1
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Takezawa Y, Shionoya M. Enzymatic synthesis of ligand-bearing oligonucleotides for the development of metal-responsive DNA materials. Org Biomol Chem 2024. [PMID: 38967487 DOI: 10.1039/d4ob00947a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Metal-mediated artificial base pairs are some of the most promising building blocks for constructing DNA-based supramolecules and functional materials. These base pairs are formed by coordination bonds between ligand-type nucleobases and a bridging metal ion and have been exploited to develop metal-responsive DNA materials and DNA-templated metal arrays. In this review, we provide an overview of methods for the enzymatic synthesis of DNA strands containing ligand-type artificial nucleotides that form metal-mediated base pairs. Conventionally, ligand-bearing DNA oligomers have been synthesized via solid-phase synthesis using a DNA synthesizer. In recent years, there has been growing interest in enzymatic methods as an alternative approach to synthesize ligand-bearing DNA oligomers, because enzymatic reactions proceed under mild conditions and do not require protecting groups. DNA polymerases are used to incorporate ligand-bearing unnatural nucleotides into DNA, and DNA ligases are used to connect artificial DNA oligomers to natural DNA fragments. Template-independent polymerases are also utilized to post-synthetically append ligand-bearing nucleotides to DNA oligomers. In addition, enzymatic replication of DNA duplexes containing metal-mediated base pairs has been intensively studied. Enzymatic methods facilitate the synthesis of DNA strands containing ligand-bearing nucleotides at both internal and terminal positions. Enzymatically synthesized ligand-bearing DNAs have been applied to metal-dependent self-assembly of DNA structures and the allosteric control of DNAzyme activity through metal-mediated base pairing. Therefore, the enzymatic synthesis of ligand-bearing oligonucleotides holds great potential in advancing the development of various metal-responsive DNA materials, such as molecular sensors and machines, providing a versatile tool for DNA supramolecular chemistry and nanotechnology.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan.
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2
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Pichon M, Hollenstein M. Controlled enzymatic synthesis of oligonucleotides. Commun Chem 2024; 7:138. [PMID: 38890393 PMCID: PMC11189433 DOI: 10.1038/s42004-024-01216-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Oligonucleotides are advancing as essential materials for the development of new therapeutics, artificial genes, or in storage of information applications. Hitherto, our capacity to write (i.e., synthesize) oligonucleotides is not as efficient as that to read (i.e., sequencing) DNA/RNA. Alternative, biocatalytic methods for the de novo synthesis of natural or modified oligonucleotides are in dire need to circumvent the limitations of traditional synthetic approaches. This Perspective article summarizes recent progress made in controlled enzymatic synthesis, where temporary blocked nucleotides are incorporated into immobilized primers by polymerases. While robust protocols have been established for DNA, RNA or XNA synthesis is more challenging. Nevertheless, using a suitable combination of protected nucleotides and polymerase has shown promises to produce RNA oligonucleotides even though the production of long DNA/RNA/XNA sequences (>1000 nt) remains challenging. We surmise that merging ligase- and polymerase-based synthesis would help to circumvent the current shortcomings of controlled enzymatic synthesis.
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Affiliation(s)
- Maëva Pichon
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, Rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, Rue du Docteur Roux, 75724, Paris Cedex 15, France.
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3
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Kissmann AK, Bolotnikov G, Li R, Müller F, Xing H, Krämer M, Gottschalk KE, Andersson J, Weil T, Rosenau F. IMPATIENT-qPCR: monitoring SELEX success during in vitro aptamer evolution. Appl Microbiol Biotechnol 2024; 108:284. [PMID: 38573322 PMCID: PMC10995058 DOI: 10.1007/s00253-024-13085-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 04/05/2024]
Abstract
SELEX (Systematic Evolution of Ligands by Exponential enrichment) processes aim on the evolution of high-affinity aptamers as binding entities in diagnostics and biosensing. Aptamers can represent game-changers as constituents of diagnostic assays for the management of instantly occurring infectious diseases or other health threats. Without in-process quality control measures SELEX suffers from low overall success rates. We present a quantitative PCR method for fast and easy quantification of aptamers bound to their targets. Simultaneous determination of melting temperatures (Tm) of each SELEX round delivers information on the evolutionary success via the correlation of increasing GC content and Tm alone with a round-wise increase of aptamer affinity to the respective target. Based on nine successful and published previous SELEX processes, in which the evolution/selection of aptamer affinity/specificity was demonstrated, we here show the functionality of the IMPATIENT-qPCR for polyclonal aptamer libraries and resulting individual aptamers. Based on the ease of this new evolution quality control, we hope to introduce it as a valuable tool to accelerate SELEX processes in general. IMPATIENT-qPCR SELEX success monitoring. Selection and evolution of high-affinity aptamers using SELEX technology with direct aptamer evolution monitoring using melting curve shifting analyses to higher Tm by quantitative PCR with fluorescence dye SYBR Green I. KEY POINTS: • Fast and easy analysis. • Universal applicability shown for a series of real successful projects.
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Affiliation(s)
- Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128, Mainz, Germany
| | - Grigory Bolotnikov
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Runliu Li
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Franziska Müller
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Hu Xing
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Kay-E Gottschalk
- Institute of Experimental Physics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Jakob Andersson
- AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210, Vienna, Austria
| | - Tanja Weil
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128, Mainz, Germany
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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4
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Kong D, Thompson IAP, Maganzini N, Eisenstein M, Soh HT. Aptamer-Antibody Chimera Sensors for Sensitive, Rapid, and Reversible Molecular Detection in Complex Samples. ACS Sens 2024; 9:1168-1177. [PMID: 38407035 DOI: 10.1021/acssensors.3c01638] [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: 02/27/2024]
Abstract
The development of receptors suitable for the continuous detection of analytes in complex, interferent-rich samples remains challenging. Antibodies are highly sensitive but difficult to engineer in order to introduce signaling functionality, while aptamer switches are easy to construct but often yield only a modest target sensitivity. We present here a programmable antibody and DNA aptamer switch (PANDAS), which combines the desirable properties of both receptors by using a nucleic acid tether to link an analyte-specific antibody to an internal strand-displacement (ISD)-based aptamer switch that recognizes the same target through different epitopes. The antibody increases PANDAS analyte binding due to its high affinity, and the effective concentration between the two receptors further enhances two-epitope binding and fluorescent aptamer signaling. We developed a PANDAS sensor for the clotting protein thrombin and show that a tuned design achieves a greater than 300-fold enhanced sensitivity compared to that of using an aptamer alone. This design also exhibits reversible binding, enabling repeated measurements with a temporal resolution of ∼10 min, and retains excellent sensitivity even in interferent-rich samples. With future development, this PANDAS approach could enable the adaptation of existing protein-binding aptamers with modest affinity to sensors that deliver excellent sensitivity and minute-scale resolution in minimally prepared biological specimens.
