1
|
Singh NK, Wang Y, Wen C, Davis B, Wang X, Lee K, Wang Y. High-affinity one-step aptamer selection using a non-fouling porous hydrogel. Nat Biotechnol 2023:10.1038/s41587-023-01973-8. [PMID: 37798416 DOI: 10.1038/s41587-023-01973-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 08/29/2023] [Indexed: 10/07/2023]
Abstract
Aptamers, commonly referred to as chemical antibodies, are used in a wide range of applications including drug delivery and biosensing. However, the process of aptamer selection poses a substantial challenge, as it requires numerous cycles of enrichment and involves issues with nonspecific binding. We present a simple, fast instrument-free method for aptamer enrichment and selection based on a diffusion-binding process in a three-dimensional non-fouling porous hydrogel with immobilized target proteins. Low-affinity aptamer candidates can be rapidly released from the hydrogel, whereas high-affinity candidates are restricted due to their strong binding to the immobilized protein targets. Consequently, a one-step enriched aptamer pool can strongly bind the protein targets. This enrichment is consistent across five proteins with isoelectric points in varying ranges. With thrombin as a representative model, the anti-thrombin aptamer identified from an enriched aptamer pool has been found to have a binding affinity that is comparable to those identified over ten cycles of selection using traditional methods.
Collapse
Affiliation(s)
- Naveen K Singh
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, Delhi, New Delhi, India
| | - Yixun Wang
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Connie Wen
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Brandon Davis
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Xuelin Wang
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Kyungsene Lee
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Yong Wang
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA.
| |
Collapse
|
2
|
Meng X, Wen K, Citartan M, Lin Q. A comparative study of aptamer isolation by conventional and microfluidic strategies. Analyst 2023; 148:787-798. [PMID: 36688616 PMCID: PMC10143297 DOI: 10.1039/d2an01767a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Aptamers are single-stranded oligonucleotide molecules that bind with high affinity and specificity to a wide range of target molecules. The method of systematic evolution of ligands by exponential enrichment (SELEX) plays an essential role in the isolation of aptamers from a randomized oligonucleotide library. To date, significant modifications and improvements of the SELEX process have been achieved, engendering various forms of SELEX from conventional SELEX to microfluidics-based full-chip SELEX. While full-chip SELEX is generally considered advantageous over conventional SELEX, there has not yet been a conclusive comparison between the methods. Herein, we present a comparative study of three SELEX strategies for aptamer isolation, including those using conventional agarose bead-based partitioning, microfluidic affinity selection, and fully integrated microfluidic affinity selection and PCR amplification. Using immunoglobulin E (IgE) as a model target molecule, we compare these strategies in terms of the time and cost for each step of the SELEX process including affinity selection, amplification, and oligonucleotide conditioning. Target-binding oligonucleotides in the enriched pools are sequenced and compared to assess the relative efficacy of the SELEX strategies. We show that the microfluidic strategies are more time- and cost-efficient than conventional SELEX.
Collapse
Affiliation(s)
- Xin Meng
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, USA.
| | - Kechun Wen
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, USA.
| | - Marimuthu Citartan
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, USA. .,Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, USA.
| |
Collapse
|
3
|
Kulabhusan PK, Pishva P, Çapkın E, Tambe P, Yüce M. Aptamer-based Emerging Tools for Viral Biomarker Detection: A Focus on SARS-CoV-2. Curr Med Chem 2023; 30:910-934. [PMID: 35156569 DOI: 10.2174/1568009622666220214101059] [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: 06/22/2021] [Revised: 11/11/2021] [Accepted: 12/19/2021] [Indexed: 11/22/2022]
Abstract
Viral infections can cause fatal illnesses to humans as well as animals. Early detection of viruses is therefore crucial to provide effective treatment to patients. Recently, the Covid-19 pandemic has undoubtedly given an alarming call to develop rapid and sensitive detection platforms. The viral diagnostic tools need to be fast, affordable, and easy to operate with high sensitivity and specificity equivalent or superior to the currently used diagnostic methods. The present detection methods include direct detection of viral antigens or measuring the response of antibodies to viral infections. However, the sensitivity and quantification of the virus are still a significant challenge. Detection tools employing synthetic binding molecules like aptamers may provide several advantages over the conventional methods that use antibodies in the assay format. Aptamers are highly stable and tailorable molecules and are therefore ideal for detection and chemical sensing applications. This review article discusses various advances made in aptamer-based viral detection platforms, including electrochemical, optical, and colorimetric methods to detect viruses, specifically SARS-Cov-2. Considering the several advantages, aptamers could be game-changing in designing high-throughput biosensors for viruses and other biomedical applications in the future.
