamer-based assays are discussed, highlighting how they utilized some of the suggested methodologies to develop commercially successful point-of-care diagnostic assays.
Collapse
Affiliation(s)
- Priya Kalra
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India.,Faculty of Pharmacy, Uttarakhand Technical University, Dehradun, India
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - John G Bruno
- Operational Technologies Corporation, San Antonio, TX, United States
| | - Tarun K Sharma
- Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, India.,AptaBharat Innovation Private Limited, Translational Health Science and Technology Institute Incubator, Faridabad, India
| |
Collapse
|