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Dou S, Liu M, Wang H, Zhou S, Marrazza G, Guo Y, Sun X, Darwish IA. Synthesis of dual models multivalent activatable aptamers based on HCR and RCA for ultrasensitive detection of Salmonella typhimurium. Talanta 2024; 275:126101. [PMID: 38631268 DOI: 10.1016/j.talanta.2024.126101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024]
Abstract
Aptamers have superior structural properties and have been widely used in bacterial detection methods. However, the problem of low affinity still exists in complex sample detection. In contrast, hybridization chain reaction (HCR)-based model I and rolling circle amplification (RCA)-based model II multivalent activatable aptamers (multi-Apts) can fulfill the need for low-cost, rapid, highly sensitive and high affinity detection of S. typhimurium. In our research, two models of multi-Apts were designed. First, a monovalent activatable aptamer (mono-Apt) was constructed by fluorescence resonance energy transfer (FRET) with an S. typhimurium aptamer and its complementary chain of BHQ1. Next, the DNA scaffold was obtained by HCR and RCA, and the multi-Apts were obtained by self-assembly of the mono-Apt with a DNA scaffold. In model I, when target was presented, the complementary chain BHQ1 was released due to the binding of multi-Apts to the target and was subsequently adsorbed by UIO66. Finally, a FRET-based fluorescence detection signal was obtained. In mode II, the multi-Apts bound to the target, and the complementary chain BHQ1 was released to become the trigger chain for the next round of amplification of HCR with a fluorescence detection signal. HCR and RCA based multi-Apts were able to detect S. typhimurium as low as 2 CFU mL-1 and 1 CFU mL-1 respectively. Multi-Apts amplification strategy provides a new method for early diagnosis of pathogenic microorganisms in foods.
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Affiliation(s)
- Shouyi Dou
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Mengyue Liu
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Haifang Wang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
| | - Shuxian Zhou
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Giovanna Marrazza
- "Ugo Schiff" Chemistry Department, University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy
| | - Yemin Guo
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China.
| | - Xia Sun
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China.
| | - Ibrahim A Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
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Krissanaprasit A, Mihalko E, Meinhold K, Simpson A, Sollinger J, Pandit S, Dupont DM, Kjems J, Brown AC, LaBean TH. A functional RNA-origami as direct thrombin inhibitor with fast-acting and specific single-molecule reversal agents in vivo model. Mol Ther 2024:S1525-0016(24)00302-2. [PMID: 38720458 DOI: 10.1016/j.ymthe.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 03/29/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Abstract
Injectable anticoagulants are widely used in medical procedures to prevent unwanted blood clotting. However, many lack safe, effective reversal agents. Here, we present new data on a previously described RNA origami-based, direct thrombin inhibitor (HEX01). We describe a new, fast-acting, specific, single-molecule reversal agent (antidote) and present in vivo data for the first time, including efficacy, reversibility, preliminary safety, and initial biodistribution studies. HEX01 contains multiple thrombin-binding aptamers appended on an RNA origami. It exhibits excellent anticoagulation activity in vitro and in vivo. The new single-molecule, DNA antidote (HEX02) reverses anticoagulation activity of HEX01 in human plasma within 30 s in vitro and functions effectively in a murine liver laceration model. Biodistribution studies of HEX01 in whole mice using ex vivo imaging show accumulation mainly in the liver over 24 h and with 10-fold lower concentrations in the kidneys. Additionally, we show that the HEX01/HEX02 system is non-cytotoxic to epithelial cell lines and non-hemolytic in vitro. Furthermore, we found no serum cytokine response to HEX01/HEX02 in a murine model. HEX01 and HEX02 represent a safe and effective coagulation control system with a fast-acting, specific reversal agent showing promise for potential drug development.
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Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, NC 27695, USA.
| | - Emily Mihalko
- Joint Department of Biomedical Engineering, College of Engineering, North Carolina State University and University of North Carolina-Chapel Hill, Raleigh, NC 27695, USA
| | - Katherine Meinhold
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Aryssa Simpson
- Joint Department of Biomedical Engineering, College of Engineering, North Carolina State University and University of North Carolina-Chapel Hill, Raleigh, NC 27695, USA
| | - Jennifer Sollinger
- Joint Department of Biomedical Engineering, College of Engineering, North Carolina State University and University of North Carolina-Chapel Hill, Raleigh, NC 27695, USA
| | - Sanika Pandit
- Joint Department of Biomedical Engineering, College of Engineering, North Carolina State University and University of North Carolina-Chapel Hill, Raleigh, NC 27695, USA
| | - Daniel M Dupont
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000 Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000 Aarhus, Denmark
| | - Ashley C Brown
- Joint Department of Biomedical Engineering, College of Engineering, North Carolina State University and University of North Carolina-Chapel Hill, Raleigh, NC 27695, USA; Comparative Medicine Institute, North Carolina State University and University of North Carolina, Chapel Hill, NC 27695, USA
| | - Thomas H LaBean
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, NC 27695, USA; Comparative Medicine Institute, North Carolina State University and University of North Carolina, Chapel Hill, NC 27695, USA.
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Park SV, Kang B, Lee M, Yoo H, Jo H, Woo S, Oh SS. In vitro selection of a trans aptamer complex for target-responsive fluorescence activation. Anal Chim Acta 2024; 1301:342465. [PMID: 38553123 DOI: 10.1016/j.aca.2024.342465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/23/2024] [Accepted: 03/10/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Most biological molecular complexes consist of multiple functional domains, yet rationally constructing such multifunctional complexes is challenging. Aptamers, the nucleic acid-based functional molecules, can perform multiple tasks including target recognition, conformational changes, and enzymatic activities, while being chemically synthesizable and tunable, and thus provide a basis for engineering enhanced functionalities through combination of multiple units. However, the conventional approach of simply combining aptamer units in a serial manner is susceptible to undesired crosstalk or interference between the aptamer units and to false interactions with non-target molecules; besides, the approach would require additional mechanisms to separate the units if they are desired to function independently. It is clearly a challenge to develop multi-aptamer complexes that preserve independent functions of each unit while avoiding undesired interference and non-specific interactions. RESULTS By directly in vitro selecting a 'trans' aptamer complex, we demonstrate that one aptamer unit ('utility module') can remain hidden or 'inactive' until a target analyte triggers the other unit ('sensing module') and separates the two aptamers. Since the operation of the utility module occurs free from the sensing module, unnecessary crosstalk between the two units can be avoided. Because the utility module is kept inactive until separated from the complex, non-specific interactions of the hidden module with noncognate targets can be naturally prevented. In our demonstration, the sensing module was selected to detect serotonin, a clinically important neurotransmitter, and the target-binding-induced structure-switching of the sensing module reveals and activates the utility module that turns on a fluorescence signal. The aptamer complex exhibited a moderately high affinity and an excellent specificity for serotonin with ∼16-fold discrimination against common neurotransmitter molecules, and displayed strong robustness to perturbations in the design, disallowing nonspecific reactions against various challenges. SIGNIFICANCE This work represents the first example of a trans aptamer complex that was in vitro selected de novo. The trans aptamer complex selected by our strategy does not require chemical modifications or immediate optimization processes to function, because the complex is directly selected to perform desired functions. This strategy should be applicable to a wide range of functional nucleic acid moieties, which will open up diverse applications in biosensing and molecular therapeutics.
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Affiliation(s)
- Soyeon V Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Byunghwa Kang
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Minjong Lee
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Hyebin Yoo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Hyesung Jo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Sungwook Woo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea.
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea.
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Jin S, Chen H, Pan K, Li R, Ma X, Yuan R, Meng X, He H. State-of-the-art electrochemical biosensors based on covalent organic frameworks and their hybrid materials. Talanta 2024; 270:125557. [PMID: 38128284 DOI: 10.1016/j.talanta.2023.125557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
As the development of global population and industry civilization, the accurate and sensitive detection of intended analytes is becoming an important and great challenge in the field of environmental, medical, and public safety. Recently, electrochemical biosensors have been constructed and used in sensing fields, such as antibiotics, pesticides, specific markers of cancer, and so on. Functional materials have been designed and prepared to enhance detection performance. Among all reported materials, covalent organic frameworks (COFs) are emerging as porous crystalline materials to construct electrochemical biosensors, because COFs have many unique advantages, including large surface area, high stability, atom-level designability, and diversity, to achieve a far better sensing performance. In this comprehensive review, we not only summarize state-of-the-art electrochemical biosensors based on COFs and their hybrid materials but also highlight and discuss some typical examples in detail. We finally provide the challenge and future perspective of COFs-based electrochemical biosensors.
