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Majumdar B, Sarma D, Yu Y, Lozoya-Colinas A, Chaput JC. Increasing the functional density of threose nucleic acid. RSC Chem Biol 2024; 5:41-48. [PMID: 38179195 PMCID: PMC10763562 DOI: 10.1039/d3cb00159h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/18/2023] [Indexed: 01/06/2024] Open
Abstract
Chemical strategies that augment genetic polymers with amino acid residues that are overrepresented on the paratope surface of an antibody offer a promising route for enhancing the binding properties of nucleic acid aptamers. Here, we describe the chemical synthesis of α-l-threofuranosyl cytidine nucleoside triphosphate (tCTP) carrying either a benzyl or phenylpropyl side chain at the pyrimidine C-5 position. Polymerase recognition studies indicate that both substrates are readily incorporated into a full-length α-l-threofuranosyl nucleic acid (TNA) product by extension of a DNA primer-template duplex with an engineered TNA polymerase. Similar primer extension reactions performed using nucleoside triphosphate mixtures containing both C-5 modified tCTP and C-5 modified tUTP substrates enable the production of doubly modified TNA strands for a panel of 20 chemotype combinations. Kinetic measurements reveal faster on-rates (kon) and tighter binding affinity constants (Kd) for engineered versions of TNA aptamers carrying chemotypes at both pyrimidine positions as compared to their singly modified counterparts. These findings expand the chemical space of evolvable non-natural genetic polymers by offering a path for improving the quality of biologically stable TNA aptamers for future clinical applications.
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Affiliation(s)
- Biju Majumdar
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - Daisy Sarma
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - Yutong Yu
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - Adriana Lozoya-Colinas
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
- Department of Chemistry, University of California Irvine CA 92697-3958 USA
- Department of Molecular Biology and Biochemistry, University of California Irvine CA 92697-3958 USA
- Department of Chemical and Biomolecular Engineering, University of California Irvine CA 92697-3958 USA
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2
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Kimoto M, Tan HP, Matsunaga KI, Binte Mohd Mislan NA, Kawai G, Hirao I. Strict Interactions of Fifth Letters, Hydrophobic Unnatural Bases, in XenoAptamers with Target Proteins. J Am Chem Soc 2023; 145:20432-20441. [PMID: 37677157 PMCID: PMC10515488 DOI: 10.1021/jacs.3c06122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Indexed: 09/09/2023]
Abstract
XenoAptamers are DNA fragments containing additional letters (unnatural bases, UBs) that bind specifically to their target proteins with high affinities (sub-nanomolar KD values). One of the UBs is the highly hydrophobic 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds), which significantly increases XenoAptamers' affinities to targets. Originally, Ds was developed as a third base pair with a complementary UB, 2-nitro-4-propynylpyrrole (Px), for replication, and thus it can be used for aptamer generation by an evolutional engineering method involving PCR amplification. However, it is unclear whether the Ds base is the best component as the hydrophobic fifth-letter ligand for interactions with target proteins. To optimize the ligand structure of the fifth letter, we prepared 13 Ds variants and examined the affinities of XenoAptamers containing these variants to target proteins. The results obtained using four XenoAptamers prepared by the replacement of Ds bases with variants indicated that subtle changes in the chemical structure of Ds significantly affect the XenoAptamer affinities. Among the variants, placing either 4-(2-thienyl)pyrrolo[2,3-b]pyridine (Ys) or 4-(2-thienyl)benzimidazole (Bs) at specific Ds positions in each original XenoAptamer greatly improved their affinities to targets. The Ys and Bs bases are variants derived by replacing only one nitrogen with a carbon in the Ds base. These results demonstrate the strict intramolecular interactions, which are not simple hydrophobic contacts between UBs and targets, thus providing a method to mature XenoAptamers' affinities to targets.
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Affiliation(s)
- Michiko Kimoto
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | - Hui Pen Tan
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | - Ken-ichiro Matsunaga
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | | | - Gota Kawai
- Chiba
Institute of Technology (CIT), Tsudanuma 2-17-1, Narashino, Chiba 275-0016, Japan
| | - Ichiro Hirao
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
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3
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Kohn EM, Konovalov K, Gomez CA, Hoover GN, Yik AKH, Huang X, Martell JD. Terminal Alkyne-Modified DNA Aptamers with Enhanced Protein Binding Affinities. ACS Chem Biol 2023; 18:1976-1984. [PMID: 37531184 DOI: 10.1021/acschembio.3c00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Nucleic acid-based receptors, known as aptamers, are relatively fast to discover and manufacture but lack the diverse functional groups of protein receptors (e.g., antibodies). The binding properties of DNA aptamers can be enhanced by attaching abiotic functional groups; for example, aromatic groups such as naphthalene slow dissociation from proteins. Although the terminal alkyne is a π-electron-rich functional group that has been used in small molecule drugs to enhance binding to proteins through noncovalent interactions, it remains unexplored for enhancing DNA aptamer binding affinity. Here, we demonstrate the utility of the terminal alkyne for improving the binding of DNA to proteins. We prepared a library of 256 terminal-alkyne-bearing variants of HD22, a DNA aptamer that binds the protein thrombin with nanomolar affinity. After a one-step thrombin-binding selection, a high-affinity aptamer containing two alkynes was discovered, exhibiting 3.2-fold tighter thrombin binding than the corresponding unmodified sequence. The tighter binding was attributable to a slower rate of dissociation from thrombin (5.2-fold slower than HD22). Molecular dynamics simulations with enhanced sampling by Replica Exchange with Solute Tempering (REST2) suggest that the π-electron-rich alkyne interacts with an asparagine side chain N-H group on thrombin, forming a noncovalent interaction that stabilizes the aptamer-protein interface. Overall, this work represents the first case of terminal alkynes enhancing the binding properties of an aptamer and underscores the utility of the terminal alkyne as an atom economical π-electron-rich functional group to enhance binding affinity with minimal steric perturbation.
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Affiliation(s)
- Eric M Kohn
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kirill Konovalov
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Christian A Gomez
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Gillian N Hoover
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Andrew Kai-Hei Yik
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Xuhui Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D Martell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, United States
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4
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Mulholland C, Jestřábová I, Sett A, Ondruš M, Sýkorová V, Manzanares CL, Šimončík O, Muller P, Hocek M. The selection of a hydrophobic 7-phenylbutyl-7-deazaadenine-modified DNA aptamer with high binding affinity for the Heat Shock Protein 70. Commun Chem 2023; 6:65. [PMID: 37024672 PMCID: PMC10079658 DOI: 10.1038/s42004-023-00862-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Nucleic acids aptamers often fail to efficiently target some proteins because of the hydrophilic character of the natural nucleotides. Here we present hydrophobic 7-phenylbutyl-7-deaadenine-modified DNA aptamers against the Heat Shock Protein 70 that were selected via PEX and magnetic bead-based SELEX. After 9 rounds of selection, the pool was sequenced and a number of candidates were identified. Following initial screening, two modified aptamers were chemically synthesised in-house and their binding affinity analysed by two methods, bio-layer interferometry and fluorescent-plate-based binding assay. The binding affinities of the modified aptamers were compared with that of their natural counterparts. The resulting modified aptamers bound with higher affinity (low nanomolar range) to the Hsp70 than their natural sequence (>5 µM) and hence have potential for applications and further development towards Hsp70 diagnostics or even therapeutics.
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Affiliation(s)
- Catherine Mulholland
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Prague, Czech Republic
| | - Ivana Jestřábová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Prague, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague 2, Prague, 12843, Czech Republic
| | - Arghya Sett
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Prague, Czech Republic
| | - Marek Ondruš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Prague, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague 2, Prague, 12843, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Prague, Czech Republic
| | - C Lorena Manzanares
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Prague, Czech Republic
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377, München, Germany
| | - Oliver Šimončík
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53, Brno, Czech Republic
| | - Petr Muller
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53, Brno, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Prague, Czech Republic.
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague 2, Prague, 12843, Czech Republic.
