1
|
Mili M, Bachu V, Kuri PR, Singh NK, Goswami P. Improving synthesis and binding affinities of nucleic acid aptamers and their therapeutics and diagnostic applications. Biophys Chem 2024; 309:107218. [PMID: 38547671 DOI: 10.1016/j.bpc.2024.107218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/21/2024] [Accepted: 03/17/2024] [Indexed: 04/22/2024]
Abstract
Nucleic acid aptamers have captivated the attention of analytical and medicinal scientists globally due to their several advantages as recognition molecules over conventional antibodies because of their small size, simple and inexpensive synthesis, broad target range, and high stability in varied environmental conditions. These recognition molecules can be chemically modified to make them resistant to nuclease action in blood serum, reduce rapid renel clearance, improve the target affinity and selectivity, and make them amenable to chemically conjugate with a support system that facilitates their selective applications. This review focuses on the development of efficient aptamer candidates and their application in clinical diagnosis and therapeutic applications. Significant advances have been made in aptamer-based diagnosis of infectious and non-infectious diseases. Collaterally, the progress made in therapeutic applications of aptamers is encouraging, as evident from their use in diagnosing cancer, neurodegenerative diseases, microbial infection, and in imaging. This review also updates the progress on clinical trials of many aptamer-based products of commercial interests. The key development and critical issues on the subject have been summarized in the concluding remarks.
Collapse
Affiliation(s)
- Malaya Mili
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India
| | - Vinay Bachu
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India
| | - Pooja Rani Kuri
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India
| | | | - Pranab Goswami
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India.
| |
Collapse
|
2
|
Laumier S, Farrow T, van Zalinge H, Seravalli L, Bosi M, Sandall I. Selection and Functionalization of Germanium Nanowires for Bio-Sensing. ACS OMEGA 2022; 7:35288-35296. [PMID: 36211075 PMCID: PMC9535719 DOI: 10.1021/acsomega.2c04775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
In this paper, we investigate the use of dielectrophoresis to align germanium nanowire arrays to realize nanowire-based diodes and their subsequent use for bio-sensing. After establishing that dielectrophoresis is a controllable and repeatable fabrication method to create devices from germanium nanowires, we use the optimum process conditions to form a series of diodes. These are subsequently functionalized with an aptamer, which is able to bind specifically to the spike protein of SARS-Cov2 and investigated as a potential sensor. We observe a linear increase in the source to drain current as the concentration of spike protein is increased from 100 fM/L to 1 nM/L.
Collapse
Affiliation(s)
- Siriny Laumier
- Department
of Electrical Engineering and Electronics, University of Liverpool, 9 Brownlow Hill, Liverpool L69 3GJ, U.K.
| | - Thomas Farrow
- Department
of Electrical Engineering and Electronics, University of Liverpool, 9 Brownlow Hill, Liverpool L69 3GJ, U.K.
| | - Harm van Zalinge
- Department
of Electrical Engineering and Electronics, University of Liverpool, 9 Brownlow Hill, Liverpool L69 3GJ, U.K.
| | - Luca Seravalli
- Institute
of Material for Electronic and Magnetism, Parco Area delle Scienze 37/A, 43124 Parma, Italia
| | - Matteo Bosi
- Institute
of Material for Electronic and Magnetism, Parco Area delle Scienze 37/A, 43124 Parma, Italia
| | - Ian Sandall
- Department
of Electrical Engineering and Electronics, University of Liverpool, 9 Brownlow Hill, Liverpool L69 3GJ, U.K.
| |
Collapse
|
3
|
Ondruš M, Sýkorová V, Hocek M. Traceless enzymatic synthesis of monodispersed hypermodified oligodeoxyribonucleotide polymers from RNA templates. Chem Commun (Camb) 2022; 58:11248-11251. [PMID: 36124894 DOI: 10.1039/d2cc03588j] [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
We have developed a new alternative for enzymatic synthesis of single-stranded hypermodified oligodeoxyribonucleotides displaying four different hydrophobic groups based on reverse transcription from RNA templates catalyzed by DNA polymerases using a set of base-modified dNTPs followed by digestion of RNA by RNases. Using mixed oligodeoxyribonucleotide primers containing a ribonucleotide at the 3'-end, RNase AT1 simultaneously digested the template and cleaved off the primer to release a fully modified oligonucleotide that can be further 3'-labelled with a fluorescent nucleotide using TdT. The resulting hypermodified oligonucleotides could find applications in selection of aptamers or other functional macromolecules.