Collapse
Affiliation(s)
- Prabir Kumar Kulabhusan
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Parsa Pishva
- Sabanci University, Faculty of Engineering and Natural Sciences, Istanbul, 34956, Turkey
| | - Eda Çapkın
- Sabanci University, Faculty of Engineering and Natural Sciences, Istanbul, 34956, Turkey
| | - Prajakta Tambe
- Wellcome-- Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Meral Yüce
- Sabanci University, SUNUM Nanotechnology Research, and Application Centre, Istanbul, 34956, Turkey
| |
Collapse
|
4
|
Olsen TR, Tapia-Alveal C, Wen K, Worgall TS, Stojanovic MN, Lin Q. Microfluidic isolation of aptamers with affinity towards multiple myeloma monoclonal immunoglobulins. Biomed Microdevices 2022; 25:3. [PMID: 36480127 PMCID: PMC11113000 DOI: 10.1007/s10544-022-00643-x] [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] [Accepted: 11/15/2022] [Indexed: 12/13/2022]
Abstract
Multiple myeloma (MM) is a bone marrow cancer of resident plasma cells that affects 125,000 patients in the U.S. with about 30,000 new cases per year. Its signature is the clonal proliferation of a single plasma cell that secretes a patient specific monoclonal immunoglobulin (M-Ig). Targeting the M-Ig in patient serum could allow sensitive and noninvasive identification of minimal residual disease in multiple myeloma. Aptamers, which are single-stranded oligonucleotides with affinity and specificity to a target molecule, have recently been introduced as affinity reagents for recognition of MM M-Igs. Here we exploit microfluidic SELEX technology to enable rapid and efficient generation of aptamers against M-Ig proteins from MM patients. We first characterize the technology by isolating aptamers with affinity towards the monoclonal antibody rituximab as a model M-Ig and then apply the technology to isolating aptamers specifically targeting M-Igs obtained from serum samples of MM patients. We demonstrate that high-affinity DNA aptamers (KD < 50 nM) for M-Ig proteins from a patient sample could be isolated via microfluidic SELEX within approximately 12 h and using less than 100 micrograms of patient M-Ig. Such aptamers can potentially be used in personalized monitoring of minimal residual disease in MM patients.
Collapse
Affiliation(s)
- Timothy R Olsen
- Department of Mechanical Engineering, Columbia University, 10027, New York, NY, USA
| | - Claudia Tapia-Alveal
- Department of Pathology and Cell Biology, Columbia University Medical Center, 10032, New York, NY, USA
| | - Kechun Wen
- Department of Mechanical Engineering, Columbia University, 10027, New York, NY, USA
| | - Tilla S Worgall
- Department of Pathology and Cell Biology, Columbia University Medical Center, 10032, New York, NY, USA
| | | | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, 10027, New York, NY, USA.