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5
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Xie B, Wang ZP, Zhang R, Zhang Z, He Y. A SERS aptasensor based on porous Au-NC nanoballoons for Staphylococcus aureus detection. Anal Chim Acta 2022; 1190:339175. [PMID: 34857128 DOI: 10.1016/j.aca.2021.339175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/05/2021] [Accepted: 10/13/2021] [Indexed: 12/14/2022]
Abstract
In this work, we developed a new approach for fabricating hollow and porous nitrogen doped carbon nanoballoons loading AuNPs (Au-NC-NBs) with a large specific surface area, a high N and Au content. The surface-enhanced Raman scattering (SERS) aptasensor based on the resulting Au-NC-NBs possess a wider linear range (10 to 107 cells/mL), a lower detection limit (3 cells/mL), better selectivity for detecting bacteria than previously reported sensors. Importantly, Au-NC-NBs SERS aptasensor also exhibits excellent performance for detecting bacteria in the real food and biological samples. This work provides a facile and versatile designing strategy for controlled construction of SERS biosensor by combination of Au nanoparticles and carbon materials, which has a great applied potential in food safety monitoring and clinical diagnosis.
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Affiliation(s)
- Beibei Xie
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, 55 Daxuecheng South Road, 401331, Shapingba, Chongqing, PR China
| | - Zhi-Peng Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, 55 Daxuecheng South Road, 401331, Shapingba, Chongqing, PR China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Ruixue Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, 55 Daxuecheng South Road, 401331, Shapingba, Chongqing, PR China
| | - Zhen Zhang
- Innovation Research Institute of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250355, PR China.
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, 55 Daxuecheng South Road, 401331, Shapingba, Chongqing, PR China.
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6
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Qi S, Duan N, Khan IM, Dong X, Zhang Y, Wu S, Wang Z. Strategies to manipulate the performance of aptamers in SELEX, post-SELEX and microenvironment. Biotechnol Adv 2022; 55:107902. [DOI: 10.1016/j.biotechadv.2021.107902] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023]
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7
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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8
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Ondruš M, Sýkorová V, Bednárová L, Pohl R, Hocek M. Enzymatic synthesis of hypermodified DNA polymers for sequence-specific display of four different hydrophobic groups. Nucleic Acids Res 2020; 48:11982-11993. [PMID: 33152081 PMCID: PMC7708046 DOI: 10.1093/nar/gkaa999] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
A set of modified 2'-deoxyribonucleoside triphosphates (dNTPs) bearing a linear or branched alkane, indole or phenyl group linked through ethynyl or alkyl spacer were synthesized and used as substrates for polymerase synthesis of hypermodified DNA by primer extension (PEX). Using the alkyl-linked dNTPs, the polymerase synthesized up to 22-mer fully modified oligonucleotide (ON), whereas using the ethynyl-linked dNTPs, the enzyme was able to synthesize even long sequences of >100 modified nucleotides in a row. In PCR, the combinations of all four modified dNTPs showed only linear amplification. Asymmetric PCR or PEX with separation or digestion of the template strand can be used for synthesis of hypermodified single-stranded ONs, which are monodispersed polymers displaying four different substituents on DNA backbone in sequence-specific manner. The fully modified ONs hybridized with complementary strands and modified DNA duplexes were found to exist in B-type conformation (B- or C-DNA) according to CD spectral analysis. The modified DNA can be replicated with high fidelity to natural DNA through PCR and sequenced. Therefore, this approach has a promising potential in generation and selection of hypermodified aptamers and other functional polymers.
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Affiliation(s)
- Marek Ondruš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department 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, CZ-16000 Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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9
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Odeh F, Nsairat H, Alshaer W, Ismail MA, Esawi E, Qaqish B, Bawab AA, Ismail SI. Aptamers Chemistry: Chemical Modifications and Conjugation Strategies. Molecules 2019; 25:E3. [PMID: 31861277 PMCID: PMC6982925 DOI: 10.3390/molecules25010003] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/14/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022] Open
Abstract
Soon after they were first described in 1990, aptamers were largely recognized as a new class of biological ligands that can rival antibodies in various analytical, diagnostic, and therapeutic applications. Aptamers are short single-stranded RNA or DNA oligonucleotides capable of folding into complex 3D structures, enabling them to bind to a large variety of targets ranging from small ions to an entire organism. Their high binding specificity and affinity make them comparable to antibodies, but they are superior regarding a longer shelf life, simple production and chemical modification, in addition to low toxicity and immunogenicity. In the past three decades, aptamers have been used in a plethora of therapeutics and drug delivery systems that involve innovative delivery mechanisms and carrying various types of drug cargos. However, the successful translation of aptamer research from bench to bedside has been challenged by several limitations that slow down the realization of promising aptamer applications as therapeutics at the clinical level. The main limitations include the susceptibility to degradation by nucleases, fast renal clearance, low thermal stability, and the limited functional group diversity. The solution to overcome such limitations lies in the chemistry of aptamers. The current review will focus on the recent arts of aptamer chemistry that have been evolved to refine the pharmacological properties of aptamers. Moreover, this review will analyze the advantages and disadvantages of such chemical modifications and how they impact the pharmacological properties of aptamers. Finally, this review will summarize the conjugation strategies of aptamers to nanocarriers for developing targeted drug delivery systems.
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Affiliation(s)
- Fadwa Odeh
- Faculty of Science, The University of Jordan, Amman 11942, Jordan; (F.O.); (H.N.); (A.A.B.)
- Hamdi Mango Center for Scientific Research, The University of Jordan, Amman 11942, Jordan
| | - Hamdi Nsairat
- Faculty of Science, The University of Jordan, Amman 11942, Jordan; (F.O.); (H.N.); (A.A.B.)
| | - Walhan Alshaer
- Cell Therapy Center, The University of Jordan, Amman 11942, Jordan
| | - Mohammad A. Ismail
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
| | - Ezaldeen Esawi
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
| | - Baraa Qaqish
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
| | - Abeer Al Bawab
- Faculty of Science, The University of Jordan, Amman 11942, Jordan; (F.O.); (H.N.); (A.A.B.)
- Hamdi Mango Center for Scientific Research, The University of Jordan, Amman 11942, Jordan
| | - Said I. Ismail
- Faculty of Medicine, The University of Jordan, Amman 11942, Jordan; (M.A.I.); (E.E.); (B.Q.); (S.I.I.)
- Qatar Genome Project, Qatar Foundation, Doha 5825, Qatar
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10
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Pourreza N, Ghomi M. Hydrogel based aptasensor for thrombin sensing by Resonance Rayleigh Scattering. Anal Chim Acta 2019; 1079:180-191. [PMID: 31387709 DOI: 10.1016/j.aca.2019.06.049] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/02/2019] [Accepted: 06/22/2019] [Indexed: 12/12/2022]
Abstract
In this research, a novel Resonance Rayleigh Scattering (RRS) aptasensor was developed for thrombin monitoring using in-situ synthesized and embedded Au nanoparticles (AuNPs) into poly vinyl alcohol -borax hydrogel (PBH). Thiolated-thrombin binding aptamer (thiolated-TBA) was attached to the surface of AuNPs embedded into PBH to design the PBH-aptasensor for thrombin detection (thiolated-TBA@AuNPs-PBH). To verify the characteristic and morphology of PBH nanocomposite, energy dispersive X-ray analysis, TEM, average particle size analizer and UV-Vis spectra were performed. The difference in RRS intensities in the absence and presence of thrombin was calculated and selected as the monitoring signal. Effect of different parameters on the RRS signal was investigated at excitation wavelength of 500 nm. Under the approved conditions, the linear detection range was validated over the concentration of 0.70 pM- 0.02 μM. The limit of detection based on 3Sb was 0.10 pM. The relative standard deviation for 5.6 pM and 3.6 nM were 4.0 and 2.7% (n = 10), respectively. The proposed aptasensor was successfully applied as an experimental model for thrombin detection in serum samples of healthy volunteers with acceptable results.