Collapse
Affiliation(s)
- Marek Ondruš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic. .,Dept. of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843, Prague 2, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic.
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic. .,Dept. of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843, Prague 2, Czech Republic
| |
Collapse
|
4
|
Wu W, Sun Q, Li T, Liu K, Jiang Y, Wang Y, Yang Y. Selection and characterization of bispecific aptamers against malachite green and leucomalachite green. Anal Biochem 2022; 658:114849. [PMID: 36150472 DOI: 10.1016/j.ab.2022.114849] [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: 04/06/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/01/2022]
Abstract
In order to develop multi-residues rapid detection, the bispecific aptamers against malachite green (MG) and leucomalachite green (LMG) were isolated by the capture systematic evolution of ligands by exponential enrichment (Capture-SELEX). After thirteen rounds of selection, the enriched ssDNA pools were sent for high-throughput sequencing. Nine aptamer candidates (A1-A9) were picked out to test their specificity by gold nanoparticles (AuNPs) colorimetric assay. Three aptamers (A2, A3, A5) with good selectivity were truncated to verify their affinity by fluorescence assay. Finally, three truncated aptamers (A2-a, A3-a, A5-a) with bispecificity and high affinity were identified. For LMG, the dissociation constant (Kd) of them were 8.4 ± 0.8 nM, 8.2 ± 1.2 nM, and 13.7 ± 1.4 nM, respectively. For MG, Kd of them were 3.4 ± 0.3 μM, 2.3 ± 0.2 μM, 3.0 ± 0.2μM. Among them, A3-a is the best. Our work will provide novel probes for the development of multi-residues rapid detection as well as opportunities for multiple target aptamer discovery.
Collapse
Affiliation(s)
- Wenwei Wu
- Agricultural College, Yanbian University, Yanji, 133002, China
| | - Qifeng Sun
- Beijing Hightrust Medical Laboratory Co., LTD, Beijing, 102600, China
| | - Tiansong Li
- College of Science, Beihua University, Jilin, 132001, China
| | - Kexin Liu
- Agricultural College, Yanbian University, Yanji, 133002, China
| | - Yan Jiang
- Agricultural College, Yanbian University, Yanji, 133002, China
| | - Yi Wang
- College of Science, Beihua University, Jilin, 132001, China.
| | - Yongjie Yang
- Agricultural College, Yanbian University, Yanji, 133002, China.
| |
Collapse
|
5
|
An Aptamer-Functionalised Schottky-Field Effect Transistor for the Detection of Proteins. BIOSENSORS 2022; 12:bios12050347. [PMID: 35624648 PMCID: PMC9138399 DOI: 10.3390/bios12050347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/09/2022] [Accepted: 05/16/2022] [Indexed: 11/21/2022]
Abstract
The outbreak of the coronavirus disease 2019 (COVID-19) in December 2019 has highlighted the need for a flexible sensing system that can quickly and accurately determine the presence of biomarkers associated with the disease. This sensing system also needs to be easily adaptable to incorporate both novel diseases as well as changes in the existing ones. Here we report the feasibility of using a simple, low-cost silicon field-effect transistor functionalised with aptamers and designed to attach to the spike protein of SARS-CoV2. It is shown that a linear response can be obtained in a concentration range of 100 fM to 10 pM. Furthermore, by using a larger range of source-drain potentials compared with other FET based sensors, it is possible to look at a wider range of device parameters to optimise the response.