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Affiliation(s)
- Shi Jin
- Department of Basic Science, Jilin Jianzhu University, Changchun, 130118, PR China
| | - Hongxu Chen
- College of Material and Textile Engineering, Jiaxing University, Jiaxing, 314001, PR China.
| | - Kexuan Pan
- College of Material and Textile Engineering, Jiaxing University, Jiaxing, 314001, PR China
| | - Ruyu Li
- Department of Materials Science and Engineering, Jilin Jianzhu University, Changchun, 130118, PR China
| | - Xingyu Ma
- Department of Materials Science and Engineering, Jilin Jianzhu University, Changchun, 130118, PR China
| | - Rongrong Yuan
- Department of Materials Science and Engineering, Jilin Jianzhu University, Changchun, 130118, PR China.
| | - Xianshu Meng
- College of Chemistry, Tianjin Key Laboratory of Structure and Performance for Functional Molecules, Tianjin Normal University, Tianjin, 300387, PR China
| | - Hongming He
- College of Chemistry, Tianjin Key Laboratory of Structure and Performance for Functional Molecules, Tianjin Normal University, Tianjin, 300387, PR China.
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Jang SJ, Kim TH. Triple multivalent aptamers within DNA tetrahedron on reduced graphene oxide electrode: Unlocking enhanced sensitivity and accelerated reactions in electrochemical sensing. Biosens Bioelectron 2024; 249:116039. [PMID: 38241797 DOI: 10.1016/j.bios.2024.116039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/21/2024]
Abstract
DNA nanostructures are emerging as promising biosensing platforms due to their programmability, predictable assembly, and compatibility with aptamers for enhanced selectivity. This study focuses on a triple-multivalent aptamer (tApt) complex immobilized on a tetrahedral DNA nanostructure (TDN) and integrated with an electrochemically reduced graphene oxide (ERGO) electrode for highly sensitive mercury ion (Hg2+) detection. Compared to a linear multivalent aptamer-modified electrode (S2/ERGO-GCE), the 3D tApt/ERGO-GCE aptasensor exhibits superior sensitivity, signal amplification, and reaction kinetics. The tApt/ERGO-GCE sensor achieves an exceptional limit of detection (LOD) of 4.1 zM, surpassing the LOD of 0.71 fM for S2/ERGO-GCE. Additionally, the tApt/ERGO-GCE sensor demonstrates faster response times, with a half-saturation time (T1/2) of 6 minutes compared to 17 minutes for S2/ERGO/GCE. The 3D tApt aptamer's superior performance is attributed to its tetrahedral DNA structure integrated on ERGO, providing multiple aptamer binding sites, facilitating oriented immobilization on the electrode surface, and enhancing analyte capture and concentration. In contrast, the linear S2 aptamers lack rigidity, resulting in a disordered orientation on the electrode surface, hindering efficient Hg2+ binding and reducing target molecule binding efficiency. This study underscores the potential of triple-multivalent aptamer-based nanostructures for ultrasensitive and rapid biosensing applications. The tApt/ERGO-GCE aptasensor's exceptional sensitivity, signal amplification, and reaction kinetics make it a promising tool for Hg2+ detection and other biosensing applications.
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Affiliation(s)
- Seung Joo Jang
- Department of Chemistry, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Tae Hyun Kim
- Department of Chemistry, Soonchunhyang University, Asan 31538, Republic of Korea.
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Janghorban M, Aradanas I, Malaeb K, Abuelazm H, Nittala A, Hu J, Murari K, Pandey R. Redox-Concatenated Aptamer Integrated Skin Mimicking Electrochemical Patch for Noninvasive Detection of Cortisol. ACS Sens 2024; 9:799-809. [PMID: 38148619 DOI: 10.1021/acssensors.3c02110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
This research focuses on developing and validating a wearable electrochemical biosensor called the concatenated aptamer integrated skin patch, also known as the Captain Patch. The main objective is to detect cortisol levels in sweat, which can provide valuable insights into an individual's health. The biosensor utilizes a corrugated surface that mimics the skin, allowing for better attachment and an improved electrochemical performance. The study demonstrates the successful application of Captain Patch on the human body by using artificially spiked sweat samples. The results indicate good measurement accuracy and conformity when the patch is worn on the body. However, for long-term usage, the patch needs to be changed every 3-4 h or worn three times a day to enable monitoring of cortisol levels. Despite the need for frequent patch changes, the cost-effectiveness and ease of operation make these skin patches suitable for longitudinal cortisol monitoring and other sweat analytes. By customization of the biorecognition probe, the developed biowearable can be used to monitor a variety of vital biomarkers. Overall, Captain Patch, with its capability of detecting specific health markers such as cortisol, hints at the future potential of wearables to offer valuable data on various other biomarkers. Our approach presents the first step in integrating a cost-effective wearable electrochemical patch integrated with a redox-concatenated aptamer for noninvasive biomarker detection. This personalized approach to monitoring can lead to improved patient outcomes and increased patient engagement in managing their health.
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Affiliation(s)
- Mohammad Janghorban
- Department of Biomedical Engineering, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Irvyne Aradanas
- Department of Biomedical Engineering, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Karem Malaeb
- Department of Biomedical Engineering, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Habiba Abuelazm
- Department of Computer Science, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Aditya Nittala
- Department of Computer Science, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Jinguang Hu
- Department of Chemical Engineering, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Kartikeya Murari
- Department of Biomedical Engineering, University of Calgary, Calgary, AB T2N 1N4, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Electrical and Software Engineering, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Richa Pandey
- Department of Biomedical Engineering, University of Calgary, Calgary, AB T2N 1N4, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
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Gutiérrez-Santana JC, Coria-Jiménez VR. Diagnosis and Therapeutic Strategies Based on Nucleic Acid Aptamers Selected against Pseudomonas aeruginosa: The Challenge of Cystic Fibrosis. ChemMedChem 2024; 19:e202300544. [PMID: 38016927 DOI: 10.1002/cmdc.202300544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 11/30/2023]
Abstract
Antimicrobial resistance (AMR) is a rapidly spreading global health problem, and approximately five million deaths associated with AMR pathogens were identified prior to the COVID-19 pandemic. Pseudomonas aeruginosa has developed increasing AMR, and in patients with cystic fibrosis (CF) colonized by this bacterium, rare phenotypes have emerged that complicate the diagnosis and treatment of the hosts, in addition to multiple associated "epidemic strains" with high morbidities and mortalities. The conjugation of aptamers with fluorochromes or nanostructures has allowed the design of new identification strategies for Pseudomonas aeruginosa with detection limits of up to 1 cell ⋅ mL-1 , and the synergy of aptamers with antibiotics, antimicrobial peptides and nanostructures has exhibited promising therapeutic qualities. Some selected aptamers against this bacterium have shown intrinsic antimicrobial activity. However, these aptamers have been poorly evaluated in clinical isolates and have shown decreased interactions for CF isolates, demonstrating, in these cases, uncommon phenotypes resulting from the selective qualities of this disease as well as the great adaptive capacity of the pathogen. Therefore, finding an aptamer or set of aptamers that have the ability to recognize strange phenotypes of this bacillus is crucial in the battle against AMR.
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Affiliation(s)
- Juan Carlos Gutiérrez-Santana
- Laboratorio de Bacteriología Experimental, Instituto Nacional de Pediatría, Insurgentes sur 3700-C, Col. Insurgentes Cuicuilco Coyoacán, 04530, Ciudad de México, México
| | - Victor Rafael Coria-Jiménez
- Laboratorio de Bacteriología Experimental, Instituto Nacional de Pediatría, Insurgentes sur 3700-C, Col. Insurgentes Cuicuilco Coyoacán, 04530, Ciudad de México, México
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Watkins Z, McHenry A, Heikenfeld J. Wearing the Lab: Advances and Challenges in Skin-Interfaced Systems for Continuous Biochemical Sensing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:223-282. [PMID: 38273210 DOI: 10.1007/10_2023_238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Continuous, on-demand, and, most importantly, contextual data regarding individual biomarker concentrations exemplify the holy grail for personalized health and performance monitoring. This is well-illustrated for continuous glucose monitoring, which has drastically improved outcomes and quality of life for diabetic patients over the past 2 decades. Recent advances in wearable biosensing technologies (biorecognition elements, transduction mechanisms, materials, and integration schemes) have begun to make monitoring of other clinically relevant analytes a reality via minimally invasive skin-interfaced devices. However, several challenges concerning sensitivity, specificity, calibration, sensor longevity, and overall device lifetime must be addressed before these systems can be made commercially viable. In this chapter, a logical framework for developing a wearable skin-interfaced device for a desired application is proposed with careful consideration of the feasibility of monitoring certain analytes in sweat and interstitial fluid and the current development of the tools available to do so. Specifically, we focus on recent advancements in the engineering of biorecognition elements, the development of more robust signal transduction mechanisms, and novel integration schemes that allow for continuous quantitative analysis. Furthermore, we highlight the most compelling and promising prospects in the field of wearable biosensing and the challenges that remain in translating these technologies into useful products for disease management and for optimizing human performance.