| |
Collapse
|
5
|
Lim H, Chang J, Kim KI, Moon Y, Lee S, Lee B, Lee JH, Lee J. On-chip selection of adenosine aptamer using graphene oxide-coated magnetic nanoparticles. BIOMICROFLUIDICS 2022; 16:044102. [PMID: 35909647 PMCID: PMC9337878 DOI: 10.1063/5.0095419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) is a method that is generally used for developing aptamers, which have arisen the promising alternatives for antibodies. However, conventional SELEX methods have limitations, such as a limited selection of target molecules, time-consuming and complex fabrication processes, and labor-intensive processes, which result in low selection yields. Here, we used (i) graphene oxide (GO)-coated magnetic nanoparticles in the selection process for separation and label-free detection and (ii) a multilayered microfluidic device manufactured using a three-dimensionally printed mold that is equipped with automated control valves to achieve precise fluid flows. The developed on-chip aptamer selection device and GO-coated magnetic nanoparticles were used to screen aptamer candidates for adenosine in eight cycles of the selection process within approximately 2 h for each cycle. Based on results from isothermal titration calorimetry, an aptamer with a dissociation constant of 18.6 ± 1.5 μM was selected. Therefore, the on-chip platform based on GO-coated magnetic nanoparticles provides a novel label-free screening technology for biosensors and micro/nanobiotechnology for achieving high-quality aptamers.
Collapse
Affiliation(s)
| | - Junhyuck Chang
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Kyung-il Kim
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Youngkwang Moon
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Saebom Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Byoungsang Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jung Heon Lee
- Authors to whom correspondence should be addressed:, Tel.: +82-31-290-7404 and , Tel.: +82-31-299-4845
| | - Jinkee Lee
- Authors to whom correspondence should be addressed:, Tel.: +82-31-290-7404 and , Tel.: +82-31-299-4845
| |
Collapse
|
6
|
Sousa DA, Carneiro M, Ferreira D, Moreira FTC, Sales MGFV, Rodrigues LR. Recent advances in the selection of cancer-specific aptamers for the development of biosensors. Curr Med Chem 2022; 29:5850-5880. [PMID: 35209816 DOI: 10.2174/0929867329666220224155037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/30/2021] [Accepted: 12/19/2021] [Indexed: 11/22/2022]
Abstract
An early diagnosis has the potential to greatly decrease cancer mortality. For that purpose, specific cancer biomarkers have been molecularly targeted by aptamer sequences to enable an accurate and rapid detection. Aptamer-based biosensors for cancer diagnostics are a promising alternative to those using antibodies, due to their high affinity and specificity to the target molecules and advantageous production. Synthetic nucleic acid aptamers are generated by in vitro Systematic Evolution of Ligands by Exponential enrichment (SELEX) methodologies that have been improved over the years to enhance the efficacy and to shorten the selection process. Aptamers have been successfully applied in electrochemical, optical, photoelectrochemical and piezoelectrical-based detection strategies. These aptasensors comprise a sensitive, accurate and inexpensive option for cancer detection being used as point-of-care devices. This review highlights the recent advances in cancer biomarkers, achievements and optimizations made in aptamer selection, as well as the different aptasensors developed for the detection of several cancer biomarkers.
Collapse
Affiliation(s)
- Diana A Sousa
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- MIT-Portugal Program, Lisbon, Portugal
| | - Mariana Carneiro
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- BioMark@ISEP, School of Engineering, Polytechnic of Porto, Porto, Portugal
| | - Débora Ferreira
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- MIT-Portugal Program, Lisbon, Portugal
| | - Felismina T C Moreira
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- BioMark@ISEP, School of Engineering, Polytechnic of Porto, Porto, Portugal
| | - Maria Goreti F V Sales
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- MIT-Portugal Program, Lisbon, Portugal
- BioMark@UC, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Lígia R Rodrigues
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
| |
Collapse
|
7
|
Liu Y, Wang N, Chan CW, Lu A, Yu Y, Zhang G, Ren K. The Application of Microfluidic Technologies in Aptamer Selection. Front Cell Dev Biol 2021; 9:730035. [PMID: 34604229 PMCID: PMC8484746 DOI: 10.3389/fcell.2021.730035] [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: 06/24/2021] [Accepted: 08/24/2021] [Indexed: 11/13/2022] Open
Abstract
Aptamers are sequences of single-strand oligonucleotides (DNA or RNA) with potential binding capability to specific target molecules, which are increasingly used as agents for analysis, diagnosis, and medical treatment. Aptamers are generated by a selection method named systematic evolution of ligands by exponential enrichment (SELEX). Numerous SELEX methods have been developed for aptamer selections. However, the conventional SELEX methods still suffer from high labor intensity, low operation efficiency, and low success rate. Thus, the applications of aptamer with desired properties are limited. With their advantages of low cost, high speed, and upgraded extent of automation, microfluidic technologies have become promising tools for rapid and high throughput aptamer selection. This paper reviews current progresses of such microfluidic systems for aptamer selection. Comparisons of selection performances with discussions on principles, structure, operations, as well as advantages and limitations of various microfluidic-based aptamer selection methods are provided.