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Affiliation(s)
- Dehui Kong
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Ian A P Thompson
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - Nicolo Maganzini
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - Michael Eisenstein
- Department of Radiology, Stanford University, Stanford, California 94305, United States
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - Hyongsok Tom Soh
- Department of Radiology, Stanford University, Stanford, California 94305, United States
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
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5
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Takezawa Y, Zhang H, Mori K, Hu L, Shionoya M. Ligase-mediated synthesis of Cu II-responsive allosteric DNAzyme with bifacial 5-carboxyuracil nucleobases. Chem Sci 2024; 15:2365-2370. [PMID: 38362437 PMCID: PMC10866359 DOI: 10.1039/d3sc05042d] [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: 09/25/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
A CuII-responsive allosteric DNAzyme has been developed by introducing bifacial 5-carboxyuracil (caU) nucleobases, which form both hydrogen-bonded caU-A and metal-mediated caU-CuII-caU base pairs. The base sequence was logically designed based on a known RNA-cleaving DNAzyme so that the caU-modified DNAzyme (caU-DNAzyme) can form a catalytically inactive structure containing three caU-A base pairs and an active form with three caU-CuII-caU pairs. The caU-DNAzyme was synthesized by joining short caU-containing fragments with a standard DNA ligase. The activity of caU-DNAzyme was suppressed without CuII, but enhanced 21-fold with the addition of CuII. Furthermore, the DNAzyme activity was turned on and off during the reaction by the addition and removal of CuII ions. Both ligase-mediated synthesis and CuII-dependent allosteric regulation were achieved by the bifacial base pairing properties of caU. This study provides a new strategy for designing stimuli-responsive DNA molecular systems.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Hanci Zhang
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Keita Mori
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Lingyun Hu
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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6
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Niogret G, Bouvier-Müller A, Figazzolo C, Joyce JM, Bonhomme F, England P, Mayboroda O, Pellarin R, Gasser G, Tucker JHR, Tanner JA, Savage GP, Hollenstein M. Interrogating Aptamer Chemical Space Through Modified Nucleotide Substitution Facilitated by Enzymatic DNA Synthesis. Chembiochem 2024; 25:e202300539. [PMID: 37837257 DOI: 10.1002/cbic.202300539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/15/2023]
Abstract
Chemical modification of aptamers is an important step to improve their performance and stability in biological media. This can be performed either during their identification (mod-SELEX) or after the in vitro selection process (post-SELEX). In order to reduce the complexity and workload of the post-SELEX modification of aptamers, we have evaluated the possibility of improving a previously reported, chemically modified aptamer by combining enzymatic synthesis and nucleotides bearing bioisosteres of the parent cubane side-chains or substituted cubane moieties. This method lowers the synthetic burden often associated with post-SELEX approaches and allowed to identify one additional sequence that maintains binding to the PvLDH target protein, albeit with reduced specificity. In addition, while bioisosteres often improve the potency of small molecule drugs, this does not extend to chemically modified aptamers. Overall, this versatile method can be applied for the post-SELEX modification of other aptamers and functional nucleic acids.
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Affiliation(s)
- Germain Niogret
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28, rue du Docteur Roux, 75015, Paris, France
| | - Alix Bouvier-Müller
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Chiara Figazzolo
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Jack M Joyce
- CSIRO Manufacturing, Clayton, VIC, 3168, Australia
- School of Chemistry, University of Sydney, Sydney, NSW, 2006, Australia
| | - Frédéric Bonhomme
- Institut Pasteur, Université Paris Cité, Department of Structural Biology and Chemistry, Unité de Chimie Biologique Epigénétique UMR CNRS 3523, 28, rue du Docteur Roux, CEDEX 15, 75724, Paris, France
| | - Patrick England
- Plateforme de Biophysique Moléculaire, C2RT, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Olena Mayboroda
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28, rue du Docteur Roux, 75015, Paris, France
| | - Riccardo Pellarin
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28, rue du Docteur Roux, 75015, Paris, France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005, Paris, France
| | - James H R Tucker
- School of Chemistry, University of Birmingham, Birmingham, B15 2TT, UK
| | - Julian A Tanner
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | | | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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7
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Picchetti P, Volpi S, Sancho-Albero M, Rossetti M, Dore MD, Trinh T, Biedermann F, Neri M, Bertucci A, Porchetta A, Corradini R, Sleiman H, De Cola L. Supramolecular Nucleic Acid-Based Organosilica Nanoparticles Responsive to Physical and Biological Inputs. J Am Chem Soc 2023; 145:22903-22912. [PMID: 37844092 PMCID: PMC10603779 DOI: 10.1021/jacs.3c04345] [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] [Received: 05/02/2023] [Indexed: 10/18/2023]
Abstract
Organosilica nanoparticles that contain responsive organic building blocks as constitutive components of the silica network offer promising opportunities for the development of innovative drug formulations, biomolecule delivery, and diagnostic tools. However, the synthetic challenges required to introduce dynamic and multifunctional building blocks have hindered the realization of biomimicking nanoparticles. In this study, capitalizing on our previous research on responsive nucleic acid-based organosilica nanoparticles, we combine the supramolecular programmability of nucleic acid (NA) interactions with sol-gel chemistry. This approach allows us to create dynamic supramolecular bridging units of nucleic acids in a silica-based scaffold. Two peptide nucleic acid-based monoalkoxysilane derivatives, which self-assemble into a supramolecular bis-alkoxysilane through direct base pairing, were chosen as the noncovalent units inserted into the silica network. In addition, a bridging functional NA aptamer leads to the specific recognition of ATP molecules. In a one-step bottom-up approach, the resulting supramolecular building blocks can be used to prepare responsive organosilica nanoparticles. The supramolecular Watson-Crick-Franklin interactions of the organosilica nanoparticles result in a programmable response to external physical (i.e., temperature) and biological (i.e., DNA and ATP) inputs and thus pave the way for the rational design of multifunctional silica materials with application from drug delivery to theranostics.
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Affiliation(s)
- Pierre Picchetti
- Karlsruhe
Institute of Technology (KIT), Institute
of Nanotechnology (INT), Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Stefano Volpi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/a, 43124 Parma, Italy
| | - María Sancho-Albero
- Department
of Molecular Biochemistry and Pharmacology, Instituto di Ricerche Farmacologiche Mario Negri, IRCCS, 20156 Milano, Italy
| | - Marianna Rossetti
- Department
of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
| | - Michael D. Dore
- Department
of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, Québec City H3A 0B8, Canada
| | - Tuan Trinh
- Department
of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, Québec City H3A 0B8, Canada
| | - Frank Biedermann
- Karlsruhe
Institute of Technology (KIT), Institute
of Nanotechnology (INT), Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Martina Neri
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/a, 43124 Parma, Italy
| | - Alessandro Bertucci
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/a, 43124 Parma, Italy
| | - Alessandro Porchetta
- Department
of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
| | - Roberto Corradini
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/a, 43124 Parma, Italy
| | - Hanadi Sleiman
- Department
of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, Québec City H3A 0B8, Canada
| | - Luisa De Cola
- Karlsruhe
Institute of Technology (KIT), Institute
of Nanotechnology (INT), Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen 76344, Germany
- Department
of Molecular Biochemistry and Pharmacology, Instituto di Ricerche Farmacologiche Mario Negri, IRCCS, 20156 Milano, Italy
- Dipartimento
DISFARM, University of Milano, via Camillo Golgi 19, 20133 Milano, Italy
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8
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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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9
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Dockerill M, Winssinger N. DNA-Encoded Libraries: Towards Harnessing their Full Power with Darwinian Evolution. Angew Chem Int Ed Engl 2023; 62:e202215542. [PMID: 36458812 DOI: 10.1002/anie.202215542] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
DNA-encoded library (DEL) technologies are transforming the drug discovery process, enabling the identification of ligands at unprecedented speed and scale. DEL makes use of libraries that are orders of magnitude larger than traditional high-throughput screens. While a DNA tag alludes to a genotype-phenotype connection that is exploitable for molecular evolution, most of the work in the field is performed with libraries where the tag serves as an amplifiable barcode but does not allow "translation" into the synthetic product it is linked to. In this Review, we cover technologies that enable the "translation" of the genetic tag into synthetic molecules, both biochemically and chemically, and explore how it can be used to harness Darwinian evolutionary pressure.