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Affiliation(s)
- Zach Watkins
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH, USA.
| | - Adam McHenry
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH, USA
| | - Jason Heikenfeld
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH, USA
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Szymanowski W, Szymanowska A, Bielawska A, Lopez-Berestein G, Rodriguez-Aguayo C, Amero P. Aptamers as Potential Therapeutic Tools for Ovarian Cancer: Advancements and Challenges. Cancers (Basel) 2023; 15:5300. [PMID: 37958473 PMCID: PMC10647731 DOI: 10.3390/cancers15215300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Ovarian cancer (OC) is the most common lethal gynecologic cause of death in women worldwide, with a high mortality rate and increasing incidence. Despite advancements in the treatment, most OC patients still die from their disease due to late-stage diagnosis, the lack of effective diagnostic methods, and relapses. Aptamers, synthetic, short single-stranded oligonucleotides, have emerged as promising anticancer therapeutics. Their ability to selectively bind to target molecules, including cancer-related proteins and receptors, has revolutionized drug discovery and biomarker identification. Aptamers offer unique insights into the molecular pathways involved in cancer development and progression. Moreover, they show immense potential as drug delivery systems, enabling targeted delivery of therapeutic agents to cancer cells while minimizing off-target effects and reducing systemic toxicity. In the context of OC, the integration of aptamers with non-coding RNAs (ncRNAs) presents an opportunity for precise and efficient gene targeting. Additionally, the conjugation of aptamers with nanoparticles allows for accurate and targeted delivery of ncRNAs to specific cells, tissues, or organs. In this review, we will summarize the potential use and challenges associated with the use of aptamers alone or aptamer-ncRNA conjugates, nanoparticles, and multivalent aptamer-based therapeutics for the treatment of OC.
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Affiliation(s)
- Wojciech Szymanowski
- Department of Biotechnology, Medical University of Bialystok, 15-222 Bialystok, Poland; (W.S.); (A.B.)
| | - Anna Szymanowska
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (G.L.-B.); (C.R.-A.)
| | - Anna Bielawska
- Department of Biotechnology, Medical University of Bialystok, 15-222 Bialystok, Poland; (W.S.); (A.B.)
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (G.L.-B.); (C.R.-A.)
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (G.L.-B.); (C.R.-A.)
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Paola Amero
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (G.L.-B.); (C.R.-A.)
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Ji D, Feng H, Liew SW, Kwok CK. Modified nucleic acid aptamers: development, characterization, and biological applications. Trends Biotechnol 2023; 41:1360-1384. [PMID: 37302912 DOI: 10.1016/j.tibtech.2023.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/30/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Aptamers are single-stranded oligonucleotides that bind to their targets via specific structural interactions. To improve the properties and performance of aptamers, modified nucleotides are incorporated during or after a selection process such as systematic evolution of ligands by exponential enrichment (SELEX). We summarize the latest modified nucleotides and strategies used in modified (mod)-SELEX and post-SELEX to develop modified aptamers, highlight the methods used to characterize aptamer-target interactions, and present recent progress in modified aptamers that recognize different targets. We discuss the challenges and perspectives in further advancing the methodologies and toolsets to accelerate the discovery of modified aptamers, improve the throughput of aptamer-target characterization, and expand the functional diversity and complexity of modified aptamers.
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Affiliation(s)
- Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Hengxin Feng
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
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11
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Cai D, Chen GL, Wang T, Zhang KH. Combination of multiple nucleic acid aptamers for precision detection of tumors based on optical methods. J Cancer Res Clin Oncol 2023; 149:7895-7903. [PMID: 36809501 DOI: 10.1007/s00432-023-04646-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 02/09/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND AND PURPOSE Nucleic acid aptamers are a novel molecular recognition tool that is functionally similar to antibodies but superior to antibodies in terms of thermal stability, structural modification, preparation, and cost, and therefore hold great promise for molecular detection. However, due to the limitations of a single aptamer in molecular detection, the multiple aptamer combination for bioanalysis has received much attention. Here, we reviewed the progress of tumor precision detection based on the combination of multiple nucleic acid aptamers and optical methods and discussed its challenges and prospects. METHODS The relevant literature in PubMed was collected and reviewed. RESULTS The combination of two or more aptamers with modern nanomaterials and analytical methods allows the fabrication of various detection systems for the simultaneous detection of different structural domains of a substance and/or different substances, including soluble tumor markers, tumor cell surface and intracellular markers, circulating tumor cells, and other tumor-related biomolecules, which has great potential for application in efficient and precise tumor detection. CONCLUSION The combination of multiple nucleic acid aptamers provides a new approach for the precise detection of tumors and will play an important role in precision medicine for tumors.
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Affiliation(s)
- Dan Cai
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Jiangxi Institute of Gastroenterology and Hepatology, No 17, Yongwai Zheng Street, Nanchang, 330006, Jiangxi, China
| | - Gui-Lin Chen
- Department of Anorectal Surgery, Chinese People's Liberation Army Joint Security Force Hospital No. 908, No 1028, Jinggangshan Avenue, Nanchang, China
| | - Ting Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Jiangxi Institute of Gastroenterology and Hepatology, No 17, Yongwai Zheng Street, Nanchang, 330006, Jiangxi, China
| | - Kun-He Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Jiangxi Institute of Gastroenterology and Hepatology, No 17, Yongwai Zheng Street, Nanchang, 330006, Jiangxi, China.
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12
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Spirov AV, Myasnikova EM. Problem of Domain/Building Block Preservation in the Evolution of Biological Macromolecules and Evolutionary Computation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:1345-1362. [PMID: 35594219 DOI: 10.1109/tcbb.2022.3175908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Structurally and functionally isolated domains in biological macromolecular evolution, both natural and artificial, are largely similar to "schemata", building blocks (BBs), in evolutionary computation (EC). The problem of preserving in subsequent evolutionary searches the already found domains / BBs is well known and quite relevant in biology as well as in EC. Both biology and EC are seeing parallel and independent development of several approaches to identifying and preserving previously identified domains / BBs. First, we notice the similarity of DNA shuffling methods in synthetic biology and multi-parent recombination algorithms in EC. Furthermore, approaches to computer identification of domains in proteins that are being developed in biology can be aligned with BB identification methods in EC. Finally, approaches to chimeric protein libraries optimization in biology can be compared to evolutionary search methods based on probabilistic models in EC. We propose to validate the prospects of mutual exchange of ideas and transfer of algorithms and approaches between evolutionary systems biology and EC in these three principal directions. A crucial aim of this transfer is the design of new advanced experimental techniques capable of solving more complex problems of in vitro evolution.
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13
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Zou Z, Younas T, Dumsday G, Haritos VS, He L. Rapid production of multimeric RNA aptamers stabilized by a designed pseudo-circular structure in E. coli. Biotechnol J 2023; 18:e2200390. [PMID: 36427490 DOI: 10.1002/biot.202200390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022]
Abstract
RNA aptamers bind specifically and selectively to various macromolecules, cell surfaces, and viruses and find broad applications as biosensors, diagnostics, and in therapeutic treatments and drug delivery. Currently, RNA aptamer production is via in vitro methods. Herein, a new E. coli-based approach has been demonstrated for the rapid production of multimeric RNA aptamer transcripts that are protected from degradation by burying the 5' and 3' ends of the transcript in a designed double-stranded spacer. Multimeric and fluorescent RNA aptamers were produced stably in vivo and readily isolated from RNase III-deficient cells, and their full functionalities were shown by binding assays and fluorescence measurements. This approach shows promise as a rapid and scalable bioprocess for the production of RNA aptamers at low cost.
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Affiliation(s)
- Zongsheng Zou
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, Australia
| | - Tayyaba Younas
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, Australia
| | - Geoff Dumsday
- CSIRO Manufacturing, Ian Wark Laboratory, Clayton, VIC, Australia
| | - Victoria S Haritos
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, Australia
| | - Lizhong He
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, Australia
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14
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Development and classification of RNA aptamers for therapeutic purposes: an updated review with emphasis on cancer. Mol Cell Biochem 2022; 478:1573-1598. [DOI: 10.1007/s11010-022-04614-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/10/2022] [Indexed: 11/26/2022]
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15
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Amanat M, Nemeth CL, Fine AS, Leung DG, Fatemi A. Antisense Oligonucleotide Therapy for the Nervous System: From Bench to Bedside with Emphasis on Pediatric Neurology. Pharmaceutics 2022; 14:2389. [PMID: 36365206 PMCID: PMC9695718 DOI: 10.3390/pharmaceutics14112389] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 09/05/2023] Open
Abstract
Antisense oligonucleotides (ASOs) are disease-modifying agents affecting protein-coding and noncoding ribonucleic acids. Depending on the chemical modification and the location of hybridization, ASOs are able to reduce the level of toxic proteins, increase the level of functional protein, or modify the structure of impaired protein to improve function. There are multiple challenges in delivering ASOs to their site of action. Chemical modifications in the phosphodiester bond, nucleotide sugar, and nucleobase can increase structural thermodynamic stability and prevent ASO degradation. Furthermore, different particles, including viral vectors, conjugated peptides, conjugated antibodies, and nanocarriers, may improve ASO delivery. To date, six ASOs have been approved by the US Food and Drug Administration (FDA) in three neurological disorders: spinal muscular atrophy, Duchenne muscular dystrophy, and polyneuropathy caused by hereditary transthyretin amyloidosis. Ongoing preclinical and clinical studies are assessing the safety and efficacy of ASOs in multiple genetic and acquired neurological conditions. The current review provides an update on underlying mechanisms, design, chemical modifications, and delivery of ASOs. The administration of FDA-approved ASOs in neurological disorders is described, and current evidence on the safety and efficacy of ASOs in other neurological conditions, including pediatric neurological disorders, is reviewed.