Collapse
Affiliation(s)
- Yang Liu
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, SAR China
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, Hong Kong, SAR China
| | - Nijia Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, SAR China
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, Hong Kong, SAR China
| | - Chiu-Wing Chan
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, SAR China
| | - Aiping Lu
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, Hong Kong, SAR China
- School of Chinese Medicine, Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, Hong Kong Baptist University, Hong Kong, Hong Kong, SAR China
| | - Yuanyuan Yu
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, Hong Kong, SAR China
- School of Chinese Medicine, Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, Hong Kong Baptist University, Hong Kong, Hong Kong, SAR China
| | - Ge Zhang
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, Hong Kong, SAR China
- School of Chinese Medicine, Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, Hong Kong Baptist University, Hong Kong, Hong Kong, SAR China
| | - Kangning Ren
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, SAR China
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, Hong Kong, SAR China
- Institute of Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon, Hong Kong, SAR China
| |
Collapse
|
8
|
Yu H, Alkhamis O, Canoura J, Liu Y, Xiao Y. Advances and Challenges in Small‐Molecule DNA Aptamer Isolation, Characterization, and Sensor Development. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202008663] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Yingzhu Liu
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| |
Collapse
|
9
|
Yu H, Alkhamis O, Canoura J, Liu Y, Xiao Y. Advances and Challenges in Small-Molecule DNA Aptamer Isolation, Characterization, and Sensor Development. Angew Chem Int Ed Engl 2021; 60:16800-16823. [PMID: 33559947 PMCID: PMC8292151 DOI: 10.1002/anie.202008663] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/16/2021] [Indexed: 12/12/2022]
Abstract
Aptamers are short oligonucleotides isolated in vitro from randomized libraries that can bind to specific molecules with high affinity, and offer a number of advantages relative to antibodies as biorecognition elements in biosensors. However, it remains difficult and labor-intensive to develop aptamer-based sensors for small-molecule detection. Here, we review the challenges and advances in the isolation and characterization of small-molecule-binding DNA aptamers and their use in sensors. First, we discuss in vitro methodologies for the isolation of aptamers, and provide guidance on selecting the appropriate strategy for generating aptamers with optimal binding properties for a given application. We next examine techniques for characterizing aptamer-target binding and structure. Afterwards, we discuss various small-molecule sensing platforms based on original or engineered aptamers, and their detection applications. Finally, we conclude with a general workflow to develop aptamer-based small-molecule sensors for real-world applications.
Collapse
Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yingzhu Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| |
Collapse
|
10
|
Bognár Z, Gyurcsányi RE. Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications. Int J Mol Sci 2020; 21:E5748. [PMID: 32796581 PMCID: PMC7461046 DOI: 10.3390/ijms21165748] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/26/2020] [Accepted: 08/06/2020] [Indexed: 12/11/2022] Open
Abstract
Nucleic acid aptamers show clear promise as diagnostic reagents, as highly specific strands were reported against a large variety of biomarkers. They have appealing benefits in terms of reproducible generation by chemical synthesis, controlled modification with labels and functionalities providing versatile means for detection and oriented immobilization, as along with high biochemical and temperature resistance. Aptamers against immunoglobulin targets-IgA, IgM, IgG and IgE-have a clear niche for diagnostic applications, therefore numerous aptamers have been selected and used in combination with a variety of detection techniques. The aim of this review is to overview and evaluate aptamers selected for the recognition of antibodies, in terms of their design, analytical properties and diagnostic applications. Aptamer candidates showed convincing performance among others to identify stress and upper respiratory tract infection through SIgA detection, for cancer cell recognition using membrane bound IgM, to detect and treat hemolytic transfusion reactions, autoimmune diseases with IgG and detection of IgE for allergy diseases. However, in general, their use still lags significantly behind what their claimed benefits and the plethora of application opportunities would forecast.
