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Hoffmann ES, De Pascali MC, Neu L, Domnick C, Soldà A, Kath-Schorr S. Reverse transcription as key step in RNA in vitro evolution with unnatural base pairs. RSC Chem Biol 2024; 5:556-566. [PMID: 38846072 PMCID: PMC11151862 DOI: 10.1039/d4cb00084f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/23/2024] [Indexed: 06/09/2024] Open
Abstract
Unnatural base pairs (UBPs) augment the chemical diversity of artificial nucleic acids and can thus enable the generation of new aptamers and catalytic nucleic acids by in vitro selection. However, owing to a lack of methodologies, the reverse transcription of UBPs, a key step in RNA aptamer selection, has not been sufficiently characterized. Here, we present a series of versatile assays to investigate the reverse transcription of the TPT3:NaM base pair as a representative for hydrophobic unnatural base pairs. We determine the fidelity and retention of the UBP for four different reverse transcriptases (RT) in the context of RNA in vitro evolution. The retention of the TPT3:NaM pair during the RNA in vitro selection process was investigated using a novel click-chemistry based electromobility shift assay. Real-time monitoring of reverse transcription kinetics revealed considerable differences in polymerase activity processing the TPT3:NaM base pair. Our findings identified SuperScript IV RT as the most efficient RT for processing the TPT3:NaM pair. Our approach can be applied universally to study newly developed UBPs, not only at the reverse transcription level, but also during PCR and in vitro transcription.
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Affiliation(s)
- Eva S Hoffmann
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne Greinstrasse 4 50939 Cologne Germany
| | - Mareike C De Pascali
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience Garching 85748 Germany
- Dynamic Biosensors GmbH Perchtinger Str. 8/10 Munich 81379 Germany
| | - Lukas Neu
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne Greinstrasse 4 50939 Cologne Germany
| | - Christof Domnick
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne Greinstrasse 4 50939 Cologne Germany
| | - Alice Soldà
- Dynamic Biosensors GmbH Perchtinger Str. 8/10 Munich 81379 Germany
| | - Stephanie Kath-Schorr
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne Greinstrasse 4 50939 Cologne Germany
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2
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Tan HP, Kimoto M, Hirao I. Advancing Genetic Alphabet Expansion: Synthesis of 7-(2-Thienyl)-Imidazo[4,5-b]pyridine (Ds) and 4-(4-Pentyne-1,2-diol)-1-Propynyl-2-Nitropyrrole (Diol-Px) for Use in Replicable Unnatural Base Pairs for PCR Applications. Curr Protoc 2024; 4:e1009. [PMID: 38572677 DOI: 10.1002/cpz1.1009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Expanding the genetic alphabet enhances DNA recombinant technologies by introducing unnatural base pairs (UBPs) beyond the standard A-T and G-C pairs, leading to biomaterials with novel and increased functionalities. Recent developments include UBPs that effectively function as a third base pair in replication, transcription, and/or translation processes. One such UBP, Ds-Px, demonstrates extremely high specificity in replication. Chemically synthesized DNA fragments containing Ds bases are amplified by PCR with the 5'-triphosphates of Ds and Px deoxyribonucleosides (dDsTP and dPxTP). The Ds-Px pair system has applications in enhanced DNA data storage, generation of high-affinity DNA aptamers, and incorporation of functional elements into RNA through transcription. This protocol describes the synthesis of the amidite derivative of Ds (dDs amidite), the triphosphate dDsTP, and the diol-modified dPxTP (Diol-dPxTP) for PCR amplifications involving the Ds-Px pair. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of Ds deoxyribonucleoside (dDs) Basic Protocol 2: Synthesis of dDs amidite Basic Protocol 3: Synthesis of dDs triphosphate (dDsTP) Basic Protocol 4: Synthesis of Pn deoxyribonucleoside (4-iodo-dPn) Basic Protocol 5: Synthesis of acetyl-protected diol-modified Px deoxyribonucleoside (Diol-dPx) Basic Protocol 6: Synthesis of Diol-dPx triphosphate (Diol-dPxTP) Basic Protocol 7: Purification of triphosphates Support Protocol 1: Synthesis of Hoffer's chlorosugar Support Protocol 2: Preparation of 0.5 M pyrophosphate in DMF Support Protocol 3: Preparation of 2 M TEAB buffer.
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3
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Wang G, Du Y, Chen T. Enzymatic Preparation of DNA with an Expanded Genetic Alphabet Using Terminal Deoxynucleotidyl Transferase and Its Applications. Methods Mol Biol 2024; 2760:133-145. [PMID: 38468086 DOI: 10.1007/978-1-0716-3658-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Efficient preparation of DNA oligonucleotides containing unnatural nucleobases (UBs) that can pair with their cognates to form unnatural base pairs (UBPs) is an essential prerequisite for the application of UBPs in vitro and in vivo. Traditional preparation of oligonucleotides containing unnatural nucleobases largely relies on solid-phase synthesis, which needs to use unstable nucleoside phosphoramidites and a DNA synthesizer, and is environmentally unfriendly and limited in product length. To overcome these limitations of solid-phase synthesis, we developed enzymatic methods for daily laboratory preparation of DNA oligonucleotides containing unnatural nucleobase dNaM, dTPT3, or one of the functionalized dTPT3 derivatives, which can be used for orthogonal DNA labeling or the preparation of DNAs containing UBP dNaM-dTPT3, one of the most successful UBPs to date, based on the template-independent polymerase terminal deoxynucleotidyl transferase (TdT). Here, we first provide a detailed procedure for the TdT-based preparation of DNA oligonucleotides containing 3'-nucleotides of dNaM, dTPT3, or one of dTPT3 derivatives. We then present the procedures for enzyme-linked oligonucleotide assay (ELONA) and imaging of bacterial cells using DNA oligonucleotides containing 3'-nucleotides of dTPT3 derivatives with different functional groups. The procedure for enzymatic synthesis of DNAs containing an internal UBP dNaM-dTPT3 is also described. Hopefully, these methods will greatly facilitate the application of UBPs and the construction of semi-synthetic organisms with an expanded genetic alphabet.