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Affiliation(s)
- Man Amanat
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christina L. Nemeth
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amena Smith Fine
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Doris G. Leung
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Genetic Muscle Disorders, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Ali Fatemi
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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16
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Chen J, Xu J, Xiang J, Wan T, Deng H, Li D. A multivalent activatable aptamer probe with ultralow background signal and high sensitivity for diagnosis of lung adenocarcinoma. Talanta 2022. [DOI: 10.1016/j.talanta.2022.124056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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17
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Liu R, Zhang F, Sang Y, Katouzian I, Jafari SM, Wang X, Li W, Wang J, Mohammadi Z. Screening, identification, and application of nucleic acid aptamers applied in food safety biosensing. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.03.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Amini R, Zhang Z, Li J, Gu J, Brennan J, Li Y. Aptamers for SARS-CoV-2: Isolation, Characterization, and Diagnostic and Therapeutic Developments. ANALYSIS & SENSING 2022; 2:e202200012. [PMID: 35574520 PMCID: PMC9082509 DOI: 10.1002/anse.202200012] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/19/2022] [Indexed: 12/17/2022]
Abstract
The SARS‐CoV‐2 virus and COVID‐19 pandemic continue to demand effective diagnostic and therapeutic solutions. Finding these solutions requires highly functional molecular recognition elements. Nucleic acid aptamers represent a possible solution. Characterized by their high affinity and specificity, aptamers can be rapidly identified from random‐sequence nucleic acid libraries. Over the past two years, many labs around the world have rushed to create diverse aptamers that target two important structural proteins of SARS‐CoV‐2: the spike (S) protein and nucleocapsid (N) protein. These have led to the identification of many aptamers that show real promise for the development of diagnostic tests and therapeutic agents for SARS‐CoV‐2. Herein we review all these developments, with a special focus on the development of diverse aptasensors for detecting SARS‐CoV‐2. These include electrochemical and optical sensors, lateral flow devices, and aptamer‐linked immobilized sorbent assays.
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Affiliation(s)
- Ryan Amini
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Zijie Zhang
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Jiuxing Li
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Jimmy Gu
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - John Brennan
- McMaster University Biointerfaces Institute CANADA
| | - Yingfu Li
- McMaster University Biochemistry and Biomedical Sciences 1280 Main Street West L8S4K1 Hamilton CANADA
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19
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Qian S, Chang D, He S, Li Y. Aptamers from random sequence space: Accomplishments, gaps and future considerations. Anal Chim Acta 2022; 1196:339511. [DOI: 10.1016/j.aca.2022.339511] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 02/07/2023]
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20
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Xu J, Xiang J, Chen J, Wan T, Deng H, Li D. High sensitivity detection of tumor cells in biological samples using a multivalent aptamer strand displacement strategy. Analyst 2022; 147:634-644. [PMID: 35040831 DOI: 10.1039/d1an01949j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Monitoring the cell surface-expressed nucleolin facilitates early cancer diagnosis. Herein, we developed a multivalent aptamer displacement strand duplex strategy on cell membranes using a multi-receptor co-recognition design for improving the sensitivity and specificity of cancer cell recognition with an ultra-low background. The AS1411 aptamer labeled with the FAM fluorophore can be quenched using a partial complementary sequence modified with a BHQ1 tag which is partially hybridized with the AS1411 aptamer to create a receptor-activating aptamer. The multi-AS1411 activable probe based on the strand displacement strategy was constructed using multiple copies of the structure-switching AS1411 aptamer (bearing a short poly-A tail) linked together using the poly-T long chain (as a scaffold) which was synthesized by Terminal Deoxynucleotidyl Transferase (TDT)-mediated extension. We demonstrated the promising efficacy and sensitivity of our method in recognizing tumor cells in both cell mixtures and clinical cytology specimens. Due to its simple and fast operation with excellent cell recognition sensitivity and accuracy, it is expected to achieve the detection of low abundance target cells. Our approach will have broad application in clinical rapid detection and personalized medicine.
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Affiliation(s)
- Jieru Xu
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Jiahui Xiang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Jialing Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Tao Wan
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Hongli Deng
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Dairong Li
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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21
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Spirov AV, Myasnikova EM. Heuristic algorithms in evolutionary computation and modular organization of biological macromolecules: Applications to in vitro evolution. PLoS One 2022; 17:e0260497. [PMID: 35085255 PMCID: PMC8794168 DOI: 10.1371/journal.pone.0260497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
Evolutionary computing (EC) is an area of computer sciences and applied mathematics covering heuristic optimization algorithms inspired by evolution in Nature. EC extensively study all the variety of methods which were originally based on the principles of selectionism. As a result, many new algorithms and approaches, significantly more efficient than classical selectionist schemes, were found. This is especially true for some families of special problems. There are strong arguments to believe that EC approaches are quite suitable for modeling and numerical analysis of those methods of synthetic biology and biotechnology that are known as in vitro evolution. Therefore, it is natural to expect that the new algorithms and approaches developed in EC can be effectively applied in experiments on the directed evolution of biological macromolecules. According to the John Holland's Schema theorem, the effective evolutionary search in genetic algorithms (GA) is provided by identifying short schemata of high fitness which in the further search recombine into the larger building blocks (BBs) with higher and higher fitness. The multimodularity of functional biological macromolecules and the preservation of already found modules in the evolutionary search have a clear analogy with the BBs in EC. It seems reasonable to try to transfer and introduce the methods of EC, preserving BBs and essentially accelerating the search, into experiments on in vitro evolution. We extend the key instrument of the Holland's theory, the Royal Roads fitness function, to problems of the in vitro evolution (Biological Royal Staircase, BioRS, functions). The specific version of BioRS developed in this publication arises from the realities of experimental evolutionary search for (DNA-) RNA-devices (aptazymes). Our numerical tests showed that for problems with the BioRS functions, simple heuristic algorithms, which turned out to be very effective for preserving BBs in GA, can be very effective in in vitro evolution approaches. We are convinced that such algorithms can be implemented in modern methods of in vitro evolution to achieve significant savings in time and resources and a significant increase in the efficiency of evolutionary search.
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Affiliation(s)
- Alexander V. Spirov
- I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Sciences, St. Petersburg, Russia
- The Institute of Scientific Information for Social Sciences RAS, Moscow, Russia
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22
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Dillen A, Lammertyn J. Paving the way towards continuous biosensing by implementing affinity-based nanoswitches on state-dependent readout platforms. Analyst 2022; 147:1006-1023. [DOI: 10.1039/d1an02308j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combining affinity-based nanoswitches with state-dependent readout platforms allows for continuous biosensing and acquisition of real-time information about biochemical processes occurring in the environment of interest.
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Affiliation(s)
- Annelies Dillen
- KU Leuven, Department of Biosystems – Biosensors Group, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
| | - Jeroen Lammertyn
- KU Leuven, Department of Biosystems – Biosensors Group, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
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23
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Zhao J, Song W, Tang Z, Chen X. Macromolecular Effects in Medicinal Chemistry ※. ACTA CHIMICA SINICA 2022. [DOI: 10.6023/a21120602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Qu N, Ying Y, Qin J, Chen AK. Rational design of self-assembled RNA nanostructures for HIV-1 virus assembly blockade. Nucleic Acids Res 2021; 50:e44. [PMID: 34967412 PMCID: PMC9071489 DOI: 10.1093/nar/gkab1282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/16/2021] [Accepted: 12/15/2021] [Indexed: 11/14/2022] Open
Abstract
Many pathological processes are driven by RNA-protein interactions, making such interactions promising targets for molecular interventions. HIV-1 assembly is one such process, in which the viral genomic RNA interacts with the viral Gag protein and serves as a scaffold to drive Gag multimerization that ultimately leads to formation of a virus particle. Here, we develop self-assembled RNA nanostructures that can inhibit HIV-1 virus assembly, achieved through hybridization of multiple artificial small RNAs with a stem-loop structure (STL) that we identify as a prominent ligand of Gag that can inhibit virus particle production via STL-Gag interactions. The resulting STL-decorated nanostructures (double and triple stem-loop structures denoted as Dumbbell and Tribell, respectively) can elicit more pronounced viral blockade than their building blocks, with the inhibition arising as a result of nanostructures interfering with Gag multimerization. These findings could open up new avenues for RNA-based therapy.