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Affiliation(s)
- Millicent Dockerill
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
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10
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Kupihár Z, Ferenc G, Petrovicz VL, Fáy VR, Kovács L, Martinek TA, Hegedüs Z. Improved Metal-Free Approach for the Synthesis of Protected Thiol Containing Thymidine Nucleoside Phosphoramidite and Its Application for the Synthesis of Ligatable Oligonucleotide Conjugates. Pharmaceutics 2023; 15:pharmaceutics15010248. [PMID: 36678876 PMCID: PMC9865093 DOI: 10.3390/pharmaceutics15010248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Oligonucleotide conjugates are versatile scaffolds that can be applied in DNA-based screening platforms and ligand display or as therapeutics. Several different chemical approaches are available for functionalizing oligonucleotides, which are often carried out on the 5' or 3' end. Modifying oligonucleotides in the middle of the sequence opens the possibility to ligate the conjugates and create DNA strands bearing multiple different ligands. Our goal was to establish a complete workflow that can be applied for such purposes from monomer synthesis to templated ligation. To achieve this, a monomer is required with an orthogonal functional group that can be incorporated internally into the oligonucleotide sequence. This is followed by conjugation with different molecules and ligation with the help of a complementary template. Here, we show the synthesis and the application of a thiol-modified thymidine nucleoside phosphoramidite to prepare ligatable oligonucleotide conjugates. The conjugations were performed both in solution and on solid phase, resulting in conjugates that can be assembled into multivalent oligonucleotides decorated with tissue-targeting peptides using templated ligation.
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Affiliation(s)
- Zoltán Kupihár
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Györgyi Ferenc
- Institute of Plant Biology, Biological Research Centre, Eötvös Lóránd Research Network, H-6726 Szeged, Hungary
| | - Vencel L. Petrovicz
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Viktória R. Fáy
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Lajos Kovács
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Tamás A. Martinek
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network, H-6720 Szeged, Hungary
- Correspondence: (T.A.M.); (Z.H.)
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
- Correspondence: (T.A.M.); (Z.H.)
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11
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Wang Q, Wang Z, He Y, Xiong B, Li Y, Wang F. Chemical and structural modification of RNA-cleaving DNAzymes for efficient biosensing and biomedical applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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12
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Aggarwal T, Hansen WA, Hong J, Ganguly A, York DM, Khare SD, Izgu EC. Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign. ACS Chem Biol 2022; 17:1924-1936. [PMID: 35776893 DOI: 10.1021/acschembio.2c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA polymerases have evolved to feature a highly conserved activity across the tree of life: formation of, without exception, internucleotidyl O-P linkages. Can this linkage selectivity be overcome by design to produce xenonucleic acids? Here, we report that the structure-guided redesign of an archaeal DNA polymerase, 9°N, exhibits a new activity undetectable in the wild-type enzyme: catalyzing the formation of internucleotidyl N-P linkages using 3'-NH2-ddNTPs. Replacing a metal-binding aspartate in the 9°N active site with asparagine was key to the emergence of this unnatural enzyme activity. MD simulations provided insights into how a single substitution enhances the productive positioning of a 3'-amino nucleophile in the active site. Further remodeling of the protein-nucleic acid interface in the finger subdomain yielded a quadruple-mutant variant (9°N-NRQS) displaying DNA-dependent NP-DNA polymerase activity. In addition, the engineered promiscuity of 9°N-NRQS was leveraged for one-pot synthesis of DNA─NP-DNA copolymers. This work sheds light on the molecular basis of substrate fidelity and latent promiscuity in enzymes.
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Affiliation(s)
- Tushar Aggarwal
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - William A Hansen
- Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - Jonathan Hong
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - Abir Ganguly
- Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey 08854, United States.,Laboratory for Biomolecular Simulation Research, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - Darrin M York
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States.,Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey 08854, United States.,Laboratory for Biomolecular Simulation Research, Rutgers University, New Brunswick, New Jersey 08854, United States.,Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States.,Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey 08854, United States.,Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Enver Cagri Izgu
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States.,Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08901, United States.,Rutgers Center for Lipid Research and New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901, United States
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13
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Shin WR, Park DY, Kim JH, Lee JP, Thai NQ, Oh IH, Sekhon SS, Choi W, Kim SY, Cho BK, Kim SC, Min J, Ahn JY, Kim YH. Structure based innovative approach to analyze aptaprobe-GPC3 complexes in hepatocellular carcinoma. J Nanobiotechnology 2022; 20:204. [PMID: 35477501 PMCID: PMC9044640 DOI: 10.1186/s12951-022-01391-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/21/2022] [Indexed: 02/07/2023] Open
Abstract
Background Glypican-3 (GPC3), a membrane-bound heparan sulfate proteoglycan, is a biomarker of hepatocellular carcinoma (HCC) progression. Aptamers specifically binding to target biomolecules have recently emerged as clinical disease diagnosis targets. Here, we describe 3D structure-based aptaprobe platforms for detecting GPC3, such as aptablotting, aptaprobe-based sandwich assay (ALISA), and aptaprobe-based imaging analysis. Results For preparing the aptaprobe–GPC3 platforms, we obtained 12 high affinity aptamer candidates (GPC3_1 to GPC3_12) that specifically bind to target GPC3 molecules. Structure-based molecular interactions identified distinct aptatopic residues responsible for binding to the paratopic nucleotide sequences (nt-paratope) of GPC3 aptaprobes. Sandwichable and overlapped aptaprobes were selected through structural analysis. The aptaprobe specificity for using in HCC diagnostics were verified through Aptablotting and ALISA. Moreover, aptaprobe-based imaging showed that the binding property of GPC3_3 and their GPC3 specificity were maintained in HCC xenograft models, which may indicate a new HCC imaging diagnosis. Conclusion Aptaprobe has the potential to be used as an affinity reagent to detect the target in vivo and in vitro diagnosing system. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12951-022-01391-z.
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Affiliation(s)
- Woo-Ri Shin
- School of Biological Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Dae-Young Park
- School of Biological Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jin-Pyo Lee
- School of Biological Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Nguyen Quang Thai
- School of Biological Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - In-Hwan Oh
- School of Biological Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Simranjeet Singh Sekhon
- School of Biological Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Wooil Choi
- Graduate School of Semiconductor and Chemical Engineering, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Sung Yeon Kim
- College of Pharmacy, Wonkwang University, Shinyoung-dong 344-2, Iksan, Jeonbuk, 570-749, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jiho Min
- Graduate School of Semiconductor and Chemical Engineering, Jeonbuk National University, Jeonju, 54896, Republic of Korea.
| | - Ji-Young Ahn
- School of Biological Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju, 28644, Republic of Korea.
| | - Yang-Hoon Kim
- School of Biological Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju, 28644, Republic of Korea.