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Affiliation(s)
- Guangyuan Wang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.
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Akiyama Y, Harada K, Miyakawa J, Kreder KJ, O’Donnell MA, Daichi M, Katoh H, Hori M, Owari K, Futami K, Ishikawa S, Ushiku T, Kume H, Homma Y, Luo Y. Th1/17 polarization and potential treatment by an anti-interferon-γ DNA aptamer in Hunner-type interstitial cystitis. iScience 2023; 26:108262. [PMID: 38026177 PMCID: PMC10663743 DOI: 10.1016/j.isci.2023.108262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/03/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Hunner-type interstitial cystitis (HIC) is a rare, enigmatic inflammatory disease of the urinary bladder with no curative treatments. In this study, we aimed to characterize the unique cellular and immunological factors specifically involved in HIC by comparing with cystitis induced by Mycobacterium bovis bacillus Calmette-Guérin, which presents similar clinicopathological features to HIC. Here, we show that T helper 1/17 +polarized immune responses accompanied by prominent overexpression of interferon (IFN)-γ, enhanced cGAS-STING cytosolic DNA sensing pathway, and increased plasma cell infiltration are the characteristic inflammatory features in HIC bladder. Further, we developed a mouse anti-IFN-γ DNA aptamer and observed that the intravesical instillation of the aptamer significantly ameliorated bladder inflammation, pelvic pain and voiding dysfunction in a recently developed murine HIC model with little migration into the blood. Our study provides the plausible basis for the clinical translation of the anti-IFN-γ DNA aptamer in the treatment of human HIC.
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Affiliation(s)
- Yoshiyuki Akiyama
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Urology, University of Iowa, Iowa City, IA, USA
| | | | - Jimpei Miyakawa
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Karl J. Kreder
- Department of Urology, University of Iowa, Iowa City, IA, USA
| | | | - Maeda Daichi
- Department of Molecular and Cellular Pathology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroto Katoh
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | | | | | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukio Homma
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Interstitial Cystitis Medicine, Faculty of Medicine, Kyorin University, Tokyo, Japan
| | - Yi Luo
- Department of Urology, University of Iowa, Iowa City, IA, USA
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5
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DeRosa M, Lin A, Mallikaratchy P, McConnell E, McKeague M, Patel R, Shigdar S. In vitro selection of aptamers and their applications. NATURE REVIEWS. METHODS PRIMERS 2023; 3:55. [PMID: 37969927 PMCID: PMC10647184 DOI: 10.1038/s43586-023-00247-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The introduction of the in-vitro evolution method known as SELEX (Systematic Evolution of Ligands by Exponential enrichment) more than 30 years ago led to the conception of versatile synthetic receptors known as aptamers. Offering many benefits such as low cost, high stability and flexibility, aptamers have sparked innovation in molecular diagnostics, enabled advances in synthetic biology and have facilitated new therapeutic approaches. The SELEX method itself is inherently adaptable and offers near limitless possibilities in yielding functional nucleic acid ligands. This Primer serves to provide guidance on experimental design and highlight new growth areas for this impactful technology.
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Affiliation(s)
- M.C. DeRosa
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - A. Lin
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
| | - P. Mallikaratchy
- Department of Molecular, Cellular, and Biomedical Sciences, City University of New York School of Medicine, New York, NY 10031, USA
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - E.M. McConnell
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - M. McKeague
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada, H3G 1Y6
| | - R. Patel
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - S. Shigdar
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, VIC 3220, Australia
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Farahbakhsh Z, Zamani M, Nasirian V, Shariati L, Kermani S, Karizmeh MS, Rafienia M. An insight into fluorescence and magnetic resonance bioimaging using a multifunctional polyethyleneimine-passivated gadocarbon dots nanoconstruct assembled with AS1411. Mikrochim Acta 2023; 190:275. [PMID: 37358641 DOI: 10.1007/s00604-023-05853-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/29/2023] [Indexed: 06/27/2023]
Abstract
A nanoassembly of PEI-passivated Gd@CDs, a type of aptamer, is presented which was designed and characterized in order to target specific cancer cells based on their recognition of the receptor nucleolin (NCL), which is overexpressed on the cell membrane of breast cancer cells for fluorescence and magnetic resonance imaging and treatment. Using hydrothermal methods, Gd-doped nanostructures were synthesized, then modified by a two-step chemical procedure for subsequent applications: the passivating of Gd@CDs with branched polyethyleneimine (PEI) (to form Gd@CDs-PEI1 and Gd@CDs-PEI2), and using AS1411 aptamer (AS) as a DNA-targeted molecule (to generate AS/Gd@CDs-PEI1 and AS/Gd@CDs-PEI2). Consequently, these nanoassemblies were constructed as a result of electrostatic interactions between cationic Gd@CDs-passivated PEI and AS aptamers, offering efficient multimodal targeting nanoassemblies for cancer cell detection. It has been demonstrated through in vitro studies that both types of AS-conjugated nanoassemblies are highly biocompatible, have high cellular uptake efficiency (equivalent concentration of AS: 0.25 μΜ), and enable targeted fluorescence imaging in nucleolin-positive MCF7 and MDA-MB-231 cancer cells compared to MCF10-A normal cells. Importantly, the as-prepared Gd@CDs, Gd@CDs-PEI1, and Gd@CDs-PEI2 exhibit higher longitudinal relaxivity values (r1) compared with the commercial Gd-DTPA, equal to 5.212, 7.488, and 5.667 mM-1s-1, respectively. Accordingly, it is concluded that the prepared nanoassemblies have the potential to become excellent candidates for cancer targeting and fluorescence/MR imaging agents, which can be applied to cancer imaging and personalized nanomedicine.