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Affiliation(s)
- Na Qu
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Yachen Ying
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China.,Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.,National Biomedical Imaging Center, Peking University, Beijing 100871, China
| | - Jinshan Qin
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China.,Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.,National Biomedical Imaging Center, Peking University, Beijing 100871, China
| | - Antony K Chen
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China.,National Biomedical Imaging Center, Peking University, Beijing 100871, China
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25
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Valero J, Civit L, Dupont DM, Selnihhin D, Reinert LS, Idorn M, Israels BA, Bednarz AM, Bus C, Asbach B, Peterhoff D, Pedersen FS, Birkedal V, Wagner R, Paludan SR, Kjems J. A serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry. Proc Natl Acad Sci U S A 2021; 118:e2112942118. [PMID: 34876524 PMCID: PMC8685691 DOI: 10.1073/pnas.2112942118] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 12/23/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has created an urgent need for new technologies to treat COVID-19. Here we report a 2'-fluoro protected RNA aptamer that binds with high affinity to the receptor binding domain (RBD) of SARS-CoV-2 spike protein, thereby preventing its interaction with the host receptor ACE2. A trimerized version of the RNA aptamer matching the three RBDs in each spike complex enhances binding affinity down to the low picomolar range. Binding mode and specificity for the aptamer-spike interaction is supported by biolayer interferometry, single-molecule fluorescence microscopy, and flow-induced dispersion analysis in vitro. Cell culture experiments using virus-like particles and live SARS-CoV-2 show that the aptamer and, to a larger extent, the trimeric aptamer can efficiently block viral infection at low concentration. Finally, the aptamer maintains its high binding affinity to spike from other circulating SARS-CoV-2 strains, suggesting that it could find widespread use for the detection and treatment of SARS-CoV-2 and emerging variants.
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Affiliation(s)
- Julián Valero
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark;
- Centre for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus DK-8000, Denmark
| | - Laia Civit
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
| | - Daniel M Dupont
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
| | - Denis Selnihhin
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Line S Reinert
- Department of Biomedicine, Aarhus University DK-8000 Aarhus, Denmark
| | - Manja Idorn
- Department of Biomedicine, Aarhus University DK-8000 Aarhus, Denmark
| | - Brett A Israels
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
- Department of Chemistry, Aarhus University, DK-8000, Aarhus, Denmark
| | - Aleksandra M Bednarz
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
- Department of Chemistry, Aarhus University, DK-8000, Aarhus, Denmark
| | - Claus Bus
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
| | - Benedikt Asbach
- Institute of Medical Microbiology and Hygiene/Molecular Microbiology (Virology), Regensburg University 93053 Regensburg, Germany
| | - David Peterhoff
- Institute of Medical Microbiology and Hygiene/Molecular Microbiology (Virology), Regensburg University 93053 Regensburg, Germany
| | - Finn S Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Victoria Birkedal
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
- Department of Chemistry, Aarhus University, DK-8000, Aarhus, Denmark
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene/Molecular Microbiology (Virology), Regensburg University 93053 Regensburg, Germany
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg 93053, Germany
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University DK-8000 Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark;
- Centre for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus DK-8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
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26
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Yoshikawa AM, Rangel A, Feagin T, Chun EM, Wan L, Li A, Moekl L, Wu D, Eisenstein M, Pitteri S, Soh HT. Discovery of indole-modified aptamers for highly specific recognition of protein glycoforms. Nat Commun 2021; 12:7106. [PMID: 34876561 PMCID: PMC8651674 DOI: 10.1038/s41467-021-26933-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
Glycosylation is one of the most abundant forms of post-translational modification, and can have a profound impact on a wide range of biological processes and diseases. Unfortunately, efforts to characterize the biological function of such modifications have been greatly hampered by the lack of affinity reagents that can differentiate protein glycoforms with robust affinity and specificity. In this work, we use a fluorescence-activated cell sorting (FACS)-based approach to generate and screen aptamers with indole-modified bases, which are capable of recognizing and differentiating between specific protein glycoforms. Using this approach, we were able to select base-modified aptamers that exhibit strong selectivity for specific glycoforms of two different proteins. These aptamers can discriminate between molecules that differ only in their glycan modifications, and can also be used to label glycoproteins on the surface of cultured cells. We believe our strategy should offer a generally-applicable approach for developing useful reagents for glycobiology research. Glycosylation is an abundant form of post-translational modification. Here the authors present a generalizable workflow for the selection of indole-modified aptamers that can recognize protein glycoforms with high specificity.
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Affiliation(s)
- Alex M Yoshikawa
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Alexandra Rangel
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Trevor Feagin
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Elizabeth M Chun
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Leighton Wan
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Anping Li
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Leonhard Moekl
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Diana Wu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Michael Eisenstein
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA.,Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Sharon Pitteri
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - H Tom Soh
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA. .,Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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27
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Behbahani M, Mohabatkar H, Hosseini B. In silico design of quadruplex aptamers against the spike protein of SARS-CoV-2. INFORMATICS IN MEDICINE UNLOCKED 2021; 26:100757. [PMID: 34664030 PMCID: PMC8514331 DOI: 10.1016/j.imu.2021.100757] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022] Open
Abstract
Nucleic acid aptamers are short sequences of nucleic acid ligands that bind to a specific target molecule. Aptamers are experimentally nominated using the well-designed SELEX (systematic evolution of ligands by exponential enrichment) method. Here, we designed a new method for diagnosis and blocking SARS-CoV-2 based on G-quadruplex aptamer. This aptamer was developed against the receptor-binding domain (RBD) region of the spike protein. In the current study, ten quadruplex DNA aptamers entitled AP1, AP2, AP3, AP4, AP5, AP6, AP7, AP8, AP9, and AP10 were designed in silico and had high HADDOCK scores. One quadruplex aptamer sequence (AP1) was selected based on the interaction with RBD of SARS-CoV-2. Results showed that AP1 aptamer could be used as an agent in the diagnosis and therapy of SARS-CoV-2, although more works are still needed.
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Affiliation(s)
- Mandana Behbahani
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jareeb St., Isfahan, 81746-73441, Iran
| | - Hassan Mohabatkar
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jareeb St., Isfahan, 81746-73441, Iran
| | - Barumand Hosseini
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jareeb St., Isfahan, 81746-73441, Iran
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Morozov D, Mironov V, Moryachkov RV, Shchugoreva IA, Artyushenko PV, Zamay GS, Kolovskaya OS, Zamay TN, Krat AV, Molodenskiy DS, Zabluda VN, Veprintsev DV, Sokolov AE, Zukov RA, Berezovski MV, Tomilin FN, Fedorov DG, Alexeev Y, Kichkailo AS. The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:316-327. [PMID: 34458013 PMCID: PMC8379633 DOI: 10.1016/j.omtn.2021.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/17/2021] [Indexed: 12/12/2022]
Abstract
Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.
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Affiliation(s)
- Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Vladimir Mironov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Roman V. Moryachkov
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Irina A. Shchugoreva
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Polina V. Artyushenko
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Galina S. Zamay
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Olga S. Kolovskaya
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Tatiana N. Zamay
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Alexey V. Krat
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Dmitry S. Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
| | - Vladimir N. Zabluda
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Dmitry V. Veprintsev
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Alexey E. Sokolov
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Ruslan A. Zukov
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
| | - Felix N. Tomilin
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8568, Japan
| | - Yuri Alexeev
- Computational Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Anna S. Kichkailo
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
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Li HK, Ye HL, Zhao XX, Sun XL, Zhu QQ, Han ZY, Yuan R, He H. Artful union of a zirconium-porphyrin MOF/GO composite for fabricating an aptamer-based electrochemical sensor with superb detecting performance. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.02.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Animesh S, Singh YD. A Comprehensive Study on Aptasensors For Cancer Diagnosis. Curr Pharm Biotechnol 2021; 22:1069-1084. [PMID: 32957883 DOI: 10.2174/1389201021999200918152721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/23/2020] [Accepted: 08/18/2020] [Indexed: 12/24/2022]
Abstract
Cancer is the most devastating disease in the present scenario, killing millions of people every year. Early detection, accurate diagnosis, and timely treatment are considered to be the most effective ways to control this disease. Rapid and efficient detection of cancer at their earliest stage is one of the most significant challenges in cancer detection and cure. Numerous diagnostic modules have been developed to detect cancer cells early. As nucleic acid equivalent to antibodies, aptamers emerge as a new class of molecular probes that can identify cancer-related biomarkers or circulating rare cancer/ tumor cells with very high specificity and sensitivity. The amalgamation of aptamers with the biosensing platforms gave birth to "Aptasensors." The advent of highly sensitive aptasensors has opened up many new promising point-of-care diagnostics for cancer. This comprehensive review focuses on the newly developed aptasensors for cancer diagnostics.