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Affiliation(s)
- Nahid Pourreza
- Department of Chemistry, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
| | - Matineh Ghomi
- Department of Chemistry, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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11
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Vasiliskov VA, Lapa SA, Kuznetsova VE, Surzhikov SA, Shershov VE, Spitsyn MA, Guseinov TO, Miftahov RA, Zasedateleva OA, Lisitsa AV, Radko SP, Zasedatelev AS, Timofeev EN, Chudinov AV. Novel 5-Alkylcarboxamide-2'-Deoxyuridine-5'-Triphosphates for Enzymatic Synthesis of Highly Modified DNA. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019030063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Lapa SA, Pavlov AS, Kuznetsova VE, Shershov VE, Spitsyn MA, Guseinov TO, Radko SP, Zasedatelev AS, Lisitsa AV, Chudinov AV. Enzymatic Preparation of Modified DNA: Study of the Kinetics by Real-Time PCR. Mol Biol 2019. [DOI: 10.1134/s0026893319030099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Lei Y, Washington J, Hili R. Efficiency and fidelity of T3 DNA ligase in ligase-catalysed oligonucleotide polymerisations. Org Biomol Chem 2019; 17:1962-1965. [PMID: 30357247 PMCID: PMC6374181 DOI: 10.1039/c8ob01958d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ligase-catalyzed oligonucleotide polymerisations (LOOPER) can readily generate libraries of diversely-modified nucleic acid polymers, which can be subjected to iterative rounds of in vitro selection to evolve functional activity. While there exist several different DNA ligases, T4 DNA ligase has most often been used for the process. Recently, T3 DNA ligase was shown to be effective in LOOPER; however, little is known about the fidelity and efficiency of this enzyme in LOOPER. In this paper we evaluate the efficiency of T3 DNA ligase and T4 DNA ligase for various codon lengths and compositions within the context of polymerisation fidelity and yield. We find that T3 DNA ligase exhibits high efficiency and fidelity with short codon lengths, but struggles with longer and more complex codon libraries, while T4 DNA ligase exhibits the opposite trend. Interestingly, T3 DNA ligase is unable to accommodate modifications at the 8-position of adenosine when integrated into short codons, which will create challenges in expanding the available codon set for the process. The limitations and strengths of the two ligases are further discussed within the context of LOOPER.
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Affiliation(s)
- Yi Lei
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA
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14
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Antipova OM, Zavyalova EG, Golovin AV, Pavlova GV, Kopylov AM, Reshetnikov RV. Advances in the Application of Modified Nucleotides in SELEX Technology. BIOCHEMISTRY (MOSCOW) 2018; 83:1161-1172. [PMID: 30472954 DOI: 10.1134/s0006297918100024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aptamers are widely used as molecular recognition elements for detecting and blocking functional biological molecules. Since the common "alphabet" of DNA and RNA consists of only four letters, the chemical diversity of aptamers is less than the diversity of protein recognition elements built of 20 amino acids. Chemical modification of nucleotides enlarges the potential of DNA/RNA aptamers. This review describes the latest achievements in a variety of approaches to aptamers selection with an extended genetic alphabet.
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Affiliation(s)
- O M Antipova
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia. .,Apto-Pharm Ltd., Moscow, 115564, Russia
| | - E G Zavyalova
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.,Apto-Pharm Ltd., Moscow, 115564, Russia
| | - A V Golovin
- Apto-Pharm Ltd., Moscow, 115564, Russia.,Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234, Russia.,Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, 119991, Russia
| | - G V Pavlova
- Apto-Pharm Ltd., Moscow, 115564, Russia.,Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, 119991, Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.,Burdenko National Scientific and Practical Center for Neurosurgery, Ministry of Healthcare of the Russian Federation, Moscow, 125047, Russia
| | - A M Kopylov
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.,Apto-Pharm Ltd., Moscow, 115564, Russia
| | - R V Reshetnikov
- Apto-Pharm Ltd., Moscow, 115564, Russia.,Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234, Russia.,Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, 119991, Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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15
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Röthlisberger P, Hollenstein M. Aptamer chemistry. Adv Drug Deliv Rev 2018; 134:3-21. [PMID: 29626546 DOI: 10.1016/j.addr.2018.04.007] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/12/2022]
Abstract
Aptamers are single-stranded DNA or RNA molecules capable of tightly binding to specific targets. These functional nucleic acids are obtained by an in vitro Darwinian evolution method coined SELEX (Systematic Evolution of Ligands by EXponential enrichment). Compared to their proteinaceous counterparts, aptamers offer a number of advantages including a low immunogenicity, a relative ease of large-scale synthesis at affordable costs with little or no batch-to-batch variation, physical stability, and facile chemical modification. These alluring properties have propelled aptamers into the forefront of numerous practical applications such as the development of therapeutic and diagnostic agents as well as the construction of biosensing platforms. However, commercial success of aptamers still proceeds at a weak pace. The main factors responsible for this delay are the susceptibility of aptamers to degradation by nucleases, their rapid renal filtration, suboptimal thermal stability, and the lack of functional group diversity. Here, we describe the different chemical methods available to mitigate these shortcomings. Particularly, we describe the chemical post-SELEX processing of aptamers to include functional groups as well as the inclusion of modified nucleoside triphosphates into the SELEX protocol. These methods will be illustrated with successful examples of chemically modified aptamers used as drug delivery systems, in therapeutic applications, and as biosensing devices.
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16
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Identification and characterization of nucleobase-modified aptamers by click-SELEX. Nat Protoc 2018; 13:1153-1180. [PMID: 29700486 DOI: 10.1038/nprot.2018.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Aptamers are single-stranded oligonucleotides that are in vitro-selected to recognize their target molecule with high affinity and specificity. As they consist of the four canonical nucleobases, their chemical diversity is limited, which in turn limits the addressable target spectrum. Introducing chemical modifications into nucleic acid libraries increases the interaction capabilities of the DNA and thereby the target spectrum. Here, we describe a protocol to select nucleobase-modified aptamers by using click chemistry (CuAAC) to introduce the preferred chemical modification. The use of click chemistry to modify the DNA library enables the introduction of a wide range of possible functionalities, which can be customized to the requirements of the target molecule and the desired application. This protocol yields modified DNA aptamers with extended interaction properties that are not accessible with the canonical set of nucleotides. After synthesis of the starting library containing a commercially available, alkyne-modified uridine (5-ethynyl-deoxyuridine (EdU)) instead of thymidine, the library is functionalized with the modification of choice by CuAAC. The thus-modified DNA is incubated with the target molecule and the best binding sequences are recovered. The chemical modification is removed during the amplification process. Therefore, this protocol is compatible with conventional amplification procedures and avoids enzymatic incompatibility problems associated with more extensive nucleobase modifications. After single-strand generation, the modification is reintroduced into the enriched library, which can then be subjected to the subsequent selection cycle. The duration of each selection cycle as outlined in the protocol is ∼1 d.
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17
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Wang Y, Ng N, Liu E, Lam CH, Perrin DM. Systematic study of constraints imposed by modified nucleoside triphosphates with protein-like side chains for use in in vitro selection. Org Biomol Chem 2018; 15:610-618. [PMID: 27942671 DOI: 10.1039/c6ob02335e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Successful selection of modified DNAzymes depends on the potential for modified nucleoside triphosphates (dNTPs) to replace their unmodified counterparts in enzyme catalyzed primer extension reactions and, once incorporated, to serve as template bases for information transfer prior to PCR amplification. To date, the most densely modified DNAzymes have been selected from three modified dNTPs: 8-histaminyl-deoxyadenosine (dAimTP), 5-guanidinoallyl-deoxyuridine (dUgaTP), and 5-aminoallyl-deoxycytidine (dCaaTP) to provide several RNA-cleaving DNAzymes with greatly enhanced rate constants compared to unmodified counterparts. Here we report biophysical and enzymatic properties of these three modified nucleosides in the context of specific oligonucleotide sequences to understand how these three modified nucleobases function in combinatorial selection. The base-pairing abilities of oligonucleotides bearing one or three modified nucleosides were investigated by thermal denaturation studies and as templates for enzymatic polymerization with both modified and unmodified dNTPs. While we address certain shortcomings in the use of modified dNTPs, we also provide key evidence of faithful incorporation and enzymatic read-out, which strongly supports their continued use in in vitro selection.
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Affiliation(s)
- Yajun Wang
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - Nicole Ng
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - Erkai Liu
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - Curtis H Lam
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
| | - David M Perrin
- Chemistry Department, UBC, 2036 Main Mall, Vancouver, BC, V6T-1Z1 Canada.