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Affiliation(s)
- Zohreh Farahbakhsh
- Department of Biology, Nourdanesh Institute of Higher Education, Meymeh, Isfahan, Iran
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Biosensor Research Center (BRC), Isfahan University of Medical Sciences (IUMS), Isfahan, Iran
| | - Mohammadreza Zamani
- Department of Biology, Nourdanesh Institute of Higher Education, Meymeh, Isfahan, Iran
| | - Vahid Nasirian
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa Hospitals and Clinics, Iowa City, IA, 52242, USA
| | - Laleh Shariati
- Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, IR, Iran
- Department of Biomaterials, Nanotechnology and Tissue Engineering, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Saeed Kermani
- Department of Bioelectric and Biomedical Engineering, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohsen Shie Karizmeh
- Department of Biomaterials, Nanotechnology and Tissue Engineering, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Rafienia
- Biosensor Research Center (BRC), Isfahan University of Medical Sciences (IUMS), Isfahan, Iran.
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7
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In vitro evolution of ribonucleases from expanded genetic alphabets. Proc Natl Acad Sci U S A 2022; 119:e2208261119. [PMID: 36279447 PMCID: PMC9636917 DOI: 10.1073/pnas.2208261119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability of nucleic acids to catalyze reactions (as well as store and transmit information) is important for both basic and applied science, the first in the context of molecular evolution and the origin of life and the second for biomedical applications. However, the catalytic power of standard nucleic acids (NAs) assembled from just four nucleotide building blocks is limited when compared with that of proteins. Here, we assess the evolutionary potential of libraries of nucleic acids with six nucleotide building blocks as reservoirs for catalysis. We compare the outcomes of in vitro selection experiments toward RNA-cleavage activity of two nucleic acid libraries: one built from the standard four independently replicable nucleotides and the other from six, with the two added nucleotides coming from an artificially expanded genetic information system (AEGIS). Results from comparative experiments suggest that DNA libraries with increased chemical diversity, higher information density, and larger searchable sequence spaces are one order of magnitude richer reservoirs of molecules that catalyze the cleavage of a phosphodiester bond in RNA than DNA libraries built from a standard four-nucleotide alphabet. Evolved AEGISzymes with nitro-carrying nucleobase Z appear to exploit a general acid–base catalytic mechanism to cleave that bond, analogous to the mechanism of the ribonuclease A family of protein enzymes and heavily modified DNAzymes. The AEGISzyme described here represents a new type of catalysts evolved from libraries built from expanded genetic alphabets.
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Kimoto M, Hirao I. Genetic Code Engineering by Natural and Unnatural Base Pair Systems for the Site-Specific Incorporation of Non-Standard Amino Acids Into Proteins. Front Mol Biosci 2022; 9:851646. [PMID: 35685243 PMCID: PMC9171071 DOI: 10.3389/fmolb.2022.851646] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/25/2022] [Indexed: 12/21/2022] Open
Abstract
Amino acid sequences of proteins are encoded in nucleic acids composed of four letters, A, G, C, and T(U). However, this four-letter alphabet coding system limits further functionalities of proteins by the twenty letters of amino acids. If we expand the genetic code or develop alternative codes, we could create novel biological systems and biotechnologies by the site-specific incorporation of non-standard amino acids (or unnatural amino acids, unAAs) into proteins. To this end, new codons and their complementary anticodons are required for unAAs. In this review, we introduce the current status of methods to incorporate new amino acids into proteins by in vitro and in vivo translation systems, by focusing on the creation of new codon-anticodon interactions, including unnatural base pair systems for genetic alphabet expansion.
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Affiliation(s)
| | - Ichiro Hirao
- *Correspondence: Michiko Kimoto, ; Ichiro Hirao,
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A review on the therapeutic applications of aptamers and aptamer-conjugated nanoparticles in cancer, inflammatory and viral diseases. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2021.103626] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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10
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Zhu G, Song P, Wu J, Luo M, Chen Z, Chen T. Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective. Front Bioeng Biotechnol 2022; 9:792489. [PMID: 35071205 PMCID: PMC8777461 DOI: 10.3389/fbioe.2021.792489] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids underlie the storage and retrieval of genetic information literally in all living organisms, and also provide us excellent materials for making artificial nanostructures and scaffolds for constructing multi-enzyme systems with outstanding performance in catalyzing various cascade reactions, due to their highly diverse and yet controllable structures, which are well determined by their sequences. The introduction of unnatural moieties into nucleic acids dramatically increased the diversity of sequences, structures, and properties of the nucleic acids, which undoubtedly expanded the toolbox for making nanomaterials and scaffolds of multi-enzyme systems. In this article, we first introduce the molecular structures and properties of nucleic acids and their unnatural derivatives. Then we summarized representative artificial nanomaterials made of nucleic acids, as well as their properties, functions, and application. We next review recent progress on constructing multi-enzyme systems with nucleic acid structures as scaffolds for cascade biocatalyst. Finally, we discuss the future direction of applying nucleic acid frameworks in the construction of nanomaterials and multi-enzyme molecular machines, with the potential contribution that unnatural nucleic acids may make to this field highlighted.