Collapse
Affiliation(s)
| | - Róbert E. Gyurcsányi
- BME “Lendület” Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary;
| |
Collapse
|
11
|
Mamet N, Amir Y, Lavi E, Bassali L, Harari G, Rusinek I, Skalka N, Debby E, Greenberg M, Zamir A, Paz A, Reiss N, Loewenthal G, Avivi I, Shimoni A, Neev G, Abu-Horowitz A, Bachelet I. Discovery of tumoricidal DNA oligonucleotides by response-directed in vitro evolution. Commun Biol 2020; 3:29. [PMID: 31941992 PMCID: PMC6962221 DOI: 10.1038/s42003-020-0756-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 12/31/2019] [Indexed: 02/07/2023] Open
Abstract
Drug discovery is challenged by ineffectiveness of drugs against variable and evolving diseases, and adverse effects due to poor selectivity. We describe a robust platform which potentially addresses these limitations. The platform enables rapid discovery of DNA oligonucleotides evolved in vitro for exerting specific and selective biological responses in target cells. The process operates without a priori target knowledge (mutations, biomarkers, etc). We report the discovery of oligonucleotides with direct, selective cytotoxicity towards cell lines, as well as patient-derived solid and hematological tumors. A specific oligonucleotide termed E8, induced selective apoptosis in triple-negative breast cancer (TNBC) cells. Polyethylene glycol-modified E8 exhibited favorable biodistribution in animals, persisting in tumors up to 48-hours after injection. E8 inhibited tumors by 50% within 10 days of treatment in patient-derived xenograft mice, and was effective in ex vivo organ cultures from chemotherapy-resistant TNBC patients. These findings highlight a drug discovery model which is target-tailored and on-demand. Noam Mamet et al. describe a platform for rapid de novo discovery of DNA oligonucleotides that directly and selectively induce apoptosis in cancer cells. They report target-tailored discovery of tumoricidal oligonucleotides against tumor cell lines as well as patient-derived tumors.
Collapse
Affiliation(s)
- Noam Mamet
- Augmanity, Rehovot, Israel.,Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Yaniv Amir
- Aummune, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
| | - Erez Lavi
- Aummune, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | | | | | | | - Nir Skalka
- Aummune, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Elinor Debby
- Aummune, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | | | | | - Anastasia Paz
- Aummune, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Neria Reiss
- Aummune, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | | | - Irit Avivi
- Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Avichai Shimoni
- BMT Department, Division of Hematology, Sheba Medical Center Tel Hashomer, Ramat-Gan, Israel
| | - Guy Neev
- Aummune, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | | | | |
Collapse
|
12
|
Fraser LA, Cheung YW, Kinghorn AB, Guo W, Shiu SCC, Jinata C, Liu M, Bhuyan S, Nan L, Shum HC, Tanner JA. Microfluidic Technology for Nucleic Acid Aptamer Evolution and Application. ACTA ACUST UNITED AC 2019; 3:e1900012. [PMID: 32627415 DOI: 10.1002/adbi.201900012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/12/2019] [Indexed: 12/18/2022]
Abstract
The intersection of microfluidics and aptamer technologies holds particular promise for rapid progress in a plethora of applications across biomedical science and other areas. Here, the influence of microfluidics on the field of aptamers, from traditional capillary electrophoresis approaches through innovative modern-day approaches using micromagnetic beads and emulsion droplets, is reviewed. Miniaturizing aptamer-based bioassays through microfluidics has the potential to transform diagnostics and embedded biosensing in the coming years.