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14
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Huang Y, Li Y, Li X. Strategies for developing DNA-encoded libraries beyond binding assays. Nat Chem 2022; 14:129-140. [PMID: 35121833 DOI: 10.1038/s41557-021-00877-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/01/2021] [Indexed: 01/01/2023]
Abstract
DNA-encoded chemical libraries (DELs) have emerged as a powerful technology in drug discovery. The wide adoption of DELs in the pharmaceutical industry and the rapid advancements of DEL-compatible chemistry have further fuelled its development and applications. In general, a DEL has been considered as a massive binding assay to identify physical binders for individual protein targets. However, recent innovations demonstrate the capability of DELs to operate in the complex milieu of biological systems. In this Perspective, we discuss the recent progress in using DNA-encoded chemical libraries to interrogate complex biological targets and their potential to identify structures that elicit function or possess other useful properties. Future breakthroughs in these aspects are expected to catapult DEL to become a momentous technology platform not only for drug discovery but also to explore fundamental biology.
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Affiliation(s)
- Yiran Huang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China.
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China. .,Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China.
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15
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Vummidi BR, Farrera-Soler L, Daguer JP, Dockerill M, Barluenga S, Winssinger N. A mating mechanism to generate diversity for the Darwinian selection of DNA-encoded synthetic molecules. Nat Chem 2022; 14:141-152. [PMID: 34873299 DOI: 10.1038/s41557-021-00829-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/30/2021] [Indexed: 12/18/2022]
Abstract
DNA-encoded library technologies enable the screening of synthetic molecules but have thus far not tapped into the power of Darwinian selection with iterative cycles of selection, amplification and diversification. Here we report a simple strategy to rapidly assemble libraries of conformationally constrained peptides that are paired in a combinatorial fashion (suprabodies). We demonstrate that the pairing can be shuffled after each amplification cycle in a process similar to DNA shuffling or mating to regenerate diversity. Using simulations, we show the benefits of this recombination in yielding a more accurate correlation of selection fitness with affinity after multiple rounds of selection, particularly if the starting library is heterogeneous in the concentration of its members. The method was validated with selections against streptavidin and applied to the discovery of PD-L1 binders. We further demonstrate that the binding of self-assembled suprabodies can be recapitulated by smaller (∼7 kDa) synthetic products that maintain the conformational constraint of the peptides.
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Affiliation(s)
- Balayeshwanth R Vummidi
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Lluc Farrera-Soler
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Jean-Pierre Daguer
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Millicent Dockerill
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland.
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16
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Le ATH, Wang TY, Krylova SM, Beloborodov SS, Krylov SN. Quantitative Characterization of Partitioning in Selection of DNA Aptamers for Protein Targets by Capillary Electrophoresis. Anal Chem 2022; 94:2578-2588. [DOI: 10.1021/acs.analchem.1c04560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- An T. H. Le
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Tong Ye Wang
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M. Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Stanislav S. Beloborodov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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17
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Electrochemical aptamer-based nanobiosensors for diagnosing Alzheimer's disease: A review. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2022; 135:112689. [DOI: 10.1016/j.msec.2022.112689] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/20/2022] [Accepted: 01/27/2022] [Indexed: 12/22/2022]
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18
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Zhu J, Huang X, Song W. Physical and Chemical Sensors on the Basis of Laser-Induced Graphene: Mechanisms, Applications, and Perspectives. ACS NANO 2021; 15:18708-18741. [PMID: 34881870 DOI: 10.1021/acsnano.1c05806] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Laser-induced graphene (LIG) is produced rapidly by directly irradiating carbonaceous precursors, and it naturally exhibits as a three-dimensional porous structure. Due to advantages such as simple preparation, time-saving, environmental friendliness, low cost, and expanding categories of raw materials, LIG and its derivatives have achieved broad applications in sensors. This has been witnessed in various fields such as wearable devices, disease diagnosis, intelligent robots, and pollution detection. However, despite LIG sensors having demonstrated an excellent capability to monitor physical and chemical parameters, the systematic review of synthesis, sensing mechanisms, and applications of them combined with comparison against other preparation approaches of graphene is still lacking. Here, graphene-based sensors for physical, biological, and chemical detection are reviewed first, followed by the introduction of general preparation methods for the laser-induced method to yield graphene. The preparation and advantages of LIG, sensing mechanisms, and the properties of different types of emerging LIG-based sensors are comprehensively reviewed. Finally, possible solutions to the problems and challenges of preparing LIG and LIG-based sensors are proposed. This review may serve as a detailed reference to guide the development of LIG-based sensors that possess properties for future smart sensors in health care, environmental protection, and industrial production.
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Affiliation(s)
- Junbo Zhu
- Department of Chemistry, Capital Normal University, Beijing 100048, China
- Beijing Key Laboratory for Optical Materials and Photonic Devices, Beijing 100048, China
| | - Xian Huang
- Department of Biomedical Engineering, Tianjin University, Tianjin 300072, China
| | - Weixing Song
- Department of Chemistry, Capital Normal University, Beijing 100048, China
- Beijing Key Laboratory for Optical Materials and Photonic Devices, Beijing 100048, China
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19
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McCloskey CM, Li Q, Yik EJ, Chim N, Ngor AK, Medina E, Grubisic I, Co Ting Keh L, Poplin R, Chaput JC. Evolution of Functionally Enhanced α-l-Threofuranosyl Nucleic Acid Aptamers. ACS Synth Biol 2021; 10:3190-3199. [PMID: 34739228 DOI: 10.1021/acssynbio.1c00481] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Synthetic genetic polymers (xeno-nucleic acids, XNAs) have the potential to transition aptamers from laboratory tools to therapeutic agents, but additional functionality is needed to compete with antibodies. Here, we describe the evolution of a biologically stable artificial genetic system composed of α-l-threofuranosyl nucleic acid (TNA) that facilitates the production of backbone- and base-modified aptamers termed "threomers" that function as high quality protein capture reagents. Threomers were discovered against two prototypical protein targets implicated in human diseases through a combination of in vitro selection and next-generation sequencing using uracil nucleotides that are uniformly equipped with aromatic side chains commonly found in the paratope of antibody-antigen crystal structures. Kinetic measurements reveal that the side chain modifications are critical for generating threomers with slow off-rate binding kinetics. These findings expand the chemical space of evolvable non-natural genetic systems to include functional groups that enhance protein target binding by mimicking the structural properties of traditional antibodies.
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Affiliation(s)
| | | | | | | | | | | | - Ivan Grubisic
- X, The Moonshot Factory, Mountain View, California 94043, United States
| | - Lance Co Ting Keh
- X, The Moonshot Factory, Mountain View, California 94043, United States
| | - Ryan Poplin
- X, The Moonshot Factory, Mountain View, California 94043, United States
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20
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Zhang J, Li X, Wei H, Li Y, Zhang G, Li Y. Sequential DNA-Encoded Building Block Fusion for the Construction of Polysubstituted Pyrazoline Core Libraries. Org Lett 2021; 23:8429-8433. [PMID: 34652930 DOI: 10.1021/acs.orglett.1c03145] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The construction of chemical libraries containing polysubstituted pyrazoline scaffolds is highly desirable for the discovery of novel chemical ligands for biological targets. Herein, we report a sequential DNA-encoded synthesis strategy for polysubstituted pyrazoline heterocycles, which fuses a broad panel of aldehydes, aryl amines, and alkenes as building blocks. Furthermore, mock library synthesis and selection demonstrated the ability of the method to produce DNA-encoded focused libraries with highly functionalized pyrazoline cores.