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18
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Renders M, Miller E, Lam CH, Perrin DM. Whole cell-SELEX of aptamers with a tyrosine-like side chain against live bacteria. Org Biomol Chem 2018; 15:1980-1989. [PMID: 28009914 DOI: 10.1039/c6ob02451c] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In an effort to expand the binding and recognition capabilities of aptamers, a nucleoside triphosphate modified with a phenol that mimics the side chain of tyrosine was used in the selection of DNA aptamers against live bacteria. Of multiple modified aptamers that were isolated against Escherichia coli DH5α cells, one aptamer displays high selectivity and affinity for the target cells and is greatly enriched for phenol-modified dU nucleotides (dUy, 47.5%). When the same sequences are synthesized with TTP, no binding is observed. Taken together, these findings highlight the value of using modified nucleotide triphosphates in aptamer selections and portends success in SELEX against an array of whole cells as targets.
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Affiliation(s)
- Marleen Renders
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
| | - Emily Miller
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
| | - Curtis H Lam
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
| | - David M Perrin
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
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19
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20
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Gao W, Li B, Yao R, Li Z, Wang X, Dong X, Qu H, Li Q, Li N, Chi H, Zhou B, Xia Z. Intuitive Label-Free SERS Detection of Bacteria Using Aptamer-Based in Situ Silver Nanoparticles Synthesis. Anal Chem 2017; 89:9836-9842. [PMID: 28803475 DOI: 10.1021/acs.analchem.7b01813] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The characteristic of an ideal bacteria-detection method should have high sensitivity and specificity, be easy to operate, and not have a time-consuming culture process. In this study, we report a new bacteria-detection strategy that can recognize bacteria quickly and directly by surface-enhanced Raman scattering (SERS) with the formation of well-defined bacteria-aptamer@AgNPs. SERS signals generated by bacteria-aptamer@AgNPs exhibited a linear dependence on bacteria (R2 = 0.9671) concentration ranging from 101 to 107 cfu/mL. The detection limit is sensitive down to 1.5 cfu/mL. Meanwhile, the bacteria SERS signal was dramatically enhanced by its specifically recognized aptamer, and the bacteria could be identified directly and visually through the SERS spectrum. This strategy eliminates the puzzling data analysis of previous studies and offers significant advantages over existing approaches, getting a critical step toward the creation of SERS-based biochips for rapid in situ bacteria detection in mixture samples.
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Affiliation(s)
- Weicun Gao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China.,College of Animal Sciences and Technology, Jilin Agricultural University , Changchun 130118, China
| | - Bo Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Ruizhi Yao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University , Daqing 163000, Heilongjiang, China
| | - Zhiping Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Xiwen Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Xiaolin Dong
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Han Qu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Qianxue Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Nan Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Hang Chi
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Bo Zhou
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
| | - Zhiping Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS Changchun 130122, China
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21
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Pfeiffer F, Rosenthal M, Siegl J, Ewers J, Mayer G. Customised nucleic acid libraries for enhanced aptamer selection and performance. Curr Opin Biotechnol 2017; 48:111-118. [PMID: 28437710 DOI: 10.1016/j.copbio.2017.03.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 03/28/2017] [Accepted: 03/30/2017] [Indexed: 12/24/2022]
Abstract
Aptamers are short single-stranded oligo(deoxy)nucleotides that are selected to bind to target molecules with high affinity and specificity. Because of their sophisticated characteristics and versatile applicability, aptamers are thought to become universal molecular probes in biotechnological and therapeutic applications. However, the variety of possible interactions with a putative target molecule is limited by the chemical repertoire of the natural nucleobases. Consequently, many desired targets are not addressable by aptamers. This obstacle is overcome by broadening the chemical diversity of aptamers, mainly achieved by nucleobase-modifications and the introduction of novel bases or base pairs. We discuss these achievements and the characteristics of the respective modified aptamers, reflected by SOMAmers (slow off-rate modified aptamers), clickmers, and aptamers bearing an expanded genetic alphabet.
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Affiliation(s)
- Franziska Pfeiffer
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Malte Rosenthal
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Julia Siegl
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Jörg Ewers
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany; Center of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany.
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22
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Abstract
Aptamers are now used ubiquitously as binding agents for a broad range of applications. Natural (unmodified) DNA and RNA aptamers have considerably less chemical diversity than protein-based ligands such as antibodies, limiting their utility. Aptamers possessing a single chemical modification have helped bridge this diversity gap. We report the selection and identification of aptamers with two diversity-enhancing chemical modifications that bind and inhibit proprotein convertase subtilisin/kexin type 9 (PCSK9), a representative human therapeutic protein target. The addition of a second modification, especially in certain pairwise combinations, resulted in significant improvements in affinity, ligand efficiency, epitope coverage, metabolic stability, and inhibitory activity. Extensively chemically functionalized aptamers have the potential to become the next generation of nucleic-acid–based ligands. The nucleobases comprising DNA and RNA aptamers provide considerably less chemical diversity than protein-based ligands, limiting their versatility. The introduction of novel functional groups at just one of the four bases in modified aptamers has recently led to dramatic improvement in the success rate of identifying nucleic acid ligands to protein targets. Here we explore the benefits of additional enhancement in physicochemical diversity by selecting modified DNA aptamers that contain amino-acid–like modifications on both pyrimidine bases. Using proprotein convertase subtilisin/kexin type 9 as a representative protein target, we identify specific pairwise combinations of modifications that result in higher affinity, metabolic stability, and inhibitory potency compared with aptamers with single modifications. Such doubly modified aptamers are also more likely to be encoded in shorter sequences and occupy nonoverlapping epitopes more frequently than aptamers with single modifications. These highly modified DNA aptamers have broad utility in research, diagnostic, and therapeutic applications.
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23
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Minagawa H, Onodera K, Fujita H, Sakamoto T, Akitomi J, Kaneko N, Shiratori I, Kuwahara M, Horii K, Waga I. Selection, Characterization and Application of Artificial DNA Aptamer Containing Appended Bases with Sub-nanomolar Affinity for a Salivary Biomarker. Sci Rep 2017; 7:42716. [PMID: 28256555 PMCID: PMC5335659 DOI: 10.1038/srep42716] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/12/2017] [Indexed: 12/21/2022] Open
Abstract
We have attained a chemically modified DNA aptamer against salivary α-amylase (sAA), which attracts researchers’ attention as a useful biomarker for assessing human psychobiological and social behavioural processes, although high affinity aptamers have not been isolated from a random natural DNA library to date. For the selection, we used the base-appended base (BAB) modification, that is, a modified-base DNA library containing (E)-5-(2-(N-(2-(N6-adeninyl)ethyl))carbamylvinyl)-uracil in place of thymine. After eight rounds of selection, a 75 mer aptamer, AMYm1, which binds to sAA with extremely high affinity (Kd < 1 nM), was isolated. Furthermore, we have successfully determined the 36-mer minimum fragment, AMYm1-3, which retains target binding activity comparable to the full-length AMYm1, by surface plasmon resonance assays. Nuclear magnetic resonance spectral analysis indicated that the minimum fragment forms a specific stable conformation, whereas the predicted secondary structures were suggested to be disordered forms. Thus, DNA libraries with BAB-modifications can achieve more diverse conformations for fitness to various targets compared with natural DNA libraries, which is an important advantage for aptamer development. Furthermore, using AMYm1, a capillary gel electrophoresis assay and lateral flow assay with human saliva were conducted, and its feasibility was demonstrated.
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Affiliation(s)
- Hirotaka Minagawa
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Kentaro Onodera
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Hiroto Fujita
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino 275-0016, Japan
| | - Joe Akitomi
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Naoto Kaneko
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Ikuo Shiratori
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Katsunori Horii
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Iwao Waga
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
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24
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Abstract
Aptamers are nucleic acid-based scaffolds that can bind with high affinity to a variety of biological targets. Aptamers are identified from large DNA or RNA libraries through a process of directed molecular evolution (SELEX). Chemical modification of nucleic acids considerably increases the functional and structural diversity of aptamer libraries and substantially increases the affinity of the aptamers. Additionally, modified aptamers exhibit much greater resistance to biodegradation. The evolutionary selection of modified aptamers is conditioned by the possibility of the enzymatic synthesis and replication of non-natural nucleic acids. Wild-type or mutant polymerases and their non-natural nucleotide substrates that can support SELEX are highlighted in the present review. A focus is made on the efforts to find the most suitable type of nucleotide modifications and the engineering of new polymerases. Post-SELEX modification as a complementary method will be briefly considered as well.