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Affiliation(s)
- Gan Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ping Song
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jing Wu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Minglan Luo
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhipeng Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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Iturriaga-Goyon E, Vivanco-Rojas O, Magaña-Guerrero FS, Buentello-Volante B, Castro-Salas I, Aguayo-Flores JE, Gracia-Mora I, Rivera-Huerta M, Sánchez-Bartés F, Garfias Y. AS1411 Nucleolin-Specific Binding Aptamers Reduce Pathological Angiogenesis through Inhibition of Nucleolin Phosphorylation. Int J Mol Sci 2021; 22:13150. [PMID: 34884955 PMCID: PMC8658263 DOI: 10.3390/ijms222313150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 12/30/2022] Open
Abstract
Proliferative retinopathies produces an irreversible type of blindness affecting working age and pediatric population of industrialized countries. Despite the good results of anti-VEGF therapy, intraocular and systemic complications are often associated after its intravitreal use, hence novel therapeutic approaches are needed. The aim of the present study is to test the effect of the AS1411, an antiangiogenic nucleolin-binding aptamer, using in vivo, ex vivo and in vitro models of angiogenesis and propose a mechanistic insight. Our results showed that AS1411 significantly inhibited retinal neovascularization in the oxygen induced retinopathy (OIR) in vivo model, as well as inhibited branch formation in the rat aortic ex vivo assay, and, significantly reduced proliferation, cell migration and tube formation in the HUVEC in vitro model. Importantly, phosphorylated NCL protein was significantly abolished in HUVEC in the presence of AS1411 without affecting NFκB phosphorylation and -21 and 221-angiomiRs, suggesting that the antiangiogenic properties of this molecule are partially mediated by a down regulation in NCL phosphorylation. In sum, this new research further supports the NCL role in the molecular etiology of pathological angiogenesis and identifies AS1411 as a novel anti-angiogenic treatment.
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Affiliation(s)
- Emilio Iturriaga-Goyon
- MD/Ph.D. (PECEM) Program, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico;
- Research Unit, Institute of Ophthalmology, Conde de Valenciana, Chimalpopoca 14, Ciudad de Mexico 06800, Mexico; (O.V.-R.); (F.S.M.-G.); (B.B.-V.); (I.C.-S.); (J.E.A.-F.)
| | - Oscar Vivanco-Rojas
- Research Unit, Institute of Ophthalmology, Conde de Valenciana, Chimalpopoca 14, Ciudad de Mexico 06800, Mexico; (O.V.-R.); (F.S.M.-G.); (B.B.-V.); (I.C.-S.); (J.E.A.-F.)
| | - Fátima Sofía Magaña-Guerrero
- Research Unit, Institute of Ophthalmology, Conde de Valenciana, Chimalpopoca 14, Ciudad de Mexico 06800, Mexico; (O.V.-R.); (F.S.M.-G.); (B.B.-V.); (I.C.-S.); (J.E.A.-F.)
| | - Beatriz Buentello-Volante
- Research Unit, Institute of Ophthalmology, Conde de Valenciana, Chimalpopoca 14, Ciudad de Mexico 06800, Mexico; (O.V.-R.); (F.S.M.-G.); (B.B.-V.); (I.C.-S.); (J.E.A.-F.)
| | - Ilse Castro-Salas
- Research Unit, Institute of Ophthalmology, Conde de Valenciana, Chimalpopoca 14, Ciudad de Mexico 06800, Mexico; (O.V.-R.); (F.S.M.-G.); (B.B.-V.); (I.C.-S.); (J.E.A.-F.)
| | - José Eduardo Aguayo-Flores
- Research Unit, Institute of Ophthalmology, Conde de Valenciana, Chimalpopoca 14, Ciudad de Mexico 06800, Mexico; (O.V.-R.); (F.S.M.-G.); (B.B.-V.); (I.C.-S.); (J.E.A.-F.)
| | - Isabel Gracia-Mora
- Unidad de Experimentación Preclínica, Department of Inorganic and Nuclear Chemistry, Faculty of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad de Mexico 04510, Mexico; (I.G.-M.); (M.R.-H.); (F.S.-B.)
| | - Marisol Rivera-Huerta
- Unidad de Experimentación Preclínica, Department of Inorganic and Nuclear Chemistry, Faculty of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad de Mexico 04510, Mexico; (I.G.-M.); (M.R.-H.); (F.S.-B.)
| | - Francisco Sánchez-Bartés
- Unidad de Experimentación Preclínica, Department of Inorganic and Nuclear Chemistry, Faculty of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad de Mexico 04510, Mexico; (I.G.-M.); (M.R.-H.); (F.S.-B.)
| | - Yonathan Garfias
- Research Unit, Institute of Ophthalmology, Conde de Valenciana, Chimalpopoca 14, Ciudad de Mexico 06800, Mexico; (O.V.-R.); (F.S.M.-G.); (B.B.-V.); (I.C.-S.); (J.E.A.-F.)
- Department of Biochemistry, Faculty of Medicine, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad de Mexico 04510, Mexico
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12
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Alamudi SH, Kimoto M, Hirao I. Uptake mechanisms of cell-internalizing nucleic acid aptamers for applications as pharmacological agents. RSC Med Chem 2021; 12:1640-1649. [PMID: 34778766 PMCID: PMC8528270 DOI: 10.1039/d1md00199j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleic acid aptamers, also regarded as chemical antibodies, show potential as targeted therapeutic and delivery agents since they possess unique advantages over antibodies. Generated by an iterative selection and amplification process from oligonucleotide libraries using cultured cells, the aptamers bind to their target molecules expressed on the cell surface. Excitingly, most aptamers also demonstrate a cell-internalizing property in native living cells, allowing them to directly enter the cells via endocytosis depending on the target. In this review, we discuss selection methods in generating cell-internalizing aptamers via a cell-based selection process, along with their challenges and optimization strategies. We highlight the cellular uptake routes adopted by the aptamers and also their intracellular fate after the uptake, to give an overview of their mechanism of action for applications as promising pharmacological agents.