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Affiliation(s)
- Sambhavi Animesh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Yengkhom D Singh
- Department of Post-Harvest Technology, College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh, 791102, India
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Mashayekhi K, Sankian M, Haftcheshmeh SM, Taheri RA, Hassanpour K, Farnoosh G. A cross-linked anti-TNF-α aptamer for neutralization of TNF-α-induced cutaneous Shwartzman phenomenon: A simple and novel approach for improving aptamers' affinity and efficiency. Biotechnol Prog 2021; 37:e3191. [PMID: 34218531 DOI: 10.1002/btpr.3191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/26/2021] [Accepted: 07/01/2021] [Indexed: 11/08/2022]
Abstract
To increase the efficiency of aptamers to their targets, a simple and novel method has been developed based on aptamer oligomerization. To this purpose, previously anti-human TNF-α aptamer named T1-T4 was trimerized through a trimethyl aconitate core for neutralization of in vitro and in vivo of TNF-α. At first, 54 mer T1-T4 aptamers with 5'-NH2 groups were covalently coupled to three ester residues in the trimethyl aconitate. In vitro activity of novel anti-TNF-α aptamer and its dissociation constant (Kd ) was done using the L929 cell cytotoxicity assay. In vivo anti-TNF-α activity of new oligomerized aptamer was assessed in a mouse model of cutaneous Shwartzman. Anchoring of three T1-T4 aptamers to trimethyl aconitate substituent results in formation of the 162 mer fragment, which was well revealed by gel electrophoresis. In vitro study indicated that the trimerization of T1-T4 aptamer significantly improved its anti-TNF-α activity compared to non-modified aptamers (P < 0.0001) from 40% to 60%. The determination of Kd showed that trimerization could effectively enhance Kd of aptamer from 67 nM to 36 nM. In vivo study showed that trimer aptamer markedly reduced mean scar size from 15.2 ± 1.2 mm to 1.6 ± 0.1 mm (P < 0.0001), which prevent the formation of skin lesions. In vitro and in vivo studies indicate that trimerization of anti-TNF-α aptamer with a novel approach could improve the anti-TNF-α activity and therapeutic efficacy. According to our findings, a new anti-TNF-α aptamer described here could be considered an appropriate therapeutic agent in treating several inflammatory diseases.
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Affiliation(s)
- Kazem Mashayekhi
- Immunology of Infectious Diseases Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran.,Department of Immunology, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Mojtaba Sankian
- Immuno-Biochemistry lab, Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Ramezan Ali Taheri
- Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Kazem Hassanpour
- Medical School, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Gholamreza Farnoosh
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Yoshitomi T, Wakui K, Miyakawa M, Yoshimoto K. Design strategy of antidote sequence for bivalent aptamer: Rapid neutralization of high-anticoagulant thrombin-binding bivalent DNA aptamer-linked M08 with HD22. Res Pract Thromb Haemost 2021; 5:e12503. [PMID: 34136744 PMCID: PMC8178692 DOI: 10.1002/rth2.12503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/09/2020] [Accepted: 12/19/2020] [Indexed: 11/10/2022] Open
Abstract
Background Bivalent thrombin-binding aptamers (TBAs) have great potential for the treatment of thrombosis because they exhibit high anticoagulant activity, and their complementary single-stranded DNA (ssDNA) sequences work as an antidote. However, a design strategy for antidote sequences against bivalent aptamers has not been established. Objectives To develop bivalent TBAs using M08, which exhibits higher anticoagulant activity than the previously reported exosite Ⅰ-binding DNA aptamers, such as HD1, an exosite Ⅱ-binding DNA aptamer (HD22) was linked to M08 with various types of linkers. In addition, short-length complementary ssDNAs were designed to neutralize the optimized bivalent aptamer effectively and rapidly. Results Among the bivalent aptamers of M08 linked to HD22 with various types of linkers, M08-T15-HD22 possessed approximately 5-fold higher anticoagulant activity than previously reported bivalent aptamers. To neutralize the activity of the 87-meric M08-T15-HD22, complementary ssDNA sequences with different lengths and hybridization segments were designed. The complementary sequence against the M08 moiety played a more important role in neutralizing than that against the HD22 moiety. Hybridization of the T15 linker in the M08-T15-HD22 with the A15 sequence in the antidote accelerated neutralization due to toehold-mediated strand displacement. Interestingly, some shorter-length antidotes showed higher neutralizing activity than the full complementary 87-meric antidote, and the shortest, 34-meric antidote, neutralized most effectively. Conclusions A pair comprising an 87-meric bivalent TBA containing M08 and a 34-meric short-length antidote with high anticoagulant and rapid neutralizing activities was developed. This design strategy of the DNA sequence can be used for other bivalent DNA aptamers and their antidotes.
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Affiliation(s)
- Toru Yoshitomi
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Tokyo Japan.,Research Center for Functional Materials National Institute for Materials Science Ibaraki Japan
| | - Koji Wakui
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Tokyo Japan
| | - Masato Miyakawa
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Tokyo Japan
| | - Keitaro Yoshimoto
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Tokyo Japan.,JST PRESTO Tokyo Japan
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Citartan M. Aptamers as the powerhouse of dot blot assays. Talanta 2021; 232:122436. [PMID: 34074421 DOI: 10.1016/j.talanta.2021.122436] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/21/2022]
Abstract
Dot blot assays have always been associated with antibodies as the main molecular recognition element, which are widely employed in a myriad of diagnostic applications. With the rising of aptamers as the equivalent molecular recognition elements of antibodies, dot blot assays are also one of the diagnostic avenues that should be scrutinized for their amenability with aptamers as the potential surrogates of antibodies. In this review, the stepwise procedures of an aptamer-based dot blot assays are underscored before reviewing the existing aptamer-based dot blot assays developed so far. Most of the applications center on monitoring the progress of SELEX and as the validatory assays to assess the potency of aptamer candidates. For the purpose of diagnostics, the current effort is still languid and as such possible suggestions to galvanize the move to spur the aptamer-based dot blot assays to a point-of-care arena are discussed.
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Affiliation(s)
- Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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34
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Alieva R, Novikov R, Tashlitsky V, Arutyunyan A, Kopylov A, Zavyalova E. Bimodular thrombin aptamers with two types of non-covalent locks. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:559-577. [PMID: 33847237 DOI: 10.1080/15257770.2021.1910297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aptamers are structured oligonucleotides that specifically bind their targets. Oligonucleotides can be assembled in large nanostructures via intermolecular duplexes or G-quadruplexes. Addition of aptamers can be used to create nanostructures that bind specifically certain targets. Here two types of self-assembling locks were used to create bimodular aptamer constructions. Well-known aptamer to thrombin was chosen as a model object. The assembly of duplex locks was more efficient at low concentrations. The functional activity of aptamer modules was nearly the same as in HD1. However, the affinity of bimodular aptamers with G-quadruplex locks to immobilized thrombin was 5-10 times higher.
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Affiliation(s)
- Rugiya Alieva
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Roman Novikov
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russian Federation
| | - Vadim Tashlitsky
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Alexander Arutyunyan
- Belozersky Research Institute of Physical Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Alexey Kopylov
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Elena Zavyalova
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation
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Improving Breast Cancer Treatment Specificity Using Aptamers Obtained by 3D Cell-SELEX. Pharmaceuticals (Basel) 2021; 14:ph14040349. [PMID: 33918832 PMCID: PMC8068899 DOI: 10.3390/ph14040349] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/26/2021] [Accepted: 04/05/2021] [Indexed: 12/24/2022] Open
Abstract
Three-dimensional spheroids of non-malignant MCF10A and malignant SKBR3 breast cells were used for subsequent 3D Cell-SELEX to generate aptamers for specific binding and treatment of breast cancer cells. Using 3D Cell-SELEX combined with Next-Generation Sequencing and bioinformatics, ten abundant aptamer families with specific structures were identified that selectively bind to SKBR3, and not to MCF10A cells. Multivalent aptamer polymers were synthesized by co-polymerization and analyzed for binding performance as well as therapeutic efficacy. Binding performance was determined by confocal fluorescence imaging and revealed specific binding and efficient internalization of aptamer polymers into SKBR3 spheroids. For therapeutic purposes, DNA sequences that intercalate the cytotoxic drug doxorubicin were co-polymerized into the aptamer polymers. Viability tests show that the drug-loaded polymers are specific and effective in killing SKBR3 breast cancer cells. Thus, the 3D-selected aptamers enhanced the specificity of doxorubicin against malignant over non-malignant breast cells. The innovative modular DNA aptamer platform based on 3D Cell SELEX and polymer multivalency holds great promise for diagnostics and treatment of breast cancer.
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Recent Progress and Opportunities for Nucleic Acid Aptamers. Life (Basel) 2021; 11:life11030193. [PMID: 33671039 PMCID: PMC7997341 DOI: 10.3390/life11030193] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/20/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
Coined three decades ago, the term aptamer and directed evolution have now reached their maturity. The concept that nucleic acid could modulate the activity of target protein as ligand emerged from basic science studies of viruses. Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular binding, which allow for therapeutic and diagnostic applications. Compared to traditional antibodies, aptamers have several advantages, including small size, flexible structure, good biocompatibility, and low immunogenicity. In vitro selection method is used to isolate aptamers that are specific for a desired target from a randomized oligonucleotide library. The first aptamer drug, Macugen, was approved by FDA in 2004, which was accompanied by many studies and clinical investigations on various targets and diseases. Despite much promise, most aptamers have failed to meet the requisite safety and efficacy standards in human clinical trials. Amid these setbacks, the emergence of novel technologies and recent advances in aptamer and systematic evolution of ligands by exponential enrichment (SELEX) design are fueling hope in this field. The unique properties of aptamer are gaining renewed interest in an era of COVID-19. The binding performance of an aptamer and reproducibility are still the key issues in tackling current hurdles in clinical translation. A thorough analysis of the aptamer binding under varying conditions and the conformational dynamics is warranted. Here, the challenges and opportunities of aptamers are reviewed with recent progress.