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Affiliation(s)
- Juan Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Xianfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Haimei Wei
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, P. R. China
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21
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Li Q, Maola VA, Chim N, Hussain J, Lozoya-Colinas A, Chaput JC. Synthesis and Polymerase Recognition of Threose Nucleic Acid Triphosphates Equipped with Diverse Chemical Functionalities. J Am Chem Soc 2021; 143:17761-17768. [PMID: 34637287 DOI: 10.1021/jacs.1c08649] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Expanding the chemical space of evolvable non-natural genetic polymers (XNAs) to include functional groups that enhance protein target binding affinity offers a promising route to therapeutic aptamers with high biological stability. Here we describe the chemical synthesis and polymerase recognition of 10 chemically diverse functional groups introduced at the C-5 position of α-l-threofuranosyl uridine nucleoside triphosphate (tUTP). We show that the set of tUTP substrates is universally recognized by the laboratory-evolved polymerase Kod-RSGA. Insights into the mechanism of TNA synthesis were obtained from a high-resolution X-ray crystal structure of the postcatalytic complex bound to the primer-template duplex. A structural analysis reveals a large cavity in the enzyme active site that can accommodate the side chain of C-5-modified tUTP substrates. Our findings expand the chemical space of evolvable nucleic acid systems by providing a synthetic route to artificial genetic polymers that are uniformly modified with diversity-enhancing functional groups.
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22
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Huang Y, Li X. Recent Advances on the Selection Methods of DNA-Encoded Libraries. Chembiochem 2021; 22:2384-2397. [PMID: 33891355 DOI: 10.1002/cbic.202100144] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/23/2021] [Indexed: 12/15/2022]
Abstract
DNA-encoded libraries (DEL) have come of age and become a major technology platform for ligand discovery in both academia and the pharmaceutical industry. Technological maturation in the past two decades and the recent explosive developments of DEL-compatible chemistries have greatly improved the chemical diversity of DELs and fueled its applications in drug discovery. A relatively less-covered aspect of DELs is the selection method. Typically, DEL selection is considered as a binding assay and the selection is conducted with purified protein targets immobilized on a matrix, and the binders are separated from the non-binding background via physical washes. However, the recent innovations in DEL selection methods have not only expanded the target scope of DELs, but also revealed the potential of the DEL technology as a powerful tool in exploring fundamental biology. In this Review, we first cover the "classic" DEL selection methods with purified proteins on solid phase, and then we discuss the strategies to realize DEL selections in solution phase. Finally, we focus on the emerging approaches for DELs to interrogate complex biological targets.
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Affiliation(s)
- Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong Science and Technology Parks, New Territories, Hong Kong SAR, China
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23
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Structural and functional analysis of the simultaneous binding of two duplex/quadruplex aptamers to human α-thrombin. Int J Biol Macromol 2021; 181:858-867. [PMID: 33864869 DOI: 10.1016/j.ijbiomac.2021.04.076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/23/2022]
Abstract
The long-range communication between the two exosites of human α-thrombin (thrombin) tightly modulates the protein-effector interactions. Duplex/quadruplex aptamers represent an emerging class of very effective binders of thrombin. Among them, NU172 and HD22 aptamers are at the forefront of exosite I and II recognition, respectively. The present study investigates the simultaneous binding of these two aptamers by combining a structural and dynamics approach. The crystal structure of the ternary complex formed by the thrombin with NU172 and HD22_27mer provides a detailed view of the simultaneous binding of these aptamers to the protein, inspiring the design of novel bivalent thrombin inhibitors. The crystal structure represents the starting model for molecular dynamics studies, which point out the cooperation between the binding at the two exosites. In particular, the binding of an aptamer to its exosite reduces the intrinsic flexibility of the other exosite, that preferentially assumes conformations similar to those observed in the bound state, suggesting a predisposition to interact with the other aptamer. This behaviour is reflected in a significant increase of the anticoagulant activity of NU172 when the inactive HD22_27mer is bound to exosite II, providing a clear evidence of the synergic action of the two aptamers.
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24
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Le ATH, Krylova SM, Beloborodov SS, Wang TY, Hili R, Johnson PE, Li F, Veedu RN, Belyanskaya S, Krylov SN. How to Develop and Prove High-Efficiency Selection of Ligands from Oligonucleotide Libraries: A Universal Framework for Aptamers and DNA-Encoded Small-Molecule Ligands. Anal Chem 2021; 93:5343-5354. [PMID: 33764056 DOI: 10.1021/acs.analchem.1c00601] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Screening molecular libraries for ligands capable of binding proteins is widely used for hit identification in the early drug discovery process. Oligonucleotide libraries provide a very high diversity of compounds, while the combination of the polymerase chain reaction and DNA sequencing allow the identification of ligands in low copy numbers selected from such libraries. Ligand selection from oligonucleotide libraries requires mixing the library with the target followed by the physical separation of the ligand-target complexes from the unbound library. Cumulatively, the low abundance of ligands in the library and the low efficiency of available separation methods necessitate multiple consecutive rounds of partitioning. Multiple rounds of inefficient partitioning make the selection process ineffective and prone to failures. There are continuing efforts to develop a separation method capable of reliably generating a pure pool of ligands in a single round of partitioning; however, none of the proposed methods for single-round selection have been universally adopted. Our analysis revealed that the developers' efforts are disconnected from each other and hindered by the lack of quantitative criteria of selection quality assessment. Here, we present a formalism that describes single-round selection mathematically and provides parameters for quantitative characterization of selection quality. We use this formalism to define a universal strategy for development and validation of single-round selection methods. Finally, we analyze the existing partitioning methods, the published single-round selection reports, and some pertinent practical considerations through the prism of this formalism. This formalism is not an experimental protocol but a framework for correct development of experimental protocols. While single-round selection is not a goal by itself and may not always suffice selection of good-quality ligands, our work will help developers of highly efficient selection approaches to consolidate their efforts under an umbrella of universal quantitative criteria of method development and assessment.
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Affiliation(s)
- An T H Le
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Stanislav S Beloborodov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Tong Y Wang
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Ryan Hili
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Philip E Johnson
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Feng Li
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University and Perron Institute for Neurological and Translational Science, Perth 6150, Australia
| | | | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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25
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Yang C, Wu KB, Deng Y, Yuan J, Niu J. Geared Toward Applications: A Perspective on Functional Sequence-Controlled Polymers. ACS Macro Lett 2021; 10:243-257. [PMID: 34336395 PMCID: PMC8320758 DOI: 10.1021/acsmacrolett.0c00855] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sequence-controlled polymers are an emerging class of synthetic polymers with a regulated sequence of monomers. In the past decade, tremendous progress has been made in the synthesis of polymers with the sophisticated sequence control approaching the level manifested in biopolymers. In contrast, the exploration of novel functions that can be achieved by controlling synthetic polymer sequences represents an emerging focus in polymer science. This Viewpoint will survey recent advances in the functional applications of sequence-controlled polymers and provide a perspective on the challenges and outlook for pursuing future applications of this fascinating class of macromolecules.
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Affiliation(s)
- Cangjie Yang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Kevin B. Wu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Yu Deng
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Jingsong Yuan
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Jia Niu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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26
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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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27
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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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28
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Ochoa S, Milam VT. Modified Nucleic Acids: Expanding the Capabilities of Functional Oligonucleotides. Molecules 2020; 25:E4659. [PMID: 33066073 PMCID: PMC7587394 DOI: 10.3390/molecules25204659] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/20/2022] Open
Abstract
In the last three decades, oligonucleotides have been extensively investigated as probes, molecular ligands and even catalysts within therapeutic and diagnostic applications. The narrow chemical repertoire of natural nucleic acids, however, imposes restrictions on the functional scope of oligonucleotides. Initial efforts to overcome this deficiency in chemical diversity included conservative modifications to the sugar-phosphate backbone or the pendant base groups and resulted in enhanced in vivo performance. More importantly, later work involving other modifications led to the realization of new functional characteristics beyond initial intended therapeutic and diagnostic prospects. These results have inspired the exploration of increasingly exotic chemistries highly divergent from the canonical nucleic acid chemical structure that possess unnatural physiochemical properties. In this review, the authors highlight recent developments in modified oligonucleotides and the thrust towards designing novel nucleic acid-based ligands and catalysts with specifically engineered functions inaccessible to natural oligonucleotides.