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Affiliation(s)
- Samira Husen Alamudi
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research (ASTAR) 31 Biopolis Way, Nanos #07-01 Singapore 138669 Singapore
| | - Michiko Kimoto
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research (ASTAR) 31 Biopolis Way, Nanos #07-01 Singapore 138669 Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research (ASTAR) 31 Biopolis Way, Nanos #07-01 Singapore 138669 Singapore
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13
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Matsunaga KI, Kimoto M, Lim VW, Tan HP, Wong YQ, Sun W, Vasoo S, Leo YS, Hirao I. High-affinity five/six-letter DNA aptamers with superior specificity enabling the detection of dengue NS1 protein variants beyond the serotype identification. Nucleic Acids Res 2021; 49:11407-11424. [PMID: 34169309 PMCID: PMC8599795 DOI: 10.1093/nar/gkab515] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 06/04/2021] [Indexed: 12/25/2022] Open
Abstract
Genetic alphabet expansion of DNA by introducing unnatural bases (UBs), as a fifth letter, dramatically augments the affinities of DNA aptamers that bind to target proteins. To determine whether UB-containing DNA (UB-DNA) aptamers obtained by affinity selection could spontaneously achieve high specificity, we have generated a series of UB-DNA aptamers (KD: 27-182 pM) targeting each of four dengue non-structural protein 1 (DEN-NS1) serotypes. The specificity of each aptamer is remarkably high, and the aptamers can recognize the subtle variants of DEN-NS1 with at least 96.9% amino acid sequence identity, beyond the capability of serotype identification (69-80% sequence identities). Our UB-DNA aptamers specifically identified two major variants of dengue serotype 1 with 10-amino acid differences in the DEN-NS1 protein (352 aa) in Singaporeans' clinical samples. These results suggest that the high-affinity UB-DNA aptamers generated by affinity selection also acquire high target specificity. Intriguingly, one of the aptamers contained two different UBs as fifth and sixth letters, which are essential for the tight binding to the target. These two types of unnatural bases with distinct physicochemical properties profoundly expand the potential of DNA aptamers. Detection methods incorporating the UB-DNA aptamers will facilitate precise diagnoses of viral infections and other diseases.
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Affiliation(s)
- Ken-Ichiro Matsunaga
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Michiko Kimoto
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Vanessa Weixun Lim
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore 308442, Singapore
| | - Hui Pen Tan
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Yu Qian Wong
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - William Sun
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Shawn Vasoo
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore 308442, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Dr., Experimental Medicine Building, Singapore 636921, Singapore
| | - Yee Sin Leo
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore 308442, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Dr., Experimental Medicine Building, Singapore 636921, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, #10-01, Singapore 117549, Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
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14
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Hybrid-Type SELEX for the Selection of Artificial Nucleic Acid Aptamers Exhibiting Cell Internalization Activity. Pharmaceutics 2021; 13:pharmaceutics13060888. [PMID: 34204006 PMCID: PMC8232673 DOI: 10.3390/pharmaceutics13060888] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid aptamers have attracted considerable attention as next-generation pharmaceutical agents and delivery vehicles for small molecule drugs and therapeutic oligonucleotides. Chemical modification is an effective approach for improving the functionality of aptamers. However, the process of selecting appropriately modified aptamers is laborious because of many possible modification patterns. Here, we describe a hybrid-type systematic evolution of ligands by exponential enrichment (SELEX) approach for the generation of the artificial nucleic acid aptamers effective against human TROP2, a cell surface protein identified by drug discovery as a promising target for cancer therapy. Capillary electrophoresis SELEX was used for the pre-screening of multiple modified nucleic acid libraries and enrichment of TROP2 binding aptamers in the first step, followed by functional screening using cell-SELEX in the second step for the generation of cell-internalizing aptamers. One representative aptamer, Tac-B1, had a nanomolar-level affinity to human TROP2 and exhibited elevated capacity for internalization by cells. Because of the growing interest in the application of aptamers for drug delivery, our hybrid selection approach has great potential for the generation of functional artificial nucleic acid aptamers with ideal modification patterns in vitro.
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15
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Tanaka K, Okuda T, Kasahara Y, Obika S. Base-modified aptamers obtained by cell-internalization SELEX facilitate cellular uptake of an antisense oligonucleotide. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 23:440-449. [PMID: 33473329 PMCID: PMC7803630 DOI: 10.1016/j.omtn.2020.11.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/20/2020] [Indexed: 12/30/2022]
Abstract
Intracellular delivery of oligonucleotides is important for their use as therapeutic drugs. The conjugation of molecules interacting with cell membrane proteins to enhance their internalization into cells is an effective strategy for delivering oligonucleotides. In the present study, we focused on creating aptamers, which are single-stranded oligonucleotides that bind target molecules with high affinity and specificity, as membrane protein-binding molecules. With an evolutionary selection approach using a random DNA library containing a uracil derivative with a hydrophobic functional group at the 5 position, we successfully obtained aptamers that are efficiently internalized into A549 cells. The efficacies of the aptamers were tested by further conjugation with MALAT1-targeting antisense oligonucleotides (ASOs), and the expression levels of MALAT1 RNA were examined. The aptamer-ASO conjugates were taken up by A549 cells, although there was no observable reduction in MALAT1 RNA levels. In contrast, the activity of the aptamer-ASO conjugate was potentiated when endosomal/lysosomal escape was enhanced by the addition of chloroquine. Thus, we showed that the hydrophobic modification of the nucleobase moiety is useful for developing highly internalizing aptamers and that endosomal/lysosomal escape is important for the intracellular delivery of ASOs by aptamers.
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Affiliation(s)
- Keisuke Tanaka
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 567-0085, Japan
| | - Takumi Okuda
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 567-0085, Japan
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 567-0085, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 567-0085, Japan
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16
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Kimoto M, Hirao I. Genetic alphabet expansion technology by creating unnatural base pairs. Chem Soc Rev 2020; 49:7602-7626. [PMID: 33015699 DOI: 10.1039/d0cs00457j] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent advancements in the creation of artificial extra base pairs (unnatural base pairs, UBPs) are opening the door to a new research area, xenobiology, and genetic alphabet expansion technologies. UBPs that function as third base pairs in replication, transcription, and/or translation enable the site-specific incorporation of novel components into DNA, RNA, and proteins. Here, we describe the UBPs developed by three research teams and their application in PCR-based diagnostics, high-affinity DNA aptamer generation, site-specific labeling of RNAs, semi-synthetic organism creation, and unnatural-amino-acid-containing protein synthesis.
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Affiliation(s)
- Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore.