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Bezerra AB, Kurian ASN, Easley CJ. Nucleic-Acid Driven Cooperative Bioassays Using Probe Proximity or Split-Probe Techniques. Anal Chem 2021; 93:198-214. [PMID: 33147015 PMCID: PMC7855502 DOI: 10.1021/acs.analchem.0c04364] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Mashreghi M, Zamani P, Karimi M, Mehrabian A, Arabsalmani M, Zarqi J, Moosavian SA, Jaafari MR. Anti-epithelial cell adhesion molecule RNA aptamer-conjugated liposomal doxorubicin as an efficient targeted therapy in mice bearing colon carcinoma tumor model. Biotechnol Prog 2020; 37:e3116. [PMID: 33369269 DOI: 10.1002/btpr.3116] [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] [Received: 10/29/2020] [Revised: 12/01/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022]
Abstract
To overcome the lack of selectivity and nonspecific biodistribution of drugs in the body, targeted delivery of chemotherapeutic agents with aptamers is a very effective method. In this strategy, aptamers could be specifically identified and attach to targeted molecules on the cancerous cells and deliver the chemotherapeutic agents to desired tissue with minimal or no damage to the normal cells. In this study, we designed anti-epithelial cell adhesion molecule (EpCAM) RNA aptamer conjugated PEGylated liposomal doxorubicin (ER-lip) to investigate its in vitro and in vivo anticancer abilities. Data showed that EpCAM aptamer was able to enhance cell uptake and cytotoxic effects of Dox in C26 cell line. The biodistribution study indicated that ER-lip enhanced the tumor accumulation of Dox compared to Caelyx. Also, double staining of isolated tumor cells with anti-CD44-PE-cy5 and anti-EpCAM Cy-7 antibodies indicated that tumor cells expressed a high level of EpCAM+ CD44+ cells (p ≤ .001) compared to cultured C26 cell line. in vivo results showed that ER-lip promoted survival and reduced tumor growth rate in animal model compared to Caelyx. In conclusion, these results suggested that the ER-lip could be served as promising formulation for the treatment of cancers with the high expression of EpCAM.
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Affiliation(s)
- Mohammad Mashreghi
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parvin Zamani
- Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Karimi
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amin Mehrabian
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahdieh Arabsalmani
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Javad Zarqi
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyedeh Alia Moosavian
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahmoud Reza Jaafari
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.,Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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Modeling SELEX for regulatory regions using Royal Road and Royal Staircase fitness functions. Biosystems 2020; 200:104312. [PMID: 33278501 DOI: 10.1016/j.biosystems.2020.104312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/11/2020] [Accepted: 11/23/2020] [Indexed: 01/24/2023]
Abstract
The field of evolutionary algorithms (EAs) emerged in the area of computer science due to transfer of ideas from biology and developed independently for several decades, enriched with techniques from probability theory, complexity theory and optimization methods. In this paper, we consider some recent results form the EAs theory transferred back into biology. The well-known biotechnological procedure SELEX (Systematic Evolution of Ligands by EXponential enrichment) is viewed as an experimental implementation of an evolutionary algorithm. Theoretical bounds on EAs runtime are applied to model SELEX search for a regulatory region consisting of promoter and enhancer sequences. A comparison of theoretical bounds to the results of computational simulation indicates some cases where the theoretical bounds give favorable prediction, while simulation requires prohibitive computational resource.
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40
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Wang CY, Lin BL, Chen CH. Targeted drug delivery using an aptamer against shared tumor-specific peptide antigen of MAGE-A3. Cancer Biol Ther 2020; 22:12-18. [PMID: 33249980 DOI: 10.1080/15384047.2020.1833156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
We developed a DNA aptamer, Ap52, against the shared tumor-specific MAGE-A3111-125 peptide antigen that was used to target multiple types of cancer cells. Here we report the in vivo study of mice implanted with pancreatic tumor cells AsPC-1, which demonstrates accumulation of phosphorothioate-modified Ap52 (ThioAp52) at the xenograft tumor following either intravenous or in situ injection. When complexed with antitumor drug doxorubicin (Dox), ThioAp52 achieves targeted delivery to four types of cancer cells, including breast, oral, pancreatic, and skin. Image analysis shows that ThioAp52-Dox complex selectively enters cancer cells, while free Dox is taken up by all cell lines. The cytotoxicity of ThioAp52-Dox for cancer cells is enhanced as compared to that for the corresponding normal/noncancerous cells. These results indicate that this aptamer against shared tumor-specific antigen can be a potential delivery vehicle for therapeutics to treat multiple cancers.
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Affiliation(s)
- Chin-Yu Wang
- Genomics Research Center, Academia Sinica , Taipei, Taiwan
| | - Bai-Ling Lin
- Genomics Research Center, Academia Sinica , Taipei, Taiwan
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Riccardi C, Napolitano E, Musumeci D, Montesarchio D. Dimeric and Multimeric DNA Aptamers for Highly Effective Protein Recognition. Molecules 2020; 25:E5227. [PMID: 33182593 PMCID: PMC7698228 DOI: 10.3390/molecules25225227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/14/2022] Open
Abstract
Multivalent interactions frequently occur in biological systems and typically provide higher binding affinity and selectivity in target recognition than when only monovalent interactions are operative. Thus, taking inspiration by nature, bivalent or multivalent nucleic acid aptamers recognizing a specific biological target have been extensively studied in the last decades. Indeed, oligonucleotide-based aptamers are suitable building blocks for the development of highly efficient multivalent systems since they can be easily modified and assembled exploiting proper connecting linkers of different nature. Thus, substantial research efforts have been put in the construction of dimeric/multimeric versions of effective aptamers with various degrees of success in target binding affinity or therapeutic activity enhancement. The present review summarizes recent advances in the design and development of dimeric and multimeric DNA-based aptamers, including those forming G-quadruplex (G4) structures, recognizing different key proteins in relevant pathological processes. Most of the designed constructs have shown improved performance in terms of binding affinity or therapeutic activity as anti-inflammatory, antiviral, anticoagulant, and anticancer agents and their number is certainly bound to grow in the next future.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini, 5, I-80131 Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
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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.
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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
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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.
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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
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Yasmeen F, Seo H, Javaid N, Kim MS, Choi S. Therapeutic Interventions into Innate Immune Diseases by Means of Aptamers. Pharmaceutics 2020; 12:pharmaceutics12100955. [PMID: 33050544 PMCID: PMC7600108 DOI: 10.3390/pharmaceutics12100955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/03/2020] [Accepted: 10/04/2020] [Indexed: 12/25/2022] Open
Abstract
The immune system plays a crucial role in the body's defense system against various pathogens, such as bacteria, viruses, and parasites, as well as recognizes non-self- and self-molecules. The innate immune system is composed of special receptors known as pattern recognition receptors, which play a crucial role in the identification of pathogen-associated molecular patterns from diverse microorganisms. Any disequilibrium in the activation of a particular pattern recognition receptor leads to various inflammatory, autoimmune, or immunodeficiency diseases. Aptamers are short single-stranded deoxyribonucleic acid or ribonucleic acid molecules, also termed "chemical antibodies," which have tremendous specificity and affinity for their target molecules. Their features, such as stability, low immunogenicity, ease of manufacturing, and facile screening against a target, make them preferable as therapeutics. Immune-system-targeting aptamers have a great potential as a targeted therapeutic strategy against immune diseases. This review summarizes components of the innate immune system, aptamer production, pharmacokinetic characteristics of aptamers, and aptamers related to innate-immune-system diseases.