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Affiliation(s)
- Sergey A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Alexander V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Edward N Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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25
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Jin NZ, Gopinath SC. Potential blood clotting factors and anticoagulants. Biomed Pharmacother 2016; 84:356-365. [DOI: 10.1016/j.biopha.2016.09.057] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/06/2016] [Accepted: 09/15/2016] [Indexed: 12/20/2022] Open
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26
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Lipi F, Chen S, Chakravarthy M, Rakesh S, Veedu RN. In vitro evolution of chemically-modified nucleic acid aptamers: Pros and cons, and comprehensive selection strategies. RNA Biol 2016; 13:1232-1245. [PMID: 27715478 PMCID: PMC5207382 DOI: 10.1080/15476286.2016.1236173] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA oligonucleotide sequences that bind to a specific target molecule with high affinity and specificity through their ability to adopt 3-dimensional structure in solution. Aptamers have huge potential as targeted therapeutics, diagnostics, delivery agents and as biosensors. However, aptamers composed of natural nucleotide monomers are quickly degraded in vivo and show poor pharmacodynamic properties. To overcome this, chemically-modified nucleic acid aptamers are developed by incorporating modified nucleotides after or during the selection process by Systematic Evolution of Ligands by EXponential enrichment (SELEX). This review will discuss the development of chemically-modified aptamers and provide the pros and cons, and new insights on in vitro aptamer selection strategies by using chemically-modified nucleic acid libraries.
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Affiliation(s)
- Farhana Lipi
- a Western Australian Neuroscience Research Institute , Perth , Australia
| | - Suxiang Chen
- a Western Australian Neuroscience Research Institute , Perth , Australia.,b Centre for Comparative Genomics, Murdoch University , Perth , Australia
| | - Madhuri Chakravarthy
- a Western Australian Neuroscience Research Institute , Perth , Australia.,b Centre for Comparative Genomics, Murdoch University , Perth , Australia
| | - Shilpa Rakesh
- a Western Australian Neuroscience Research Institute , Perth , Australia
| | - Rakesh N Veedu
- a Western Australian Neuroscience Research Institute , Perth , Australia.,b Centre for Comparative Genomics, Murdoch University , Perth , Australia
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27
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Teramoto N, Imanishi Y, Ito Y. In Vitro Selection of Ligase Ribozymes Containing 2'-Amino Groups. J BIOACT COMPAT POL 2016. [DOI: 10.1177/088391150001500402] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Novel ribozymes containing 2'-amino groups in the side chains were in vitro selected to accelerate their ligation reaction rates with oligodeoxynucleotides. The ligation rate of random sequenced RNAs in the starting pool was accelerated by incorporation of 2'-amino-2'-deoxyuridine and N6-(6-aminohexyl)adenosine. The incorporation of the amino group enhanced the activity of non-selected RNAs independent of the incorporation site. In vitro selection using 2'-amino-2'-deoxyuridine instead of uridine produced more active ribozymes. In this case, the activity of ribozyme was reduced when N6-(6-aminohexyl)adenosine was incorporated into the selected RNAs instead of natural adenosine. The presence of amino groups as well as the incorporation site affected the activity of the in vitro selected ribozyme. It seems that RNAs with tertiary structures suitable for the ligation reaction were selected by the in vitro method.
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Affiliation(s)
- Naozumi Teramoto
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 660-8501 Japan
| | - Yukio Imanishi
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma 630-0101 Japan
| | - Yoshihiro Ito
- Department of Biological Science and Technology, Faculty of Engineering, The University of Tokushima, Tokushima 770-8506 Japan
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28
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Miao Y, Gan N, Ren HX, Li T, Cao Y, Hu F, Yan Z, Chen Y. A triple-amplification colorimetric assay for antibiotics based on magnetic aptamer-enzyme co-immobilized platinum nanoprobes and exonuclease-assisted target recycling. Analyst 2016; 140:7663-71. [PMID: 26442572 DOI: 10.1039/c5an01142f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Herein, an ultrasensitive and selective colorimetric assay for antibiotics, using chloramphenicol (CAP) as the model analyte, was developed based on magnetic aptamer-HRP-platinum composite probes and exonuclease-assisted target recycling. The composite probes were prepared through immunoreactions between the double stranded DNA antibody (anti-DNA) labeled on core-shell Fe3O4@Au nanoparticles (AuMNP-anti-DNA) as the capture probe, and the double stranded aptamer (aptamer hybrid with its complementary oligonucleotides) labeled on Pt@HRP nanoparticles as the nanotracer (ds-Apt-HRP-PtNPs). When the CAP samples were incubated with the probes for 30 min at room temperature, they could be captured by the aptamer to form a nanotracer-CAP complex, which was then released into the supernatant after magnetic separation. This is because the anti-DNA on the capture probes cannot recognize the single strand aptamer-CAP complex. The exonuclease I (Exo I) added into the supernatant can further digest the aptamer-CAP from the 3'-end of the aptamer and the CAP in the aptamer-CAP complex can be released again, which can further participate in a new cycling process to react with the probes. Pt and HRP in the nanotracer could both catalyze and dual amplify the absorbance at 650 nm ascribed to the 3,3',5,5'-tetramethylbenzidine (TMB)-H2O2 system. Moreover, Exo I can assist the target recycling, which can further amplify the signal. Thus, the triple amplified signal can be quantified by ultraviolet-visible spectroscopy. The experimental results showed that the CAP detection possessed a linear range of 0.001-10 ng mL(-1) and a detection limit of 0.0003 ng mL(-1) (S/N = 3). The assay was successfully employed to detect CAP in milk, which is much more facile, time saving, and sensitive than the commercial ELISA kits.
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Affiliation(s)
- Yangbao Miao
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Ning Gan
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Hong-Xia Ren
- Key Laboratory of Asymmetric Synthesis and Chirotechnology of Sichuan Province, Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Tianhua Li
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Yuting Cao
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Futao Hu
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Zhongdan Yan
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Yinji Chen
- Faculty of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, 210000, China
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29
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Kong D, Yeung W, Hili R. Generation of Synthetic Copolymer Libraries by Combinatorial Assembly on Nucleic Acid Templates. ACS COMBINATORIAL SCIENCE 2016; 18:355-70. [PMID: 27275512 DOI: 10.1021/acscombsci.6b00059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent advances in nucleic acid-templated copolymerization have expanded the scope of sequence-controlled synthetic copolymers beyond the molecular architectures witnessed in nature. This has enabled the power of molecular evolution to be applied to synthetic copolymer libraries to evolve molecular function ranging from molecular recognition to catalysis. This Review seeks to summarize different approaches available to generate sequence-defined monodispersed synthetic copolymer libraries using nucleic acid-templated polymerization. Key concepts and principles governing nucleic acid-templated polymerization, as well as the fidelity of various copolymerization technologies, will be described. The Review will focus on methods that enable the combinatorial generation of copolymer libraries and their molecular evolution for desired function.
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Affiliation(s)
- Dehui Kong
- Department of Chemistry, University of Georgia, 140 Cedar
Street, Athens, Georgia 30602, United States
| | - Wayland Yeung
- Department of Chemistry, University of Georgia, 140 Cedar
Street, Athens, Georgia 30602, United States
| | - Ryan Hili
- Department of Chemistry, University of Georgia, 140 Cedar
Street, Athens, Georgia 30602, United States
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30
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Fareed J. Antithrombin Agents as Anticoagulants and Antithrombotics: Implications in Drug Development. Clin Appl Thromb Hemost 2016. [DOI: 10.1177/107602969800400403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Antithrombin agents of recombinant and synthetic origin are now validated in experimental models as useful an ticoagulant and antithrombic drugs. Several clinical trials in cluding surgical anticoagulation, management of coronary syn dromes, adjunct to thrombolytic agents and treatment of throm boembolism have also shown the comparative efficacy of these agents in reference to heparin. Argatroban and hirudin are now available for specific clinical indications such as thrombotic and ischemic stroke and alternate anticoagulants for heparin- induced thrombocytopenia (HIT) patients in Japan and Euro pean countries, respectively. While these agents produce strong anticoagulant effects, their mechanism of action is distinct from that of heparins, thus these agents should be used carefully using specific guidelines provided for each product. Thrombin inhibitors are effective anticoagulants however, their therapeu tic index is narrower than heparin and as such their nonopti mized use is potentially associated with hemorrhagic compli cations.