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17
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Uemachi H, Kasahara Y, Tanaka K, Okuda T, Yoneda Y, Obika S. Discovery of cell-internalizing artificial nucleic acid aptamers for lung fibroblasts and targeted drug delivery. Bioorg Chem 2020; 105:104321. [PMID: 33074117 DOI: 10.1016/j.bioorg.2020.104321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 09/24/2020] [Indexed: 12/31/2022]
Abstract
Lung fibroblasts play major roles in the lung repair/fibrosis process through synthesis and remodeling of extracellular matrix. Those aberrant activations and elevated proliferations are associated with several fibrotic lung diseases, such as idiopathic pulmonary fibrosis (IPF). Targeting fibroblasts is a promising approach for preventing aberrant remodeling of lung architecture and protect irreversible pulmonary fibrosis. In this study, we developed an aptamer that can target lung fibroblasts and explored its potential as a delivery vehicle of cytotoxic agents intracellularly. The aptamer was discovered from artificial nucleic acid libraries through cell-based systematic evolution of ligands by exponential enrichment (cell-SELEX). This indole-modified aptamer can bind to LL97A cells, a fibroblast cell line derived from IPF patients, with high affinity (Kd = 70 nM). It also showed affinity to other lung fibroblasts, while cross-reactivity to epithelial cells was minimal. An aptamer-monomethyl auristatin F (MMAF) conjugate was generated by hybridizing with complementary DNA linked to MMAF. The resulting aptamer-MMAF conjugate inhibited proliferation of fibroblasts but appeared non-toxic to non-targeted epithelial cells. Our results show that artificial nucleic acid aptamer may potentially be used for fibroblast-specific therapy and diagnostic applications.
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Affiliation(s)
- Hiro Uemachi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 567-0085, Japan; DSP Cancer Institute, Sumitomo Dainippon Pharma Co., Ltd., Osaka 554-0022, Japan
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 567-0085, Japan.
| | - Keisuke Tanaka
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 567-0085, Japan
| | - Takumi Okuda
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 567-0085, Japan
| | - Yoshihiro Yoneda
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 567-0085, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 567-0085, Japan
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18
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Duffy K, Arangundy-Franklin S, Holliger P. Modified nucleic acids: replication, evolution, and next-generation therapeutics. BMC Biol 2020; 18:112. [PMID: 32878624 PMCID: PMC7469316 DOI: 10.1186/s12915-020-00803-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Modified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the limitations of first-generation nucleic acid therapeutics. Indeed, several therapeutics based on modified nucleic acids have recently been approved and many more are under clinical evaluation. XNAs can provide increased biostability and furthermore are now increasingly amenable to in vitro evolution, accelerating lead discovery. Here, we review the most recent discoveries in this dynamic field with a focus on progress in the enzymatic replication and functional exploration of XNAs.
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Affiliation(s)
- Karen Duffy
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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19
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Kumar Kulabhusan P, Hussain B, Yüce M. Current Perspectives on Aptamers as Diagnostic Tools and Therapeutic Agents. Pharmaceutics 2020; 12:E646. [PMID: 32659966 PMCID: PMC7407196 DOI: 10.3390/pharmaceutics12070646] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022] Open
Abstract
Aptamers are synthetic single-stranded DNA or RNA sequences selected from combinatorial oligonucleotide libraries through the well-known in vitro selection and iteration process, SELEX. The last three decades have witnessed a sudden boom in aptamer research, owing to their unique characteristics, like high specificity and binding affinity, low immunogenicity and toxicity, and ease in synthesis with negligible batch-to-batch variation. Aptamers can specifically bind to the targets ranging from small molecules to complex structures, making them suitable for a myriad of diagnostic and therapeutic applications. In analytical scenarios, aptamers are used as molecular probes instead of antibodies. They have the potential in the detection of biomarkers, microorganisms, viral agents, environmental pollutants, or pathogens. For therapeutic purposes, aptamers can be further engineered with chemical stabilization and modification techniques, thus expanding their serum half-life and shelf life. A vast number of antagonistic aptamers or aptamer-based conjugates have been discovered so far through the in vitro selection procedure. However, the aptamers face several challenges for its successful clinical translation, and only particular aptamers have reached the marketplace so far. Aptamer research is still in a growing stage, and a deeper understanding of nucleic acid chemistry, target interaction, tissue distribution, and pharmacokinetics is required. In this review, we discussed aptamers in the current diagnostics and theranostics applications, while addressing the challenges associated with them. The report also sheds light on the implementation of aptamer conjugates for diagnostic purposes and, finally, the therapeutic aptamers under clinical investigation, challenges therein, and their future directions.
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Affiliation(s)
| | - Babar Hussain
- Faculty of Life Sciences, University of Central Punjab, Lahore 54000, Pakistan;
| | - Meral Yüce
- SUNUM Nanotechnology Research and Application Centre, Sabanci University, Istanbul 34956, Turkey
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20
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Müller D, Trucks S, Schwalbe H, Hengesbach M. Genetic Code Expansion Facilitates Position-Selective Modification of Nucleic Acids and Proteins. Chempluschem 2020; 85:1233-1243. [PMID: 32515171 DOI: 10.1002/cplu.202000150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/11/2020] [Indexed: 12/12/2022]
Abstract
Transcription and translation obey to the genetic code of four nucleobases and 21 amino acids evolved over billions of years. Both these processes have been engineered to facilitate the use of non-natural building blocks in both nucleic acids and proteins, enabling researchers with a decent toolbox for structural and functional analyses. Here, we review the most common approaches for how labeling of both nucleic acids as well as proteins in a site-selective fashion with either modifiable building blocks or spectroscopic probes can be facilitated by genetic code expansion. We emphasize methodological approaches and how these can be adapted for specific modifications, both during as well as after biomolecule synthesis. These modifications can facilitate, for example, a number of different spectroscopic analysis techniques and can under specific circumstances even be used in combination.