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Affiliation(s)
- Steven Ochoa
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Valeria T. Milam
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA;
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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29
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Jose J, Thomas AM, Mendonsa D, Al-Sanea MM, Uddin MS, Parambi DGT, Charyulu RN, Mathew B. Aptamers in Drug Design: An Emerging Weapon to Fight a Losing Battle. Curr Drug Targets 2020; 20:1624-1635. [PMID: 31362673 DOI: 10.2174/1389450120666190729121747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 11/22/2022]
Abstract
Implementation of novel and biocompatible polymers in drug design is an emerging and rapidly growing area of research. Even though we have a large number of polymer materials for various applications, the biocompatibility of these materials remains as a herculean task for researchers. Aptamers provide a vital and efficient solution to this problem. They are usually small (ranging from 20 to 60 nucleotides, single-stranded DNA or RNA oligonucleotides which are capable of binding to molecules possessing high affinity and other properties like specificity. This review focuses on different aspects of Aptamers in drug discovery, starting from its preparation methods and covering the recent scenario reported in the literature regarding their use in drug discovery. We address the limitations of Aptamers and provide valuable insights into their future potential in the areas regarding drug discovery research. Finally, we explained the major role of Aptamers like medical imaging techniques, application as synthetic antibodies, and the most recent application, which is in combination with nanomedicines.
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Affiliation(s)
- Jobin Jose
- Department of Pharmaceutics, N.G.S.M. Institute of Pharmaceutical Sciences, NITTE Deemed to be University, Mangalore, India
| | - Aaron Mathew Thomas
- Department of Pharmaceutics, N.G.S.M. Institute of Pharmaceutical Sciences, NITTE Deemed to be University, Mangalore, India
| | - Darewin Mendonsa
- Department of Pharmaceutics, N.G.S.M. Institute of Pharmaceutical Sciences, NITTE Deemed to be University, Mangalore, India
| | - Mohammad M Al-Sanea
- College of Pharmacy, Department of Pharmaceutical Chemistry, Jouf University, Sakaka, Al Jouf-2014, Saudi Arabia
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh.,Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
| | - Della Grace Thomas Parambi
- College of Pharmacy, Department of Pharmaceutical Chemistry, Jouf University, Sakaka, Al Jouf-2014, Saudi Arabia
| | - R Narayana Charyulu
- Department of Pharmaceutics, N.G.S.M. Institute of Pharmaceutical Sciences, NITTE Deemed to be University, Mangalore, India
| | - Bijo Mathew
- Division of Drug Design and Medicinal Chemistry Research Lab, Department of Pharmaceutical Chemistry, Ahalia School of Pharmacy, Palakkad 678557, Kerala, India
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30
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Li L, Xu S, Yan H, Li X, Yazd HS, Li X, Huang T, Cui C, Jiang J, Tan W. Nucleic Acid Aptamers for Molecular Diagnostics and Therapeutics: Advances and Perspectives. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Long Li
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
| | - Shujuan Xu
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha 410082 China
| | - He Yan
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha 410082 China
| | - Xiaowei Li
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
| | - Hoda Safari Yazd
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
| | - Xiang Li
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
| | - Tong Huang
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha 410082 China
- Institute of Cancer and Basic Medicine (IBMC) Chinese Academy of Sciences The Cancer Hospital of the University of Chinese Academy of Sciences Hangzhou Zhejiang 310022 China
| | - Jianhui Jiang
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha 410082 China
| | - Weihong Tan
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha 410082 China
- Institute of Molecular Medicine (IMM) Renji Hospital State Key Laboratory of Oncogenes and Related Genes Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
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31
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Li L, Xu S, Yan H, Li X, Yazd HS, Li X, Huang T, Cui C, Jiang J, Tan W. Nucleic Acid Aptamers for Molecular Diagnostics and Therapeutics: Advances and Perspectives. Angew Chem Int Ed Engl 2020; 60:2221-2231. [PMID: 32282107 DOI: 10.1002/anie.202003563] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Indexed: 12/11/2022]
Abstract
The advent of SELEX (systematic evolution of ligands by exponential enrichment) technology has shown the ability to evolve artificial ligands with affinity and specificity able to meet growing clinical demand for probes that can, for example, distinguish between the target leukemia cells and other cancer cells within the matrix of heterogeneity, which characterizes cancer cells. Though antibodies are the conventional and ideal choice as a molecular recognition tool for many applications, aptamers complement the use of antibodies due to many unique advantages, such as small size, low cost, and facile chemical modification. This Minireview will focus on the novel applications of aptamers and SELEX, as well as opportunities to develop molecular tools able to meet future clinical needs in biomedicine.
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Affiliation(s)
- Long Li
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Shujuan Xu
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - He Yan
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Xiaowei Li
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Hoda Safari Yazd
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Xiang Li
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Tong Huang
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Jianhui Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Weihong Tan
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China.,Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
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32
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Yu F, Yuan Z, Zhang D, Liu Y, Zhao Q, Wang H. High-affinity and undissociated capillary electrophoresis for DNA strand exchange analysis. Chem Commun (Camb) 2020; 56:7403-7406. [PMID: 32514506 DOI: 10.1039/d0cc02844d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
By identification of a super-stable protein-DNA-affinity system, we developed a free-solution capillary electrophoresis approach for rapid and sensitive detection of fundamentally important DNA strand exchange reactions mediated by recombinases. We further extended this assay for identification of hyper-recombinases generated from bioengineering and detection of single DNA mismatches caused by replication error.
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Affiliation(s)
- Fangzhi Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, No. 18 Shuangqing Road, Beijing 100085, P. R. China.
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33
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Evolution of abiotic cubane chemistries in a nucleic acid aptamer allows selective recognition of a malaria biomarker. Proc Natl Acad Sci U S A 2020; 117:16790-16798. [PMID: 32631977 DOI: 10.1073/pnas.2003267117] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nucleic acid aptamers selected through systematic evolution of ligands by exponential enrichment (SELEX) fold into exquisite globular structures in complex with protein targets with diverse translational applications. Varying the chemistry of nucleotides allows evolution of nonnatural nucleic acids, but the extent to which exotic chemistries can be integrated into a SELEX selection to evolve nonnatural macromolecular binding interfaces is unclear. Here, we report the identification of a cubane-modified aptamer (cubamer) against the malaria biomarker Plasmodium vivax lactate dehydrogenase (PvLDH). The crystal structure of the complex reveals an unprecedented binding mechanism involving a multicubane cluster within a hydrophobic pocket. The binding interaction is further stabilized through hydrogen bonding via cubyl hydrogens, previously unobserved in macromolecular binding interfaces. This binding mechanism allows discriminatory recognition of P. vivax over Plasmodium falciparum lactate dehydrogenase, thereby distinguishing these highly conserved malaria biomarkers for diagnostic applications. Together, our data demonstrate that SELEX can be used to evolve exotic nucleic acids bearing chemical functional groups which enable remarkable binding mechanisms which have never been observed in biology. Extending to other exotic chemistries will open a myriad of possibilities for functional nucleic acids.