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Affiliation(s)
- Jawed Fareed
- Departments of Pathology and Pharmacology, Loyola University Medical Center, Maywood, Illinois, U.S.A
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31
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Dellafiore MA, Montserrat JM, Iribarren AM. Modified Nucleoside Triphosphates for In-vitro Selection Techniques. Front Chem 2016; 4:18. [PMID: 27200340 PMCID: PMC4854868 DOI: 10.3389/fchem.2016.00018] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/05/2016] [Indexed: 12/22/2022] Open
Abstract
The development of SELEX (Selective Enhancement of Ligands by Exponential Enrichment) provides a powerful tool for the search of functional oligonucleotides with the ability to bind ligands with high affinity and selectivity (aptamers) and for the discovery of nucleic acid sequences with diverse enzymatic activities (ribozymes and DNAzymes). This technique has been extensively applied to the selection of natural DNA or RNA molecules but, in order to improve chemical and structural diversity as well as for particular applications where further chemical or biological stability is necessary, the extension of this strategy to modified oligonucleotides is desirable. Taking into account these needs, this review intends to collect the research carried out during the past years, focusing mainly on the use of modified nucleotides in SELEX and the development of mutant enzymes for broadening nucleoside triphosphates acceptance. In addition, comments regarding the synthesis of modified nucleoside triphosphate will be briefly discussed.
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Affiliation(s)
- María A Dellafiore
- Laboratorio de Química de Ácidos Nucleicos, INGEBI (CONICET) Ciudad Autónoma de Buenos Aires, Argentina
| | - Javier M Montserrat
- Laboratorio de Química de Ácidos Nucleicos, INGEBI (CONICET)Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Ciencias, Universidad Nacional de General SarmientoLos Polvorines, Argentina
| | - Adolfo M Iribarren
- Laboratorio de Química de Ácidos Nucleicos, INGEBI (CONICET)Ciudad Autónoma de Buenos Aires, Argentina; Laboratorio de Biotransformaciones, Universidad Nacional de QuilmesBernal, Argentina
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32
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Meek KN, Rangel AE, Heemstra JM. Enhancing aptamer function and stability via in vitro selection using modified nucleic acids. Methods 2016; 106:29-36. [PMID: 27012179 DOI: 10.1016/j.ymeth.2016.03.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 11/29/2022] Open
Abstract
Nucleic acid aptamers have emerged as a promising alternative to antibodies for use as recognition elements in therapeutics, bioimaging, and analytical applications. A key benefit that aptamers possess relative to antibodies is their ability to be chemically synthesized. This advantage, coupled with the broad range of modified nucleotide building blocks that can be constructed using chemical synthesis, has enabled the discovery and development of modified aptamers having extraordinary affinity, specificity, and biostability. Early efforts to generate modified aptamers focused on selection of a native DNA or RNA aptamer, followed by post-selection trial-and-error testing of modifications. However, recent advances in polymerase engineering and templated nucleic acid synthesis have enabled the direct selection of aptamers having modified backbones and nucleobases. This review will discuss these technological advances and highlight the improvements in aptamer function that have been realized through in vitro selection of non-natural nucleic acids.
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Affiliation(s)
- Kirsten N Meek
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, 315 S 1400 E, Salt Lake City, UT 84112, United States
| | - Alexandra E Rangel
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, 315 S 1400 E, Salt Lake City, UT 84112, United States
| | - Jennifer M Heemstra
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, 315 S 1400 E, Salt Lake City, UT 84112, United States.
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33
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Zhu Q, Liu G, Kai M. DNA Aptamers in the Diagnosis and Treatment of Human Diseases. Molecules 2015; 20:20979-97. [PMID: 26610462 PMCID: PMC6332121 DOI: 10.3390/molecules201219739] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/16/2015] [Accepted: 11/16/2015] [Indexed: 02/07/2023] Open
Abstract
Aptamers have a promising role in the field of life science and have been extensively researched for application as analytical tools, therapeutic agents and as vehicles for targeted drug delivery. Compared with RNA aptamers, DNA aptamers have inherent advantages in stability and facility of generation and synthesis. To better understand the specific potential of DNA aptamers, an overview of the progress in the generation and application of DNA aptamers in human disease diagnosis and therapy are presented in this review. Special attention is given to researches that are relatively close to practical application. DNA aptamers are expected to have great potential in the diagnosis and treatment of human diseases.
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Affiliation(s)
- Qinchang Zhu
- Faculty of Pharmaceutical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
| | - Ge Liu
- Department of Genomic Epidemiology, Research Center for Environment and Developmental Medical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka 812-8582, Japan.
| | - Masaaki Kai
- Faculty of Pharmaceutical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
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Generation of Aptamers with an Expanded Chemical Repertoire. Molecules 2015; 20:16643-71. [PMID: 26389865 PMCID: PMC6332006 DOI: 10.3390/molecules200916643] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 08/28/2015] [Accepted: 09/01/2015] [Indexed: 01/03/2023] Open
Abstract
The enzymatic co-polymerization of modified nucleoside triphosphates (dN*TPs and N*TPs) is a versatile method for the expansion and exploration of expanded chemical space in SELEX and related combinatorial methods of in vitro selection. This strategy can be exploited to generate aptamers with improved or hitherto unknown properties. In this review, we discuss the nature of the functionalities appended to nucleoside triphosphates and their impact on selection experiments. The properties of the resulting modified aptamers will be described, particularly those integrated in the fields of biomolecular diagnostics, therapeutics, and in the expansion of genetic systems (XNAs).
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35
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Abstract
Aptamers, as a novel class of molecular probes for diagnosis, imaging and targeting therapy, have attracted increasing attention in recent years. Aptamers are generated from libraries of single-stranded nucleic acids against different molecules via the "systematic evolution of ligands by exponential enrichment" (SELEX) method. SELEX is a repetitive process of a sequential selection procedure in which a DNA or RNA library pool is incubated separately with target and control molecules to select specific oligonucleotide aptamers with high affinities and specificities. Cell-SELEX is a modified version of the SELEX process in which whole living cells are used as targets for the aptamers. Dendritic cell (DC) targeting, as a new therapeutic approach, can improve the efficiency of immunotherapy in the treatment of allergies and cancers. DCs use various receptors to continuously induce adaptive immunity via capture and presentation of antigens to naïve T cells. DCs are considered as the best targets in modulating immune responses against cancer, autoimmunity, allergy and transplantation. Aptamers, as a new agent, can be applied in DC targeting. The purpose of this review is to present some general concepts of aptamer production and DC targeting by aptamer molecules.
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Affiliation(s)
- A Ganji
- a Student Research Committee , Mashhad University of Medical Sciences , Mashhad , Iran .,b Immunology Research Center, Medical School, Mashhad University of Medical Sciences , Mashhad , Iran , and
| | - A Varasteh
- c Allergy Research Center, Medical School, Mashhad University of Medical Sciences , Mashhad , Iran
| | - M Sankian
- b Immunology Research Center, Medical School, Mashhad University of Medical Sciences , Mashhad , Iran , and
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36
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Identification and Characterization of an eIF4e DNA Aptamer That Inhibits Proliferation With High Throughput Sequencing. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e217. [PMID: 25514650 PMCID: PMC4272410 DOI: 10.1038/mtna.2014.70] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/06/2014] [Indexed: 12/19/2022]
Abstract
Development of DNA aptamer screens that are both simple and informative can increase the success rate of DNA aptamer selection and induce greater adoption. High eIF4e levels contribute to malignancies, thus eIF4e presents itself as a valuable target for DNA aptamer-based inhibition screen. Here, we demonstrate a method for the rapid selection of looped DNA aptamers against eIF4e by combining negative selection and purification in a single step, followed by characterization with high throughput sequencing. The resulting aptamers show functional binding to eIF4e and inhibit translation initiation in biochemical assays. When transfected into cells, eIF4e aptamers cause a dramatic loss of cell proliferation in tumor cells as seen with eIF4e knockdown with antisense oligonucleotides, shRNAs, and siRNAs, hinting at therapeutic possibilities. With the large data set provided by high throughput sequencing, we demonstrate that selection happens in waves and that sequencing data can be used to infer aptamer structure. Lastly, we show that ligation of looped aptamers can enhance their functional effects. These results demonstrate a rapid protocol to screen and optimize aptamers against macromolecules of interest.