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Affiliation(s)
- Diana Müller
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
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21
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Thevendran R, Sarah S, Tang TH, Citartan M. Strategies to bioengineer aptamer-driven nanovehicles as exceptional molecular tools for targeted therapeutics: A review. J Control Release 2020; 323:530-548. [PMID: 32380206 DOI: 10.1016/j.jconrel.2020.04.051] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 02/06/2023]
Abstract
Aptamers are a class of folded nucleic acid strands capable of binding to different target molecules with high affinity and selectivity. Over the years, they have gained a substantial amount of interest as promising molecular tools for numerous medical applications, particularly in targeted therapeutics. However, only the different treatment approaches and current developments of aptamer-drug therapies have been discussed so far, ignoring the crucial technical and functional aspects of constructing a therapeutically effective aptamer-driven drug delivery system that translates to improved in-vivo performance. Hence, this paper provides a comprehensive review of the strategies used to improve the therapeutic performance of aptamer-guided delivery systems. We focus on the different functional features such as drug deployment, payload capacity, in-vivo stability and targeting efficiency to further our knowledge in enhancing the cell-specific delivery of aptamer-drug conjugates. Each reported strategy is critically discussed to emphasize both the benefits provided in comparison with other similar techniques and to outline their potential drawbacks with respect to the molecular properties of the aptamers, the drug and the system to be designed. The molecular architecture and design considerations for an efficient aptamer-based delivery system are also briefly elaborated.
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Affiliation(s)
- Ramesh Thevendran
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Shigdar Sarah
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3216, Australia
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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22
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Kiggins C, Skinner A, Resendiz MJE. 7,8-Dihydro-8-oxoguanosine Lesions Inhibit the Theophylline Aptamer or Change Its Selectivity. Chembiochem 2020; 21:1347-1355. [PMID: 31845489 PMCID: PMC7297664 DOI: 10.1002/cbic.201900684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Indexed: 12/15/2022]
Abstract
Aptamers are attractive constructs due to their high affinity/selectivity towards a target. Here 7,8-dihydro-8-oxoguanosine (8-oxoG) has been used, due in part to its unique H-bonding capabilities (Watson-Crick or Hoogsteen), to expand the "RNA alphabet". Its impact on the theophylline RNA aptamer was explored by modifying its binding pocket at positions G11, G25, or G26. Structural probing, with RNases A and T1 , showed that modification at G11 leads to a drastic structural change, whereas the G25-/G26-modified analogues exhibited cleavage patterns similar to that of the canonical construct. The recognition properties towards three xanthine derivatives were then explored through thermophoresis. Modifying the aptamer at position G11 led to binding inhibition. Modification at G25, however, changed the selectivity towards theobromine (Kd ≈160 μm), with a poor affinity for theophylline (Kd >1.5 mm) being observed. Overall, 8-oxoG can have an impact on the structures of aptamers in a position-dependent manner, leading to altered target selectivity.
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Affiliation(s)
- Courtney Kiggins
- Present address: Department of ChemistryU.S. Air Force Academy2355 Fairchild DriveUSAF AcademyColorado SpringsCO80840USA
| | - Austin Skinner
- Department of ChemistryUniversity of Colorado Denver1151 Arapahoe Street, Science Building Room 4145DenverCO80204USA
| | - Marino J. E. Resendiz
- Department of ChemistryUniversity of Colorado Denver1151 Arapahoe Street, Science Building Room 4145DenverCO80204USA
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23
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Kimoto M, Hirao I. New Research Area, Xenobiology, by Integrating Chemistry and Biology. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, A*STAR
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24
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Kimoto M, Soh SHG, Hirao I. Sanger Gap Sequencing for Genetic Alphabet Expansion of DNA. Chembiochem 2020; 21:2287-2296. [DOI: 10.1002/cbic.202000057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/19/2020] [Indexed: 01/03/2023]
Affiliation(s)
- Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
| | - Si Hui Gabriella Soh
- Institute of Bioengineering and Nanotechnology, A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
- Raffles Institution 1 Raffles Institution Lane Singapore 575954 Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
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25
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Marx A, Betz K. The Structural Basis for Processing of Unnatural Base Pairs by DNA Polymerases. Chemistry 2020; 26:3446-3463. [PMID: 31544987 PMCID: PMC7155079 DOI: 10.1002/chem.201903525] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/17/2019] [Indexed: 12/16/2022]
Abstract
Unnatural base pairs (UBPs) greatly increase the diversity of DNA and RNA, furthering their broad range of molecular biological and biotechnological approaches. Different candidates have been developed whereby alternative hydrogen-bonding patterns and hydrophobic and packing interactions have turned out to be the most promising base-pairing concepts to date. The key in many applications is the highly efficient and selective acceptance of artificial base pairs by DNA polymerases, which enables amplification of the modified DNA. In this Review, computational as well as experimental studies that were performed to characterize the pairing behavior of UBPs in free duplex DNA or bound to the active site of KlenTaq DNA polymerase are highlighted. The structural studies, on the one hand, elucidate how base pairs lacking hydrogen bonds are accepted by these enzymes and, on the other hand, highlight the influence of one or several consecutive UBPs on the structure of a DNA double helix. Understanding these concepts facilitates optimization of future UBPs for the manifold fields of applications.