Collapse
|
6
|
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]
|
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
|
Ashley J, Schaap-Johansen AL, Mohammadniaei M, Naseri M, Marcatili P, Prado M, Sun Y. Terminal deoxynucleotidyl transferase-mediated formation of protein binding polynucleotides. Nucleic Acids Res 2021; 49:1065-1074. [PMID: 33398328 PMCID: PMC7826267 DOI: 10.1093/nar/gkaa1263] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 11/16/2022] Open
Abstract
Terminal deoxynucleotidyl transferase (TdT) enzyme plays an integral part in the V(D)J recombination, allowing for the huge diversity in expression of immunoglobulins and T-cell receptors within lymphocytes, through their unique ability to incorporate single nucleotides into oligonucleotides without the need of a template. The role played by TdT in lymphocytes precursors found in early vertebrates is not known. In this paper, we demonstrated a new screening method that utilises TdT to form libraries of variable sized (vsDNA) libraries of polynucleotides that displayed binding towards protein targets. The extent of binding and size distribution of each vsDNA library towards their respective protein target can be controlled through the alteration of different reaction conditions such as time of reaction, nucleotide ratio and initiator concentration raising the possibility for the rational design of aptamers prior to screening. The new approach, allows for the screening of aptamers based on size as well as sequence in a single round, which minimises PCR bias. We converted the protein bound sequences to dsDNA using rapid amplification of variable ends assays (RAVE) and sequenced them using next generation sequencing. The resultant aptamers demonstrated low nanomolar binding and high selectivity towards their respective targets.
Collapse
Affiliation(s)
- Jon Ashley
- Technical University of Denmark, Department of Health Technology, Kgs. Lyngby 2800, Denmark.,International Iberian Nanotechnology Laboratory (INL), Av. Mestre José Veiga Braga 4715-330, Portugal
| | | | - Mohsen Mohammadniaei
- Technical University of Denmark, Department of Health Technology, Kgs. Lyngby 2800, Denmark
| | - Maryam Naseri
- Technical University of Denmark, Department of Health Technology, Kgs. Lyngby 2800, Denmark
| | - Paolo Marcatili
- Technical University of Denmark, Department of Health Technology, Kgs. Lyngby 2800, Denmark
| | - Marta Prado
- International Iberian Nanotechnology Laboratory (INL), Av. Mestre José Veiga Braga 4715-330, Portugal
| | - Yi Sun
- Technical University of Denmark, Department of Health Technology, Kgs. Lyngby 2800, Denmark
| |
Collapse
|
9
|
Komarova N, Barkova D, Kuznetsov A. Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology. Int J Mol Sci 2020; 21:E8774. [PMID: 33233573 PMCID: PMC7699794 DOI: 10.3390/ijms21228774] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HTS) meets this demand of SELEX. Analysis of the data obtained from sequencing of the libraries produced during and after aptamer isolation provides an informative basis for precise aptamer identification and for examining the structure and function of nucleic acid ligands. This review discusses the technical aspects and the potential of the integration of HTS with SELEX.
Collapse
Affiliation(s)
- Natalia Komarova
- Scientific-Manufacturing Complex Technological Centre, 1–7 Shokin Square, Zelenograd, 124498 Moscow, Russia; (D.B.); (A.K.)
| | | | | |
Collapse
|
10
|
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
|
11
|
Komarova N, Kuznetsov A. Inside the Black Box: What Makes SELEX Better? Molecules 2019; 24:E3598. [PMID: 31591283 PMCID: PMC6804172 DOI: 10.3390/molecules24193598] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023] Open
Abstract
Aptamers are small oligonucleotides that are capable of binding specifically to a target, with impressive potential for analysis, diagnostics, and therapeutics applications. Aptamers are isolated from large nucleic acid combinatorial libraries using an iterative selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Since being implemented 30 years ago, the SELEX protocol has undergone many modifications and improvements, but it remains a laborious, time-consuming, and costly method, and the results are not always successful. Each step in the aptamer selection protocol can influence its results. This review discusses key technical points of the SELEX procedure and their influence on the outcome of aptamer selection.