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37
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Anandhakumar C, Kizaki S, Bando T, Pandian GN, Sugiyama H. Advancing Small-Molecule-Based Chemical Biology with Next-Generation Sequencing Technologies. Chembiochem 2014; 16:20-38. [DOI: 10.1002/cbic.201402556] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Indexed: 12/24/2022]
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38
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Nucleic Acid Ligands With Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e201. [PMID: 25291143 PMCID: PMC4217074 DOI: 10.1038/mtna.2014.49] [Citation(s) in RCA: 347] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/12/2014] [Indexed: 12/30/2022]
Abstract
Limited chemical diversity of nucleic acid libraries has long been suspected to be a major constraining factor in the overall success of SELEX (Systematic Evolution of Ligands by EXponential enrichment). Despite this constraint, SELEX has enjoyed considerable success over the past quarter of a century as a result of the enormous size of starting libraries and conformational richness of nucleic acids. With judicious introduction of functional groups absent in natural nucleic acids, the “diversity gap” between nucleic acid–based ligands and protein-based ligands can be substantially bridged, to generate a new class of ligands that represent the best of both worlds. We have explored the effect of various functional groups at the 5-position of uracil and found that hydrophobic aromatic side chains have the most profound influence on the success rate of SELEX and allow the identification of ligands with very low dissociation rate constants (named Slow Off-rate Modified Aptamers or SOMAmers). Such modified nucleotides create unique intramolecular motifs and make direct contacts with proteins. Importantly, SOMAmers engage their protein targets with surfaces that have significantly more hydrophobic character compared with conventional aptamers, thereby increasing the range of epitopes that are available for binding. These improvements have enabled us to build a collection of SOMAmers to over 3,000 human proteins encompassing major families such as growth factors, cytokines, enzymes, hormones, and receptors, with additional SOMAmers aimed at pathogen and rodent proteins. Such a large and growing collection of exquisite affinity reagents expands the scope of possible applications in diagnostics and therapeutics.
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39
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Coiled-coil peptide based sensor for ultra-sensitive thrombin detection. Biosens Bioelectron 2014; 55:26-31. [DOI: 10.1016/j.bios.2013.11.070] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/15/2013] [Accepted: 11/25/2013] [Indexed: 01/21/2023]
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40
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Hollenstein M, Smith CC, Räz M. Nucleoside triphosphates--from synthesis to biochemical characterization. J Vis Exp 2014:51385. [PMID: 24747811 PMCID: PMC4162383 DOI: 10.3791/51385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The traditional strategy for the introduction of chemical functionalities is the use of solid-phase synthesis by appending suitably modified phosphoramidite precursors to the nascent chain. However, the conditions used during the synthesis and the restriction to rather short sequences hamper the applicability of this methodology. On the other hand, modified nucleoside triphosphates are activated building blocks that have been employed for the mild introduction of numerous functional groups into nucleic acids, a strategy that paves the way for the use of modified nucleic acids in a wide-ranging palette of practical applications such as functional tagging and generation of ribozymes and DNAzymes. One of the major challenges resides in the intricacy of the methodology leading to the isolation and characterization of these nucleoside analogues. In this video article, we present a detailed protocol for the synthesis of these modified analogues using phosphorous(III)-based reagents. In addition, the procedure for their biochemical characterization is divulged, with a special emphasis on primer extension reactions and TdT tailing polymerization. This detailed protocol will be of use for the crafting of modified dNTPs and their further use in chemical biology.
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Affiliation(s)
| | | | - Michael Räz
- Department of Chemistry and Biochemistry, University of Bern
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41
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Stovall GM, Bedenbaugh RS, Singh S, Meyer AJ, Hatala PJ, Ellington AD, Hall B. In vitro selection using modified or unnatural nucleotides. ACTA ACUST UNITED AC 2014; 56:9.6.1-33. [PMID: 25606981 DOI: 10.1002/0471142700.nc0906s56] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Incorporation of modified nucleotides into in vitro RNA or DNA selections offers many potential advantages, such as the increased stability of selected nucleic acids against nuclease degradation, improved affinities, expanded chemical functionality, and increased library diversity. This unit provides useful information and protocols for in vitro selection using modified nucleotides. It includes a discussion of when to use modified nucleotides; protocols for evaluating and optimizing transcription reactions, as well as confirming the incorporation of the modified nucleotides; protocols for evaluating modified nucleotide transcripts as template in reverse transcription reactions; protocols for the evaluation of the fidelity of modified nucleotides in the replication and the regeneration of the pool; and a protocol to compare modified nucleotide pools and selection conditions.
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Affiliation(s)
- Gwendolyn M Stovall
- The University of Texas at Austin, Austin, Texas; Altermune Technologies LLC, Austin, Texas
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42
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Kong HY, Byun J. Nucleic Acid aptamers: new methods for selection, stabilization, and application in biomedical science. Biomol Ther (Seoul) 2014; 21:423-34. [PMID: 24404332 PMCID: PMC3879913 DOI: 10.4062/biomolther.2013.085] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 11/05/2013] [Accepted: 11/05/2013] [Indexed: 12/19/2022] Open
Abstract
The adoption of oligonucleotide aptamer is well on the rise, serving an ever increasing demand for versatility in biomedical field. Through the SELEX (Systematic Evolution of Ligands by EXponential enrichment), aptamer that can bind to specific target with high affinity and specificity can be obtained. Aptamers are single-stranded nucleic acid molecules that can fold into complex threedimensional structures, forming binding pockets and clefts for the specific recognition and tight binding of any given molecular target. Recently, aptamers have attracted much attention because they not only have all of the advantages of antibodies, but also have unique merits such as thermal stability, ease of synthesis, reversibility, and little immunogenicity. The advent of novel technologies is revolutionizing aptamer applications. Aptamers can be easily modified by various chemical reactions to introduce functional groups and/or nucleotide extensions. They can also be conjugated to therapeutic molecules such as drugs, drug containing carriers, toxins, or photosensitizers. Here, we discuss new SELEX strategies and stabilization methods as well as applications in drug delivery and molecular imaging.
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Affiliation(s)
- Hoon Young Kong
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, Dankook University, Yongin 448-701, Republic of Korea
| | - Jonghoe Byun
- Department of Molecular Biology, Institute of Nanosensor and Biotechnology, Dankook University, Yongin 448-701, Republic of Korea
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43
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Lollo B, Steele F, Gold L. Beyond antibodies: new affinity reagents to unlock the proteome. Proteomics 2014; 14:638-44. [PMID: 24395722 DOI: 10.1002/pmic.201300187] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 11/28/2013] [Accepted: 12/16/2013] [Indexed: 12/20/2022]
Abstract
Antibodies have been the workhorse reagents of protein capture and quantification since their 1959 debut in the RIAs developed by Yalow and Berson. However, there are technical challenges to the use of antibodies in highly multiplexed arrays aimed at measuring hundreds or even thousands of proteins at one time. We describe here a recently developed class of synthetic protein-binding reagents (slow off-rate modified aptamer). We discuss the chemical makeup and protein binding specifications of slow off-rate modified aptamer reagents, compare them to traditional aptamers and antibodies, briefly describe the novel proteomic assay that takes advantage of their unique properties, and provide several examples of their multiple applications to biomarker discovery and validation across a range of biomedical science questions.