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34
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Kong D, Movahedi M, Mahdavi-Amiri Y, Yeung W, Tiburcio T, Chen D, Hili R. Evolutionary Outcomes of Diversely Functionalized Aptamers Isolated from in Vitro Evolution. ACS Synth Biol 2020; 9:43-52. [PMID: 31774997 DOI: 10.1021/acssynbio.9b00222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Expanding the chemical diversity of aptamers remains an important thrust in the field in order to increase their functional potential. Previously, our group developed LOOPER, which enables the incorporation of up to 16 unique modifications throughout a ssDNA sequence, and applied it to the in vitro evolution of thrombin binders. As LOOPER-derived highly modified nucleic acids polymers are governed by two interrelated evolutionary variables, namely, functional modifications and sequence, the evolution of this polymer contrasts with that of canonical DNA. Herein we provide in-depth analysis of the evolution, including structure-activity relationships, mapping of evolutionary pressures on the library, and analysis of plausible evolutionary pathways that resulted in the first LOOPER-derived aptamer, TBL1. A detailed picture of how TBL1 interacts with thrombin and how it may mimic known peptide binders of thrombin is also proposed. Structural modeling and folding studies afford insights into how the aptamer displays critical modifications and also how modifications enhance the structural stability of the aptamer. A discussion of benefits and potential limitations of LOOPER during in vitro evolution is provided, which will serve to guide future evolutions of this highly modified class of aptamers.
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Affiliation(s)
- Dehui Kong
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - Matina Movahedi
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Yasaman Mahdavi-Amiri
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Wayland Yeung
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - Tristan Tiburcio
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Dickson Chen
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Ryan Hili
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
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35
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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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36
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Xu Y, Huang K, Lopez A, Xu W, Liu J. Freezing promoted hybridization of very short DNA oligonucleotides. Chem Commun (Camb) 2019; 55:10300-10303. [PMID: 31397452 DOI: 10.1039/c9cc04608a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Shorter DNA probes provide better specificity for hybridization, but they may not form stable duplexes at room temperature. In this study, we used thiazole orange to follow DNA hybridization upon freezing and achieved stable 5-mer duplex DNA. Using multiple short probes in tandem, long DNA could also be studied. This study provides insights into DNA hybridization in the frozen state and expands the application of freezing for nucleic acid chemistry.
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Affiliation(s)
- Yuancong Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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37
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Yan J, Xiong H, Cai S, Wen N, He Q, Liu Y, Peng D, Liu Z. Advances in aptamer screening technologies. Talanta 2019; 200:124-144. [DOI: 10.1016/j.talanta.2019.03.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/20/2019] [Accepted: 03/02/2019] [Indexed: 02/07/2023]
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38
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Nucleic acid enzymes based on functionalized nucleosides. Curr Opin Chem Biol 2019; 52:93-101. [PMID: 31307007 DOI: 10.1016/j.cbpa.2019.06.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/28/2019] [Accepted: 06/06/2019] [Indexed: 12/29/2022]
Abstract
Nucleic acid-based enzymes have recently joined their proteinaceous counterparts as important biocatalysts. While RNA enzymes (ribozymes) are found in nature, deoxyribozymes or DNAzymes are man-made entities. Numerous ribozymes and DNAzymes have been identified by Darwinian selection methods to catalyze a broad array of chemical transformations. Despite these important advances, practical applications involving nucleic acid enzymes are often plagued by relatively poor pharmacokinetic properties and cellular uptake, rapid degradation by nucleases and/or by the limited chemical arsenal carried by natural DNA and RNA. In this review, the two main chemical approaches for the modification of nucleic acid-based catalysts, particularly DNAzymes, are described. These methods aim at improving the functional properties of nucleic acid enzymes by mitigating some of these shortcomings. In this context, recent developments in the post-SELEX processing of existing nucleic acid catalysts as well as efforts for the selection of DNAzymes and ribozymes with modified nucleoside triphosphates are summarized.
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39
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Shi H, Lei Y, Ge J, He X, Cui W, Ye X, Liu J, Wang K. A Simple, pH-Activatable Fluorescent Aptamer Probe with Ultralow Background for Bispecific Tumor Imaging. Anal Chem 2019; 91:9154-9160. [PMID: 31185714 DOI: 10.1021/acs.analchem.9b01828] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Activatable aptamer probes (AAPs) are promising in molecular imaging of tumors, but the reported shape-switching-dependent AAPs are still challenged by unsatisfied noise suppression, poor stability, and sophisticated sequence design. To address the problem, we constructed a pH-activatable aptamer probe (pH-AAP) by utilizing an acid-labile acetal linker as the responsive element to be fused with a tumor-targeted aptamer. Specifically, a Cy5-labeled aptamer was connected with the quencher BHQ2 through the acetal group, thus generating pH-AAP with quenched fluorescence. Due to the stable proximity of Cy5 to BHQ2, pH-AAP was found to have ultralow background with a quenching efficiency as high as 98%. In comparison with shape-switching-dependent AAPs, the noise suppression of pH-AAP was well maintained for a much longer time in both serum and mouse body, thus showing a robust fluorescence stability. By a combination of the fluorescence recovery induced by acid hydrolysis of acetal linkers and the tumor-targeted recognition of aptamers, pH-AAP could either specifically anchor the extracellular pH-activated signals on the target cell surface in an acidic tumor microenvironment or be activated by acidic lysosomes after it was internalized into target cells. As proof of concept, in vitro evaluation and in vivo imaging of A549 lung cancer cells were performed by using S6 aptamer as a demonstration. It was indicated that pH-AAP realized washing-free, bispecific, and contrast-enhanced tumor imaging. The strategy is simple and free of sequence modification, which promises to provide a universal platform for sensitive and precise tumor diagnosis.
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Affiliation(s)
- Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China
| | - Yanli Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China.,School of Chemistry and Food Engineering , Changsha University of Science and Technology , Changsha 410076 , People's Republic of China
| | - Jia Ge
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China
| | - Wensi Cui
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China
| | - Xiaosheng Ye
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology , Hunan University , Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082 , People's Republic of China
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Verdonck L, Buyst D, de Vries AM, Gheerardijn V, Madder A, Martins JC. Tethered imidazole mediated duplex stabilization and its potential for aptamer stabilization. Nucleic Acids Res 2019; 46:11671-11686. [PMID: 30418582 PMCID: PMC6294506 DOI: 10.1093/nar/gky1062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/01/2018] [Indexed: 12/15/2022] Open
Abstract
Previous investigations of the impact of an imidazole-tethered thymidine in synthetic DNA duplexes, monitored using UV and NMR spectroscopy, revealed a base context dependent increase in thermal stability of these duplexes and a striking correlation with the imidazolium pKa. Unrestrained molecular dynamics (MD) simulations demonstrated the existence of a hydrogen bond between the imidazolium and the Hoogsteen side of a nearby guanosine which, together with electrostatic interactions, form the basis of the so-called pKa-motif responsible for these duplex-stabilizing and pKa-modulating properties. Here, the robustness and utility of this pKa-motif was explored by introducing multiple imidazole-tethered thymidines at different positions on the same dsDNA duplex. For all constructs, sequence based expectations as to pKa-motif formation were supported by MD simulations and experimentally validated using NOESY. Based on the analysis of the pKa values and melting temperatures, guidelines are formulated to assist in the rational design of oligonucleotides modified with imidazolium-tethered thymidines for increased thermal stability that should be generally applicable, as demonstrated through a triply modified construct. In addition, a proof-of-principle study demonstrating enhanced stability of the l-argininamide binding aptamer modified with an imidazole-tethered thymidine in the presence and absence of ligand, demonstrates its potential for the design of more stable aptamers.