Collapse
Affiliation(s)
- Natalia Komarova
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
| | - Alexander Kuznetsov
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
| |
Collapse
|
12
|
Zhou Y, Qi X, Liu Y, Zhang F, Yan H. DNA-Nanoscaffold-Assisted Selection of Femtomolar Bivalent Human α-Thrombin Aptamers with Potent Anticoagulant Activity. Chembiochem 2019; 20:2494-2503. [PMID: 31083763 DOI: 10.1002/cbic.201900265] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Indexed: 11/11/2022]
Abstract
Multivalent aptamers that interact with their target proteins through multiple sites exhibit much stronger binding strengths than their monovalent counterparts. In this work, we have designed a single-stranded DNA (ssDNA) library (1015 molecules, each 145 nt) based on a predefined DNA nanostructure designed to present two random-loop sites for bivalent aptamer evolution. From this library, a group of ultra-strong bivalent aptamers against human α-thrombin (with apparent KD values of ≈340 fm) were easily identified through a simple seven-round conventional systematic evolution of ligands by exponential enrichment (SELEX) procedure. The dominant bivalent aptamers consist of two components, one binding to exosite I and the other to exosite II. The best of these bivalent aptamers show strong allosteric attenuation of the thrombin cleavage activity and also display an extremely potent anticoagulation effect in human plasma, demonstrating their great potential in therapeutic applications. The method developed here can easily be adapted to conventional SELEX techniques, opening a new route for fast selection of multivalent aptamers with superior binding affinity for other targets.
Collapse
Affiliation(s)
- Yu Zhou
- The Biodesign Institute and School of Molecular Science, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85281, USA
| | - Xiaodong Qi
- The Biodesign Institute and School of Molecular Science, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85281, USA
| | - Yan Liu
- The Biodesign Institute and School of Molecular Science, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85281, USA
| | - Fei Zhang
- The Biodesign Institute and School of Molecular Science, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85281, USA
| | - Hao Yan
- The Biodesign Institute and School of Molecular Science, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85281, USA
| |
Collapse
|
13
|
Matysiak S, Hellmuth K, El-Sagheer AH, Shivalingam A, Ariyurek Y, de Jong M, Hollestelle MJ, Out R, Brown T. Searching for avidity by chemical ligation of combinatorially self-assembled DNA-encoded ligand libraries. Org Biomol Chem 2018; 16:48-52. [DOI: 10.1039/c7ob02119d] [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
DNA encoded ligands are self-assembled into bivalent complexes and chemically ligated to link their identities.
Collapse
Affiliation(s)
| | | | - Afaf H. El-Sagheer
- Department of Chemistry
- University of Oxford
- Chemistry Research Laboratory
- Oxford
- UK
| | - Arun Shivalingam
- Department of Chemistry
- University of Oxford
- Chemistry Research Laboratory
- Oxford
- UK
| | - Yavuz Ariyurek
- Leiden Genome Technology Center
- Leiden University Medical Center
- Leiden
- The Netherlands
| | | | - Martine J. Hollestelle
- Dep. Immunophathology and Blood Coagulation
- Sanquin Diagnostic Services
- Amsterdam
- The Netherlands
| | - Ruud Out
- Piculet-Biosciences BV
- 2333BD Leiden
- The Netherlands
| | - Tom Brown
- Department of Chemistry
- University of Oxford
- Chemistry Research Laboratory
- Oxford
- UK
| |
Collapse
|
14
|
|
15
|
Witt M, Phung NL, Stalke A, Walter JG, Stahl F, von Neuhoff N, Scheper T. Comparing two conventional methods of emulsion PCR and optimizing of Tegosoft-based emulsion PCR. Eng Life Sci 2017; 17:953-958. [PMID: 32624844 DOI: 10.1002/elsc.201700047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/26/2017] [Accepted: 07/14/2017] [Indexed: 12/25/2022] Open
Abstract
The selection of aptamers represents a promising route in the development of high affinity ligands. In these processes the formation of by-products is a common problem during the PCR-based amplification of complex oligonucleotide libraries. One approach to overcome this drawback is to separate each template oligonucleotide into an individual reaction compartment provided by a droplet. This method, termed emulsion PCR (ePCR), has already emerged to a standard method in sample preparation for 2nd generation sequencing. In this work, we compare different literature protocols that have been developed to generate stable emulsions for ePCR. We investigate different emulsification methods and evaluate the importance of the initial template concentration. We demonstrate that emulsion stability is of utmost importance for the successful inhibition of by-product formation and give an optimized protocol for generation of an emulsified PCR.