Collapse
Affiliation(s)
- Lewis A Fraser
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Yee-Wai Cheung
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Wei Guo
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), China
| | - Simon Chi-Chin Shiu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Chandra Jinata
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Mengping Liu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Soubhagya Bhuyan
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Lang Nan
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), China
| | - Julian A Tanner
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| |
Collapse
|
13
|
Yu F, Li H, Sun W, Zhao Y, Xu D, He F. Selection of aptamers against Lactoferrin based on silver enhanced and fluorescence-activated cell sorting. Talanta 2018; 193:110-117. [PMID: 30368278 DOI: 10.1016/j.talanta.2018.09.063] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/13/2018] [Accepted: 09/18/2018] [Indexed: 02/07/2023]
Abstract
We report a novel method for efficiently screening aptamers from a complex ssDNA library based on silver decahedral nanoparticles (AgNP) and fluorescence activated cell sorting (FACS). In this method, target protein (lactoferrin) and negative proteins (α-lactalbumin, β-lactoglobulin, bovine serum albumin, casein) were respectively immobilized on polystyrene microspheres (PS) to form PSLac, PSα-Lac, PSβ-Lac, PSBSA and PSCas. PSLac was firstly interacted with Cy5 labeled library (Lib), then hybridized with Cy5 modified silver decahedral nanoparticles (AgNPCy5) to form PSLac/Lib/AgNPCy5 conjugates. FACS was used to separate and collect PSLac/Lib/AgNPCy5 conjugates from complicated complex. AgNP was used to increase the fluorescence intensity in the selecting process and choose non-self-hybridization of Lib. Six aptamers (Ylac1, Ylac4, Ylac5, Ylac6, Ylac8 and Ylac9) were obtained after five-round of selection. These aptamers showed good specificity towards lactoferrin in the presence of negative proteins. The equilibrium dissociation constants (Kd) of six aptamers were calculated and all were in the nanomolar range. In a word, AgNP-FACS SELEX (AgFACS-SELEX) is a rapid, sensitive and highly efficient method for screening aptamers.
Collapse
Affiliation(s)
- Fang Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210046, China
| | - Hui Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210046, China.
| | - Wei Sun
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yaju Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210046, China
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210046, China.
| | - Fuchu He
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210046, China; State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China.
| |
Collapse
|
14
|
Sinha A, Gopinathan P, Chung YD, Lin HY, Li KH, Ma HP, Huang PC, Shiesh SC, Lee GB. An integrated microfluidic platform to perform uninterrupted SELEX cycles to screen affinity reagents specific to cardiovascular biomarkers. Biosens Bioelectron 2018; 122:104-112. [PMID: 30245322 DOI: 10.1016/j.bios.2018.09.040] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/04/2018] [Accepted: 09/12/2018] [Indexed: 12/19/2022]
Abstract
As cardiovascular diseases (CVD) are responsible for millions of deaths annually, there is a need for rapid and sensitive diagnosis of CVD at earlier stages. Aptamers generated by systematic evolution of ligands by exponential enrichment (SELEX) processes have been shown to be superior to conventional antibody-based cardiac biomarker detection. However, SELEX is a complicated, lengthy procedure requiring multiple rounds of extraction/amplification and well-trained personnel. To circumvent such issue, we designed an automated, miniaturized SELEX platform for the screening of aptamers towards three protein biomarkers associated with CVDs: N-terminal pro-peptide of B-type natriuretic peptide, human cardiac troponin I, and fibrinogen. The developed microfluidic platform was equipped with microfluidic devices capable of sample transport and mixing along with an on-chip nucleic acid amplification module such that the entire screening process (5 rounds of selection in 8 h.) could be performed consecutively on a single chip while consuming only 35 µL of reagents in each cycle. This system may therefore serve as a promising, sensitive, cost-effective platform for the selection of aptamers specific for CVD biomarkers.