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Affiliation(s)
- Lars Verdonck
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium.,Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Dieter Buyst
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium.,NMR Expertise Centre, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Anne-Mare de Vries
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium.,Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Vicky Gheerardijn
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - José C Martins
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
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41
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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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Abstract
This chapter provides a brief introduction to followed by discussion of recent preclinical studies on potential aptamer drugs grouped into two broad categories, namely, “aptamer structures” and “non-ocular diseases.” Examples of aptamer-based targeting of drugs are then described. Next is an overview of the status of nearly 30 clinical trials of aptamer drugs currently listed in ClinicalTrials.gov, which is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world, and is a service of the US National Institutes of Health. This overview includes brief descriptions of each study sponsor, aptamer drug, disease(s), and type of study, as well as separate tables for completed studies, withdrawn or terminated studies, and active studies. The final section discusses Conclusions and Prospects.
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Affiliation(s)
- G. Zon
- TriLink BioTechnologies 9955 Mesa Rim Road San Diego 92121 USA
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43
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Lichtor PA, Chen Z, Elowe NH, Chen JC, Liu DR. Side chain determinants of biopolymer function during selection and replication. Nat Chem Biol 2019; 15:419-426. [PMID: 30742124 PMCID: PMC6430648 DOI: 10.1038/s41589-019-0229-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/12/2019] [Indexed: 12/21/2022]
Abstract
The chemical functionalities within biopolymers determine their physical properties and biological activities. The relationship between the side-chains available to a biopolymer population and the potential functions of the resulting polymers, however, has proven difficult to study experimentally. Using seven sets of chemically diverse charged, polar, and nonpolar side-chains, we performed cycles of artificial translation, in vitro selections for binding to either PCSK9 or IL-6 protein, and replication on libraries of random side-chain-functionalized nucleic acid polymers. Polymer sequence convergence, bulk population target binding, affinity of individual polymers, and head-to-head competition among post-selection libraries collectively indicate that polymer libraries with nonpolar side-chains outperformed libraries lacking these side-chains. The presence of nonpolar groups, resembling functionality present in proteins but missing from natural nucleic acids, thus may be strong determinants of binding activity. This factor may contribute to the apparent evolutionary advantage of proteins over their nucleic acid precursors for some molecular recognition tasks.
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Affiliation(s)
- Phillip A Lichtor
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Zhen Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Nadine H Elowe
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jonathan C Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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44
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Guo C, Mahdavi-Amiri Y, Hili R. Influence of Linker Length on Ligase-Catalyzed Oligonucleotide Polymerization. Chembiochem 2019; 20:793-799. [PMID: 30458067 DOI: 10.1002/cbic.201800616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Indexed: 01/07/2023]
Abstract
Ligase-catalyzed oligonucleotide polymerization (LOOPER) that enables the sequence-defined generation of DNA with up to 16 different modifications has recently been developed. This approach was used to develop new classes of diversely modified DNA aptamers for molecular recognition through in vitro evolution. The modifications in LOOPER are appended by use of a long hexane-1,6-diamine linker, which could negatively impact binding thermodynamics. Here we explore the incorporation of modifications with the aid of shorter linkers and the use of commercially available phosphoramidites and assess their efficiency and fidelity of incorporation. We observed that shorter linkers are less tolerated during LOOPER, with very short linkers providing high levels of error and sequence bias. An ethane-1,2-diamine linker was found to be optimal in terms of yield, efficiency, and bias; however, codon adjustment was necessary. This shorter-linker anticodon set for LOOPER should prove valuable in exploring the impact of diverse chemical modifications on the molecular function of DNA.
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Affiliation(s)
- Chun Guo
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, GA, 30602, USA
| | - Yasaman Mahdavi-Amiri
- Department of Chemistry, Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Ryan Hili
- Department of Chemistry, Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
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45
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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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46
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Yu F, Zhao Q, Zhang D, Yuan Z, Wang H. Affinity Interactions by Capillary Electrophoresis: Binding, Separation, and Detection. Anal Chem 2018; 91:372-387. [PMID: 30392351 DOI: 10.1021/acs.analchem.8b04741] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fangzhi Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing , 100085 , China.,University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing , 100085 , China.,University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Dapeng Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing , 100085 , China
| | - Zheng Yuan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing , 100085 , China.,University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing , 100085 , China.,University of Chinese Academy of Sciences , Beijing , 100049 , China
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47
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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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48
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Kestemont D, Renders M, Leonczak P, Abramov M, Schepers G, Pinheiro VB, Rozenski J, Herdewijn P. XNA ligation using T4 DNA ligase in crowding conditions. Chem Commun (Camb) 2018; 54:6408-6411. [PMID: 29872779 DOI: 10.1039/c8cc02414f] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
T4 DNA ligase is capable of ligating 2'OMe-RNA duplexes, HNA, LNA and FANA mixed sequences in the presence of 10% w/v PEG8000 and 3 M betaine. The enzymatic joining of oligonucleotides containing multiple consecutive XNA nucleotides at the ligation site has not been reported before.
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Affiliation(s)
- Donaat Kestemont
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49 box 1041, 3000 Leuven, Belgium.
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49
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Mei H, Liao JY, Jimenez RM, Wang Y, Bala S, McCloskey C, Switzer C, Chaput JC. Synthesis and Evolution of a Threose Nucleic Acid Aptamer Bearing 7-Deaza-7-Substituted Guanosine Residues. J Am Chem Soc 2018; 140:5706-5713. [PMID: 29667819 DOI: 10.1021/jacs.7b13031] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In vitro selection experiments carried out on artificial genetic polymers require robust and faithful methods for copying genetic information back and forth between DNA and xeno-nucleic acids (XNA). Previously, we have shown that Kod-RI, an engineered polymerase developed to transcribe DNA templates into threose nucleic acid (TNA), can function with high fidelity in the absence of manganese ions. However, the transcriptional efficiency of this enzyme diminishes greatly when individual templates are replaced with libraries of DNA sequences, indicating that manganese ions are still required for in vitro selection. Unfortunately, the presence of manganese ions in the transcription mixture leads to the misincorporation of tGTP nucleotides opposite dG residues in the templating strand, which are detected as G-to-C transversions when the TNA is reverse transcribed back into DNA. Here we report the synthesis and fidelity of TNA replication using 7-deaza-7-modified guanosine base analogues in the DNA template and incoming TNA nucleoside triphosphate. Our findings reveal that tGTP misincorporation occurs via a Hoogsteen base pair in which the incoming tGTP residue adopts a syn conformation with respect to the sugar. Substitution of tGTP for 7-deaza-7-phenyl tGTP enabled the synthesis of TNA polymers with >99% overall fidelity. A TNA library containing the 7-deaza-7-phenyl guanine analogue was used to evolve a biologically stable TNA aptamer that binds to HIV reverse transcriptase with low nanomolar affinity.
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Affiliation(s)
| | | | | | | | | | | | - Christopher Switzer
- Department of Chemistry , University of California , Riverside , California 92521 , United States
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50
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Chaput JC. Made in translation. Nat Chem 2018; 10:379-381. [DOI: 10.1038/s41557-018-0034-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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