Collapse
Affiliation(s)
- Martin Witt
- Institute of Technical Chemistry Leibniz University Hannover Hannover Germany
| | - Ngoc Linh Phung
- Institute of Technical Chemistry Leibniz University Hannover Hannover Germany
| | - Amelie Stalke
- Institute for Cellular and Molecular Pathology Hannover Medical School Hannover Germany
| | | | - Frank Stahl
- Institute of Technical Chemistry Leibniz University Hannover Hannover Germany
| | - Nils von Neuhoff
- Department of Pediatric Hematology-Oncology University of Duisburg-Essen Essen Germany
| | - Thomas Scheper
- Institute of Technical Chemistry Leibniz University Hannover Hannover Germany
| |
Collapse
|
16
|
Yüce M, Ullah N, Budak H. Trends in aptamer selection methods and applications. Analyst 2016; 140:5379-99. [PMID: 26114391 DOI: 10.1039/c5an00954e] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aptamers are target specific ssDNA, RNA or peptide sequences generated by an in vitro selection and amplification method called SELEX (Systematic Evolution of Ligands by EXponential Enrichment), which involves repetitive cycles of binding, recovery and amplification steps. Aptamers have the ability to bind with a variety of targets such as drugs, proteins, heavy metals, and pathogens with high specificity and selectivity. Aptamers are similar to monoclonal antibodies regarding their binding affinities, but they offer a number of advantages over the existing antibody-based detection methods, which make the aptamers promising diagnostic and therapeutic tools for future biomedical and analytical applications. The aim of this review article is to provide an overview of the recent advancements in aptamer screening methods along with a concise description of the major application areas of aptamers including biomarker discovery, diagnostics, imaging and nanotechnology.
Collapse
Affiliation(s)
- Meral Yüce
- Sabanci University, Nanotechnology Research and Application Centre, 34956, Istanbul, Turkey.
| | | | | |
Collapse
|
17
|
Trends in the Design and Development of Specific Aptamers Against Peptides and Proteins. Protein J 2016; 35:81-99. [DOI: 10.1007/s10930-016-9653-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
18
|
Ouellet E, Foley JH, Conway EM, Haynes C. Hi-Fi SELEX: A High-Fidelity Digital-PCR Based Therapeutic Aptamer Discovery Platform. Biotechnol Bioeng 2016; 112:1506-22. [PMID: 25727321 DOI: 10.1002/bit.25581] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 02/14/2015] [Indexed: 12/30/2022]
Abstract
Current technologies for aptamer discovery typically leverage the systematic evolution of ligands by exponential enrichment (SELEX) concept by recursively panning semi-combinatorial ssDNA or RNA libraries against a molecular target. The expectation is that this iterative selection process will be sufficiently stringent to identify a candidate pool of specific high-affinity aptamers. However, failure of this process to yield promising aptamers is common, due in part to (i) limitations in library designs, (ii) retention of non-specific aptamers during screening rounds, (iii) excessive accumulation of amplification artifacts, and (iv) the use of screening criteria (binding affinity) that does not reflect therapeutic activity. We report a new selection platform, High-Fidelity (Hi-Fi) SELEX, that introduces fixed-region blocking elements to safeguard the functional diversity of the library. The chemistry of the target-display surface and the composition of the equilibration solvent are engineered to strongly inhibit non-specific retention of aptamers. Partition efficiencies approaching 10(6) are thereby realized. Retained members are amplified in Hi-Fi SELEX by digital PCR in a manner that ensures both elimination of amplification artifacts and stoichiometric conversion of amplicons into the single-stranded library required for the next selection round. Improvements to aptamer selections are first demonstrated using human α-thrombin as the target. Three clinical targets (human factors IXa, X, and D) are then subjected to Hi-Fi SELEX. For each, rapid enrichment of ssDNA aptamers offering an order-nM mean equilibrium dissociation constant (Kd) is achieved within three selection rounds, as quantified by a new label-free qPCR assay reported here. Therapeutic candidates against factor D are identified.