Collapse
Affiliation(s)
- Anirban Sinha
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan
| | - Priya Gopinathan
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Da Chung
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Hsin-Ying Lin
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Kuang-Hsien Li
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Hsi-Pin Ma
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Po-Chiun Huang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Shu-Chu Shiesh
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
| | - Gwo-Bin Lee
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan; Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
| |
Collapse
|
15
|
Nakatsuka N, Cao HH, Deshayes S, Melkonian AL, Kasko AM, Weiss PS, Andrews AM. Aptamer Recognition of Multiplexed Small-Molecule-Functionalized Substrates. ACS APPLIED MATERIALS & INTERFACES 2018; 10:23490-23500. [PMID: 29851335 PMCID: PMC6087467 DOI: 10.1021/acsami.8b02837] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Aptamers are chemically synthesized oligonucleotides or peptides with molecular recognition capabilities. We investigated recognition of substrate-tethered small-molecule targets, using neurotransmitters as examples, and fluorescently labeled DNA aptamers. Substrate regions patterned via microfluidic channels with dopamine or l-tryptophan were selectively recognized by previously identified dopamine or l-tryptophan aptamers, respectively. The on-substrate dissociation constant determined for the dopamine aptamer was comparable to, though, slightly greater than the previously determined solution dissociation constant. Using prefunctionalized neurotransmitter-conjugated oligo(ethylene glycol) alkanethiols and microfluidics patterning, we produced multiplexed substrates to capture and to sort aptamers. Substrates patterned with l-3,4-dihydroxyphenylalanine, l- threo-dihydroxyphenylserine, and l-5-hydroxytryptophan enabled comparison of the selectivity of the dopamine aptamer for different targets via simultaneous determination of in situ binding constants. Thus, beyond our previous demonstrations of recognition by protein binding partners (i.e., antibodies and G-protein-coupled receptors), strategically optimized small-molecule-functionalized substrates show selective recognition of nucleic acid binding partners. These substrates are useful for side-by-side target comparisons and future identification and characterization of novel aptamers targeting neurotransmitters or other important small molecules.
Collapse
Affiliation(s)
- Nako Nakatsuka
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Huan H. Cao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Stephanie Deshayes
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Arin L. Melkonian
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Andrea M. Kasko
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Paul S. Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Anne M. Andrews
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience & Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles, Los Angeles, CA 90095, United States
| |
Collapse
|
16
|
Human genomic DNA isolation from whole blood using a simple microfluidic system with silica- and polymer-based stationary phases. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 74:10-20. [DOI: 10.1016/j.msec.2016.12.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/06/2016] [Accepted: 12/22/2016] [Indexed: 10/20/2022]
|
17
|
Olsen TR, Tapia-Alveal C, Yang KA, Zhang X, Pereira LJ, Farmakidis N, Pei R, Stojanovic MN, Lin Q. INTEGRATED MICROFLUIDIC SELEX USING FREE SOLUTION ELECTROKINETICS. JOURNAL OF THE ELECTROCHEMICAL SOCIETY 2017; 164:B3122-B3129. [PMID: 29170564 PMCID: PMC5697788 DOI: 10.1149/2.0191705jes] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) offers a powerful method to isolate affinity oligonucleotides known as aptamers, which can then be used in a wide range of applications from drug delivery to biosensing. However, conventional SELEX methods rely on labor intensive and time consuming benchtop operations. A simplified microfluidic approach is presented which allows integration of the affinity selection and amplification stages of SELEX for the isolation of target-binding oligonucleotides by combining bead-based biochemical reactions with free solution electrokinetic oligonucleotide transfer. Free solution electrokinetics allows coupling of affinity selection and amplification for closed loop oligonucleotide enrichment without the need for offline processes, flow handling components or gel components, while bead based selection and amplification allow efficient manipulation of reagents and reaction products thereby realizing on-chip loop closure and integration of the entire SELEX process. Thus the approach is capable of multi-round enrichment of oligonucleotides using simple transfer processes while maintaining a high level of device integration, as demonstrated by the isolation of an aptamer pool against a protein target (IgA) with significantly higher binding affinity than the starting library in approximately 4 hours of processing time.