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44
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Szeto K, Latulippe DR, Ozer A, Pagano JM, White BS, Shalloway D, Lis JT, Craighead HG. RAPID-SELEX for RNA aptamers. PLoS One 2013; 8:e82667. [PMID: 24376564 PMCID: PMC3869713 DOI: 10.1371/journal.pone.0082667] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 10/26/2013] [Indexed: 01/11/2023] Open
Abstract
Aptamers are high-affinity ligands selected from DNA or RNA libraries via SELEX, a repetitive in vitro process of sequential selection and amplification steps. RNA SELEX is more complicated than DNA SELEX because of the additional transcription and reverse transcription steps. Here, we report a new selection scheme, RAPID-SELEX (RNA Aptamer Isolation via Dual-cycles SELEX), that simplifies this process by systematically skipping unnecessary amplification steps. Using affinity microcolumns, we were able to complete a multiplex selection for protein targets, CHK2 and UBLCP1, in a third of the time required for analogous selections using a conventional SELEX approach. High-throughput sequencing of the enriched pools from both RAPID and SELEX revealed many identical candidate aptamers from the starting pool of 5×1015 sequences. For CHK2, the same sequence was preferentially enriched in both selections as the top candidate and was found to bind to its respective target. These results demonstrate the efficiency and, most importantly, the robustness of our selection scheme. RAPID provides a generalized approach that can be used with any selection technology to accelerate the rate of aptamer discovery, without compromising selection performance.
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Affiliation(s)
- Kylan Szeto
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| | - David R Latulippe
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| | - Abdullah Ozer
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - John M Pagano
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Brian S White
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - David Shalloway
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Harold G Craighead
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
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45
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Kasahara Y, Irisawa Y, Fujita H, Yahara A, Ozaki H, Obika S, Kuwahara M. Capillary electrophoresis-systematic evolution of ligands by exponential enrichment selection of base- and sugar-modified DNA aptamers: target binding dominated by 2'-O,4'-C-methylene-bridged/locked nucleic acid primer. Anal Chem 2013; 85:4961-7. [PMID: 23662585 DOI: 10.1021/ac400058z] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chemically modified DNA aptamers specific to human α-thrombin were obtained from oligodeoxyribonucleotide (ODN) libraries by using a capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX) method. These libraries contained 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides (B/L nucleotides) in the primer region and/or C5-modified thymidine bearing N(6)-ethyladenine (t) in the nonprimer region. Modified DNA aptamers showed high binding affinities to the target, with dissociation constants (Kd) values in the range of subnanomolar to several ten nanomolar levels. The introduction of base modification significantly suppressed the frequency of G-quadruplex motifs, which are often seen in thrombin-binding DNA aptamers. The resulting alternatives contained the 10-mer consensus sequence t5Gt2G2, which is frequently found in modified DNA aptamers with subnanomolar protein binding affinities. Furthermore, some base- and sugar-modified DNA aptamers with the 12-mer consensus sequence t2G2tC(A/G)A2G2t displayed binding activities that were dependent on the presence of B/L nucleotides in the primer region. Such aptamers were interestingly not recovered from a natural DNA library or from DNA libraries modified with either B/L nucleotides or t's. This emerging characteristic binding property will enable the creation of a direct selection methodology for DNA-based molecular switches that are triggered by chemical conversion of B/L nucleotides introduced to constant sequence regions in ODN libraries.
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Affiliation(s)
- Yuuya Kasahara
- Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, Japan
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46
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Orava EW, Abdul-Wahid A, Huang EHB, Mallick AI, Gariépy J. Blocking the attachment of cancer cells in vivo with DNA aptamers displaying anti-adhesive properties against the carcinoembryonic antigen. Mol Oncol 2013; 7:799-811. [PMID: 23656757 DOI: 10.1016/j.molonc.2013.03.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/27/2013] [Accepted: 03/31/2013] [Indexed: 01/28/2023] Open
Abstract
The formation of metastatic foci occurs through a series of cellular events, initiated by the attachment and aggregation of cancer cells leading to the establishment of micrometastases. We report the derivation of synthetic DNA aptamers bearing anti-adhesive properties directed at cancer cells expressing the carcinoembryonic antigen (CEA). Two DNA aptamers targeting the homotypic and heterotypic IgV-like binding domain of CEA were shown to block the cell adhesion properties of CEA, while not recognizing other IgV-like domains of CEACAM family members that share strong sequence and structural homologies. More importantly, the pre-treatment of CEA-expressing tumour cells with these aptamers prior to their intraperitoneal implantation resulted in the prevention of peritoneal tumour foci formation. Taken together, these results highlight the effectiveness of targeting the cell adhesion properties of cancer cells with aptamers in preventing tumour implantation.
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Affiliation(s)
- Erik W Orava
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
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47
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Tolle F, Mayer G. Dressed for success – applying chemistry to modulate aptamer functionality. Chem Sci 2013. [DOI: 10.1039/c2sc21510a] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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48
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Hollenstein M. Nucleoside triphosphates--building blocks for the modification of nucleic acids. Molecules 2012; 17:13569-91. [PMID: 23154273 PMCID: PMC6268876 DOI: 10.3390/molecules171113569] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 11/07/2012] [Accepted: 11/09/2012] [Indexed: 11/16/2022] Open
Abstract
Nucleoside triphosphates are moldable entities that can easily be functionalized at various locations. The enzymatic polymerization of these modified triphosphate analogues represents a versatile platform for the facile and mild generation of (highly) functionalized nucleic acids. Numerous modified triphosphates have been utilized in a broad palette of applications spanning from DNA-tagging and -labeling to the generation of catalytic nucleic acids. This review will focus on the recent progress made in the synthesis of modified nucleoside triphosphates as well as on the understanding of the mechanisms underlying their polymerase acceptance. In addition, the usefulness of chemically altered dNTPs in SELEX and related methods of in vitro selection will be highlighted, with a particular emphasis on the generation of modified DNA enzymes (DNAzymes) and DNA-based aptamers.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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49
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Kasahara Y, Kuwahara M. Artificial specific binders directly recovered from chemically modified nucleic acid libraries. J Nucleic Acids 2012; 2012:156482. [PMID: 23094139 PMCID: PMC3472525 DOI: 10.1155/2012/156482] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 08/19/2012] [Indexed: 11/18/2022] Open
Abstract
Specific binders comprised of nucleic acids, that is, RNA/DNA aptamers, are attractive functional biopolymers owing to their potential broad application in medicine, food hygiene, environmental analysis, and biological research. Despite the large number of reports on selection of natural DNA/RNA aptamers, there are not many examples of direct screening of chemically modified nucleic acid aptamers. This is because of (i) the inferior efficiency and accuracy of polymerase reactions involving transcription/reverse-transcription of modified nucleotides compared with those of natural nucleotides, (ii) technical difficulties and additional time and effort required when using modified nucleic acid libraries, and (iii) ambiguous efficacies of chemical modifications in binding properties until recently; in contrast, the effects of chemical modifications on biostability are well studied using various nucleotide analogs. Although reports on the direct screening of a modified nucleic acid library remain in the minority, chemical modifications would be essential when further functional expansion of nucleic acid aptamers, in particular for medical and biological uses, is considered. This paper focuses on enzymatic production of chemically modified nucleic acids and their application to random screenings. In addition, recent advances and possible future research are also described.
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Affiliation(s)
- Yuuya Kasahara
- Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu 376-8515, Japan
| | - Masayasu Kuwahara
- Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu 376-8515, Japan
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50
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Hoon S, Zhou B, Janda KD, Brenner S, Scolnick J. Aptamer selection by high-throughput sequencing and informatic analysis. Biotechniques 2012; 51:413-6. [PMID: 22150332 DOI: 10.2144/000113786] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 11/03/2011] [Indexed: 11/23/2022] Open
Abstract
Traditional methods for selecting aptamers require multiple rounds of selection and optimization in order to identify aptamers that bind with high affinity to their targets. Here we describe an assay that requires only one round of positive selection followed by high-throughput DNA sequencing and informatic analysis in order to select high-affinity aptamers. The assay is flexible, requires less hands on time, and can be used by laboratories with minimal expertise in aptamer biology to quickly select high-affinity aptamers to a target of interest. This assay has been utilized to successfully identify aptamers that bind to thrombin with dissociation constants in the nanomolar range.
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Affiliation(s)
- Shawn Hoon
- Molecular Engineering Lab, Agency for Science Technology and Research, Singapore
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