Collapse
|
19
|
Elle IC, Karlsen KK, Terp MG, Larsen N, Nielsen R, Derbyshire N, Mandrup S, Ditzel HJ, Wengel J. Selection of LNA-containing DNA aptamers against recombinant human CD73. MOLECULAR BIOSYSTEMS 2016; 11:1260-70. [PMID: 25720604 DOI: 10.1039/c5mb00045a] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
LNA-containing DNA aptamers against CD73 (human ecto-5'-nucleotidase), a protein frequently overexpressed in solid tumours, were isolated by SELEX. A pre-defined stem-loop library, containing LNA in the forward primer region, was enriched with CD73 binding sequences through six rounds of SELEX with recombinant his-tagged CD73 immobilised on anti-his plates. Enriched pools isolated from rounds one, three and six were subjected to next-generation sequencing and analysed for enrichment using custom bioinformatics software. The software identified aptamer sequences via the primers and then performed several steps including sequence unification, clustering and alignment to identify enriched sequences. Three enriched sequences were synthesised for further analysis, two of which showed sequence similarities. These sequences exhibited binding to the recombinant CD73 with KD values of 10 nM and 3.5 nM when tested by surface plasmon resonance. Truncated variants of these aptamers and variants where the LNA nucleotides were substituted for the DNA equivalent also exhibited affinity for the recombinant CD73 in the low nanomolar range. In enzyme inhibition assays with recombinant CD73 the aptamer sequences were able to decrease the activity of the protein. However, the aptamers exhibited no binding to cellular CD73 by flow cytometry analysis likely since the epitope recognised by the aptamer was not available for binding on the cellular protein.
Collapse
Affiliation(s)
- Ida C Elle
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Fukaya T, Abe K, Savory N, Tsukakoshi K, Yoshida W, Ferri S, Sode K, Ikebukuro K. Improvement of the VEGF binding ability of DNA aptamers through in silico maturation and multimerization strategy. J Biotechnol 2015; 212:99-105. [PMID: 26302839 DOI: 10.1016/j.jbiotec.2015.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 07/25/2015] [Accepted: 08/17/2015] [Indexed: 11/28/2022]
Abstract
Aptamers are mainly selected by in vitro selection using random nucleic acid libraries. These aptamers have often shown insufficient affinity for biomedical applications. We improved DNA aptamer binding affinity for vascular endothelial growth factor (VEGF) through in silico maturation (ISM) and aptamer multimerization. ISM is one of a number of evolutionary approaches and aptamer multimerization is one of several semi-rational strategies to improve function. We first reselected VEGF-binding aptamers using a partially randomized DNA library and identified two aptamers with higher binding ability than that of a known aptamer. We conducted ISM using the re-selected aptamers to optimize the key loop sequences created by a three-way junction structure. After five ISM rounds, we identified aptamer 2G19 [dissociation constant (Kd), 52 nM] as a local optimum of the defined search space. We characterized the aptamer and found that a specific stem-loop structure was involved in aptamer VEGF recognition. To further improve its affinity for VEGF, we multimerized 2G19 or its stem-loop structure. The designed SL5-trivalent aptamer (Kd, 0.37 nM) with three binding motifs significantly increased binding affinity, representing a 500-fold improvement from systematic evolution of ligands by exponential enrichment-selected aptamers.
Collapse
Affiliation(s)
- Takahiro Fukaya
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Koichi Abe
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Nasa Savory
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology, Japan
| | - Stefano Ferri
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Koji Sode
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan.
| |
Collapse
|
21
|
Kobori S, Nomura Y, Miu A, Yokobayashi Y. High-throughput assay and engineering of self-cleaving ribozymes by sequencing. Nucleic Acids Res 2015; 43:e85. [PMID: 25829176 PMCID: PMC4513843 DOI: 10.1093/nar/gkv265] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/17/2015] [Indexed: 01/20/2023] Open
Abstract
Self-cleaving ribozymes are found in all domains of life and are believed to play important roles in biology. Additionally, self-cleaving ribozymes have been the subject of extensive engineering efforts for applications in synthetic biology. These studies often involve laborious assays of multiple individual variants that are either designed rationally or discovered through selection or screening. However, these assays provide only a limited view of the large sequence space relevant to the ribozyme function. Here, we report a strategy that allows quantitative characterization of greater than 1000 ribozyme variants in a single experiment. We generated a library of predefined ribozyme variants that were converted to DNA and analyzed by high-throughput sequencing. By counting the number of cleaved and uncleaved reads of every variant in the library, we obtained a complete activity profile of the ribozyme pool which was used to both analyze and engineer allosteric ribozymes.
Collapse
Affiliation(s)
- Shungo Kobori
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA
| | - Yoko Nomura
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA
| | - Anh Miu
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA
| | - Yohei Yokobayashi
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
| |
Collapse
|