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Affiliation(s)
- Andreas Marx
- Department of ChemistryKonstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstrasse 1078464KonstanzGermany
| | - Karin Betz
- Department of ChemistryKonstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstrasse 1078464KonstanzGermany
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26
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Novel Aptamers Selected on Living Cells for Specific Recognition of Triple-Negative Breast Cancer. iScience 2020; 23:100979. [PMID: 32222697 PMCID: PMC7103779 DOI: 10.1016/j.isci.2020.100979] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/02/2020] [Accepted: 03/09/2020] [Indexed: 02/08/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a high heterogeneous group of tumors with a distinctly aggressive nature and high rates of relapse. So far, the lack of any known targetable proteins has not allowed a specific anti-tumor treatment. Therefore, the identification of novel agents for specific TNBC targeting and treatment is desperately needed. Here, by integrating cell-SELEX (Systematic Evolution of Ligands by EXponential enrichment) for the specific recognition of TNBC cells with high-throughput sequencing technology, we identified a panel of 2′-fluoropyrimidine-RNA aptamers binding to TNBC cells and their cisplatin- and doxorubicin-resistant derivatives at low nanomolar affinity. These aptamers distinguish TNBC cells from both non-malignant and non-TNBC breast cancer cells and are able to differentiate TNBC histological specimens. Importantly, they inhibit TNBC cell capacity of growing in vitro as mammospheres, indicating they could also act as anti-tumor agents. Therefore, our newly identified aptamers are a valuable tool for selectively dealing with TNBC. Six 2′FPy-RNA aptamers were obtained by TNBC Cell-SELEX/NGS They distinguish TNBC cells from non-malignant and non-TNBC breast cancer cells They differentiate TNBC histological specimens by aptamer-based staining They inhibit TNBC cell lines capacity of growing in vitro as mammospheres
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27
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Kimoto M, Shermane Lim YW, Hirao I. Molecular affinity rulers: systematic evaluation of DNA aptamers for their applicabilities in ELISA. Nucleic Acids Res 2019; 47:8362-8374. [PMID: 31392985 PMCID: PMC6895277 DOI: 10.1093/nar/gkz688] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/09/2019] [Accepted: 07/30/2019] [Indexed: 12/15/2022] Open
Abstract
Many nucleic acid aptamers that bind to target molecules have been reported as antibody alternatives. However, while the affinities of aptamers vary widely, little is known about the relationship between the affinities and their applicabilities for practical use. Here, we developed molecular affinity rulers: a series of DNA aptamers with different affinities that bind to the same area of target molecules, to measure the aptamer and its device applicabilities. For the ruler preparation, we used high-affinity DNA aptamers containing a hydrophobic unnatural base (Ds) as the fifth base. By replacing Ds bases with A bases in Ds-DNA aptamers targeting VEGF165 and interferon-γ, we prepared two sets of DNA aptamers with dissociation constants (KD) ranging from 10−12 to 10−8 M. Using these molecular affinity rulers, we evaluated the sensitivity of DNA aptamers in ELISA (enzyme-linked immunosorbent assay), which showed the clear relationship between aptamer affinities and their detection sensitivities. In sandwich-type ELISA using combinations of aptamers and antibodies, aptamers with KD values lower than ∼10−9 M were required for sufficient sensitivities (limit of detection (LOD) < 10 pM) and signal intensities, but optimizations improved the lower-affinity aptamers’ applicabilities. These aptamer affinity rulers could be useful for evaluating and improving aptamer applicabilities.
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Affiliation(s)
- Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Yun Wei Shermane Lim
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore.,NUS High School of Mathematics and Science, 20 Clementi Avenue 1, Singapore 129957, Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
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28
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Tan Y, Li Y, Tang F. Nucleic Acid Aptamer: A Novel Potential Diagnostic and Therapeutic Tool for Leukemia. Onco Targets Ther 2019; 12:10597-10613. [PMID: 31824168 PMCID: PMC6900352 DOI: 10.2147/ott.s223946] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/14/2019] [Indexed: 12/23/2022] Open
Abstract
Leukemia immunotherapy has been dominant via using synthetic antibodies to target cluster of differentiation (CD) molecules, nevertheless inevitable cytotoxicity and immunogenicity would limit its development. Recently, increasing reports have focused on nucleic acid aptamers, a class of high-affinity nucleic acid ligands. Aptamers purportedly serve as “chemical antibodies”, have negligible cytotoxicity and low immunogenicity, and would be widely applied for the therapy and diagnosis of various diseases, especially leukemia. In the preclinical applications, nucleic acid aptamers have displayed the augmented specificity and selectivity via recognizing targets on leukemia cells based on unique three-dimensional conformations. As small molecules with nucleic acid characteristics, aptamers need to be chemically modified to resist nuclease degradation, renal clearance and improve binding affinities. Moreover, aptamers can be linked with neoteric detection techniques to enhance sensitivity and selectivity of diagnosis and therapy. In this review, we summarized aptamers’ preparation, chemical modification and conjugation, and discussed the application of aptamers in diagnosis and treatment of leukemia through highly specifically recognizing target molecules. Significantly, the application prospect of aptamers in fusion genes would be introduced.
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Affiliation(s)
- Yuan Tan
- Department of Clinical Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
| | - Yuejin Li
- Department of Clinical Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
| | - Faqing Tang
- Department of Clinical Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
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McConnell EM, Cozma I, Morrison D, Li Y. Biosensors Made of Synthetic Functional Nucleic Acids Toward Better Human Health. Anal Chem 2019; 92:327-344. [PMID: 31656066 DOI: 10.1021/acs.analchem.9b04868] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Erin M McConnell
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
| | - Ioana Cozma
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1.,Department of Surgery, Division of General Surgery , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
| | - Devon Morrison
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
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Bing T, Zhang N, Shangguan D. Cell-SELEX, an Effective Way to the Discovery of Biomarkers and Unexpected Molecular Events. ACTA ACUST UNITED AC 2019; 3:e1900193. [PMID: 32648677 DOI: 10.1002/adbi.201900193] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/26/2019] [Indexed: 12/15/2022]
Abstract
Cell-SELEX can not only generate aptamers for specific cell isolation/detection, diagnosis, and therapy, but also lead to the discovery of biomarkers and unexpected molecular events. However, most cell-SELEX research is concentrated on aptamer generation and applications. In this progress report, recent research progress with cell-SELEX in terms of the discovery of biomarkers and unexpected molecular events is highlighted. In particular, the key technical challenges for cell-SELEX-based biomarker discovery, namely, the methods for identification and validation of target proteins of aptamers, are discussed in detail. Finally, the prospects of the applications of cell-SELEX in this field now and in the near future are described. It is expected that this report will attract attention to the benefit of cell-SELEX and provide a practical reference for biomedical researchers.
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Affiliation(s)
- Tao Bing
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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