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Riccardi C, Napolitano E, Platella C, Musumeci D, Melone MAB, Montesarchio D. Anti-VEGF DNA-based aptamers in cancer therapeutics and diagnostics. Med Res Rev 2020; 41:464-506. [PMID: 33038031 DOI: 10.1002/med.21737] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/12/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022]
Abstract
The vascular endothelial growth factor (VEGF) family and its receptors play fundamental roles not only in physiological but also in pathological angiogenesis, characteristic of cancer progression. Aiming at finding putative treatments for several malignancies, various small molecules, antibodies, or protein-based drugs have been evaluated in vitro and in vivo as VEGF inhibitors, providing efficient agents approved for clinical use. Due to the high clinical importance of VEGF, also a great number of anti-VEGF nucleic acid-based aptamers-that is, oligonucleotides able to bind with high affinity and specificity a selected biological target-have been developed as promising agents in anticancer strategies. Notable research efforts have been made in optimization processes of the identified aptamers, searching for increased target affinity and/or bioactivity by exploring structural analogues of the lead compounds. This review is focused on recent studies devoted to the development of DNA-based aptamers designed to target VEGF. Their therapeutic potential as well as their significance in the construction of highly selective biosensors is here discussed.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.,Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and Inter-University Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.,Institute of Biostructures and Bioimages, Naples, Italy
| | - Mariarosa A B Melone
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and Inter-University Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, Naples, Italy.,Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
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Kumar S, Mandal D, El-Mowafi SA, Mozaffari S, Tiwari RK, Parang K. Click-Free Synthesis of a Multivalent Tricyclic Peptide as a Molecular Transporter. Pharmaceutics 2020; 12:pharmaceutics12090842. [PMID: 32899170 PMCID: PMC7558522 DOI: 10.3390/pharmaceutics12090842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 01/19/2023] Open
Abstract
The cellular delivery of cell-impermeable and water-insoluble molecules remains an ongoing challenge to overcome. Previously, we reported amphipathic cyclic peptides c[WR]4 and c[WR]5 consisting of alternate arginine and tryptophan residues as nuclear-targeting molecular transporters. These peptides contain an optimal balance of positive charge and hydrophobicity, which is required for interactions with the phospholipid bilayer to facilitate their application as a drug delivery system. To further optimize them, we synthesized and evaluated a multivalent tricyclic peptide as an efficient molecular transporter. The monomeric cyclic peptide building blocks were synthesized using Fmoc/tBu solid-phase chemistry and cyclization in the solution and conjugated with each other through an amide bond to afford the tricyclic peptide, which demonstrated modest antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA), Klebsiella pneumoniae, Pseudomonas aeruginosa, and Escherichia coli (E. coli) with a minimum inhibitory concentration (MIC) of 64–128 µg/mL. The tricyclic peptide was found to be nontoxic up to 30 µM in the breast cancer cell lines (MDA-MB-231). The presence of tricyclic peptide enhanced cellular uptakes of fluorescently-labeled phosphopeptide (F’-GpYEEI, 18-fold), anti-HIV drugs (lamivudine (F’-3TC), emtricitabine (F’-FTC), and stavudine (F’-d4T), 1.7–12-fold), and siRNA (3.3-fold) in the MDA-MB-231 cell lines.
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Affiliation(s)
- Sumit Kumar
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, Chapman University School of Pharmacy, Irvine, CA 92618, USA; (S.K.); (D.M.); (S.A.E.-M.); (S.M.)
- Department of Chemistry, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Haryana 131039, India
| | - Dindyal Mandal
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, Chapman University School of Pharmacy, Irvine, CA 92618, USA; (S.K.); (D.M.); (S.A.E.-M.); (S.M.)
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar 751024, India
| | - Shaima Ahmed El-Mowafi
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, Chapman University School of Pharmacy, Irvine, CA 92618, USA; (S.K.); (D.M.); (S.A.E.-M.); (S.M.)
- Peptide Chemistry Department, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Saghar Mozaffari
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, Chapman University School of Pharmacy, Irvine, CA 92618, USA; (S.K.); (D.M.); (S.A.E.-M.); (S.M.)
| | - Rakesh Kumar Tiwari
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, Chapman University School of Pharmacy, Irvine, CA 92618, USA; (S.K.); (D.M.); (S.A.E.-M.); (S.M.)
- Correspondence: (R.K.T.); (K.P.); Tel.: +1-714-516-5483 (R.K.T.); +1-714-516-5489 (K.P.)
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, Chapman University School of Pharmacy, Irvine, CA 92618, USA; (S.K.); (D.M.); (S.A.E.-M.); (S.M.)
- Correspondence: (R.K.T.); (K.P.); Tel.: +1-714-516-5483 (R.K.T.); +1-714-516-5489 (K.P.)
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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.
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Affiliation(s)
- Victoria Calzada
- Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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Eilers A, Witt S, Walter J. Aptamer-Modified Nanoparticles in Medical Applications. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 174:161-193. [PMID: 32157319 DOI: 10.1007/10_2020_124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Since aptamers have been selected against a broad range of target structures of medical interest and nanoparticles are available with diverse properties, aptamer-modified nanoparticles can be used in various diagnostic and therapeutic applications. While the aptamer is responsible for specificity and affinity of the conjugate, the nanoparticles' function varies from signal generation in diagnostic approaches to drug loading in drug delivery systems. Within this chapter different medical applications of aptamer-modified nanoparticles will be summarized and underlying principles will be described.
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Affiliation(s)
- Alina Eilers
- Institut für Technische Chemie, Hannover, Germany
| | - Sandra Witt
- Institut für Technische Chemie, Hannover, Germany
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Riccardi C, Napolitano E, Platella C, Musumeci D, Montesarchio D. G-quadruplex-based aptamers targeting human thrombin: Discovery, chemical modifications and antithrombotic effects. Pharmacol Ther 2020; 217:107649. [PMID: 32777331 DOI: 10.1016/j.pharmthera.2020.107649] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
First studies on thrombin-inhibiting DNA aptamers were reported in 1992, and since then a large number of anticoagulant aptamers has been discovered. TBA - also named HD1, a 15-mer G-quadruplex (G4)-forming oligonucleotide - is the best characterized thrombin binding aptamer, able to specifically recognize the protein exosite I, thus inhibiting the conversion of soluble fibrinogen into insoluble fibrin strands. Unmodified nucleic acid-based aptamers, in general, and TBA in particular, exhibit limited pharmacokinetic properties and are rapidly degraded in vivo by nucleases. In order to improve the biological performance of aptamers, a widely investigated strategy is the introduction of chemical modifications in their backbone at the level of the nucleobases, sugar moieties or phosphodiester linkages. Besides TBA, also other thrombin binding aptamers, able to adopt a well-defined G4 structure, e.g. mixed duplex/quadruplex sequences, as well as homo- and hetero-bivalent constructs, have been identified and optimized. Considering the growing need of new efficient anticoagulant agents associated with the strong therapeutic potential of these thrombin inhibitors, the research on thrombin binding aptamers is still a very hot and intriguing field. Herein, we comprehensively described the state-of-the-art knowledge on the DNA-based aptamers targeting thrombin, especially focusing on the optimized analogues obtained by chemically modifying the oligonucleotide backbone, and their biological performances in therapeutic applications.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Department of Advanced Medical and Surgical Sciences, 2(nd) Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini, 5, I-80131 Naples, Italy.
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
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Guzman NA, Guzman DE. A Two-Dimensional Affinity Capture and Separation Mini-Platform for the Isolation, Enrichment, and Quantification of Biomarkers and Its Potential Use for Liquid Biopsy. Biomedicines 2020; 8:biomedicines8080255. [PMID: 32751506 PMCID: PMC7459796 DOI: 10.3390/biomedicines8080255] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023] Open
Abstract
Biomarker detection for disease diagnosis, prognosis, and therapeutic response is becoming increasingly reliable and accessible. Particularly, the identification of circulating cell-free chemical and biochemical substances, cellular and subcellular entities, and extracellular vesicles has demonstrated promising applications in understanding the physiologic and pathologic conditions of an individual. Traditionally, tissue biopsy has been the gold standard for the diagnosis of many diseases, especially cancer. More recently, liquid biopsy for biomarker detection has emerged as a non-invasive or minimally invasive and less costly method for diagnosis of both cancerous and non-cancerous diseases, while also offering information on the progression or improvement of disease. Unfortunately, the standardization of analytical methods to isolate and quantify circulating cells and extracellular vesicles, as well as their extracted biochemical constituents, is still cumbersome, time-consuming, and expensive. To address these limitations, we have developed a prototype of a portable, miniaturized instrument that uses immunoaffinity capillary electrophoresis (IACE) to isolate, concentrate, and analyze cell-free biomarkers and/or tissue or cell extracts present in biological fluids. Isolation and concentration of analytes is accomplished through binding to one or more biorecognition affinity ligands immobilized to a solid support, while separation and analysis are achieved by high-resolution capillary electrophoresis (CE) coupled to one or more detectors. When compared to other existing methods, the process of this affinity capture, enrichment, release, and separation of one or a panel of biomarkers can be carried out on-line with the advantages of being rapid, automated, and cost-effective. Additionally, it has the potential to demonstrate high analytical sensitivity, specificity, and selectivity. As the potential of liquid biopsy grows, so too does the demand for technical advances. In this review, we therefore discuss applications and limitations of liquid biopsy and hope to introduce the idea that our affinity capture-separation device could be used as a form of point-of-care (POC) diagnostic technology to isolate, concentrate, and analyze circulating cells, extracellular vesicles, and viruses.
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Affiliation(s)
- Norberto A. Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08816, USA
- Correspondence: ; Tel.: +1-908-510-5258
| | - Daniel E. Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08816, USA
- Department of Internal Medicine, University of California at San Francisco, San Francisco, CA 94143, USA; or
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