Collapse
Affiliation(s)
- Timothy R Olsen
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | | | - Kyung-Ae Yang
- Department of Medicine, Columbia University, New York, NY, USA
| | - Xin Zhang
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | | | | | - Renjun Pei
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China
| | | | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| |
Collapse
|
18
|
Enomoto J, Kageyama T, Osaki T, Bonalumi F, Marchese F, Gautieri A, Bianchi E, Dubini G, Arrigoni C, Moretti M, Fukuda J. Catch-and-Release of Target Cells Using Aptamer-Conjugated Electroactive Zwitterionic Oligopeptide SAM. Sci Rep 2017; 7:43375. [PMID: 28266533 PMCID: PMC5339905 DOI: 10.1038/srep43375] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/23/2017] [Indexed: 11/18/2022] Open
Abstract
Nucleic acid aptamers possess attractive features such as specific molecular recognition, high-affinity binding, and rapid acquisition and replication, which could be feasible components for separating specific cells from other cell types. This study demonstrates that aptamers conjugated to an oligopeptide self-assembled monolayer (SAM) can be used to selectively trap human hepatic cancer cells from cell mixtures containing normal human hepatocytes or human fibroblasts. Molecular dynamics calculations have been performed to understand how the configurations of the aptamers are related to the experimental results of selective cell capture. We further demonstrate that the captured hepatic cancer cells can be detached and collected along with electrochemical desorption of the oligopeptide SAM, and by repeating these catch-and-release processes, target cells can be enriched. This combination of capture with aptamers and detachment with electrochemical reactions is a promising tool in various research fields ranging from basic cancer research to tissue engineering applications.
Collapse
Affiliation(s)
- Junko Enomoto
- Graduate School of Engineering, Yokohama National University, Japan
| | - Tatsuto Kageyama
- Graduate School of Engineering, Yokohama National University, Japan
| | - Tatsuya Osaki
- Graduate School of Engineering, Yokohama National University, Japan
| | - Flavia Bonalumi
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Italy
| | - Francesca Marchese
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Italy
| | - Alfonso Gautieri
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Italy
| | - Elena Bianchi
- Department of Chemistry, Politecnico di Milan, Italy
| | | | - Chiara Arrigoni
- Cell and Tissue Engineering Laboratory, IRCCS Galeazzi Orthopaedic Institute, Italy
| | - Matteo Moretti
- Cell and Tissue Engineering Laboratory, IRCCS Galeazzi Orthopaedic Institute, Italy
- Regenerative Medicine Technologies Lab, Ente Ospedaliero Cantonale, Switzerland
- Swiss Institute for Regenerative Medicine, Switzerland
- Cardiocentro Ticino, Switzerland
| | - Junji Fukuda
- Graduate School of Engineering, Yokohama National University, Japan
| |
Collapse
|
19
|
Olsen T, Zhu J, Kim J, Pei R, Stojanovic MN, Lin Q. An Integrated Microfluidic SELEX Approach Using Combined Electrokinetic and Hydrodynamic Manipulation. SLAS Technol 2017; 22:63-72. [PMID: 27418370 PMCID: PMC5417355 DOI: 10.1177/2211068216659255] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This article presents a microfluidic approach for the integration of the process of aptamer selection via systematic evolution of ligands by exponential enrichment (SELEX). The approach employs bead-based biochemical reactions in which affinity-selected target-binding oligonucleotides are electrokinetically transferred for amplification, while the amplification product is transferred back for affinity selection via pressure-driven fluid flow. The hybrid approach simplifies the device design and operation procedures by reduced pressure-driven flow control requirements and avoids the potentially deleterious exposure of targets to electric fields prior to and during affinity selection. In addition, bead-based reactions are used to achieve the on-chip coupling of affinity selection and amplification of target-binding oligonucleotides, thereby realizing on-chip loop closure and integration of the entire SELEX process without requiring offline procedures. The microfluidic approach is thus capable of closed-loop, multiround aptamer enrichment as demonstrated by selection of DNA aptamers against the protein immunoglobulin E with high affinity ( KD = 12 nM) in a rapid manner (4 rounds in approximately 10 h).
Collapse
Affiliation(s)
- Timothy Olsen
- 1 Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Jing Zhu
- 1 Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Jinho Kim
- 1 Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Renjun Pei
- 2 Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China
| | | | - Qiao Lin
- 1 Department of Mechanical Engineering, Columbia University, New York, NY, USA
| |
Collapse
|