1
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Steinbuch KB, Cong D, Rodriguez AJ, Tor Y. Emissive Guanosine Analog Applicable for Real-Time Live Cell Imaging. ACS Chem Biol 2024; 19:1836-1841. [PMID: 39101365 PMCID: PMC11334113 DOI: 10.1021/acschembio.4c00398] [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: 06/07/2024] [Revised: 07/16/2024] [Accepted: 07/26/2024] [Indexed: 08/06/2024]
Abstract
A new emissive guanosine analog CF3thG, constructed by a single trifluoromethylation step from the previously reported thG, displays red-shifted absorption and emission spectra compared to its precursor. The impact of solvent type and polarity on the photophysical properties of CF3thG suggests that the electronic effects of the trifluoromethyl group dominate its behavior and demonstrates its susceptibility to microenvironmental polarity changes. In vitro transcription initiations using T7 RNA polymerase, initiated with CF3thG, result in highly emissive 5'-labeled RNA transcripts, demonstrating the tolerance of the enzyme toward the analog. Viability assays with HEK293T cells displayed no detrimental effects at tested concentrations, indicating the safety of the analog for cellular applications. Live cell imaging of the free emissive guanosine analog using confocal microscopy was facilitated by its red-shifted absorption and emission and adequate brightness. Real-time live cell imaging demonstrated the release of the guanosine analog from HEK293T cells at concentration-gradient conditions, which was suppressed by the addition of guanosine.
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Affiliation(s)
- Kfir B. Steinbuch
- Department of Chemistry and
Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, United
States
| | - Deyuan Cong
- Department of Chemistry and
Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, United
States
| | - Anthony J. Rodriguez
- Department of Chemistry and
Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, United
States
| | - Yitzhak Tor
- Department of Chemistry and
Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, United
States
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2
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Lemdani K, Marlin R, Mayet C, Perkov V, Pascal Q, Ripoll M, Relouzat F, Dhooge N, Bossevot L, Dereuddre-Bosquet N, Dargazanli G, Thibaut-Duprey K, Haensler J, Chapon C, Prost C, Le Grand R. Distinct dynamics of mRNA LNPs in mice and nonhuman primates revealed by in vivo imaging. NPJ Vaccines 2024; 9:113. [PMID: 38902327 PMCID: PMC11189915 DOI: 10.1038/s41541-024-00900-5] [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: 12/07/2023] [Accepted: 06/03/2024] [Indexed: 06/22/2024] Open
Abstract
The characterization of vaccine distribution to relevant tissues after in vivo administration is critical to understanding their mechanisms of action. Vaccines based on mRNA lipid nanoparticles (LNPs) are now being widely considered against infectious diseases and cancer. Here, we used in vivo imaging approaches to compare the trafficking of two LNP formulations encapsulating mRNA following intramuscular administration: DLin-MC3-DMA (MC3) and the recently developed DOG-IM4. The mRNA formulated in DOG-IM4 LNPs persisted at the injection site, whereas mRNA formulated in MC3 LNPs rapidly migrated to the draining lymph nodes. Furthermore, MC3 LNPs induced the fastest increase in blood neutrophil counts after injection and greater inflammation, as shown by IL-1RA, IL-15, CCL-1, and IL-6 concentrations in nonhuman primate sera. These observations highlight the influence of the nature of the LNP on mRNA vaccine distribution and early immune responses.
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Affiliation(s)
- Katia Lemdani
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
- Sanofi, Marcy-L'étoile, France
| | - Romain Marlin
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Céline Mayet
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | | | - Quentin Pascal
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | | | - Francis Relouzat
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Nina Dhooge
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Laetitia Bossevot
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Nathalie Dereuddre-Bosquet
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | | | | | | | - Catherine Chapon
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | | | - Roger Le Grand
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France.
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3
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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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4
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Zhang Y, Gao Z, Yang X, Xu Q, Lu Y. Leveraging high-throughput screening technologies in targeted mRNA delivery. Mater Today Bio 2024; 26:101101. [PMID: 38883419 PMCID: PMC11176929 DOI: 10.1016/j.mtbio.2024.101101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/06/2024] [Accepted: 05/25/2024] [Indexed: 06/18/2024] Open
Abstract
Messenger ribonucleic acid (mRNA) has emerged as a promising molecular preventive and therapeutic approach that opens new avenues for healthcare. Although the use of delivery systems, especially lipid nanoparticles (LNPs), greatly improves the efficiency and stability of mRNA, mRNA tends to accumulate in the liver and hardly penetrates physiological barriers to reach the target site after intravenous injection. Hence, the rational design of targeting strategies aimed at directing mRNA to specific tissues and cells remains an enormous challenge in mRNA therapy. High-throughput screening (HTS) is a cutting-edge targeted technique capable of synthesizing chemical compound libraries for the large-scale experiments to validate the efficiency of mRNA delivery system. In this review, we firstly provide an overview of conventional low-throughput targeting strategies. Then the latest advancements in HTS techniques for mRNA targeted delivery, encompassing optimizing structures of large-scale delivery vehicles and developing large-scale surface ligands, as well as the applications of HTS techniques in extrahepatic systemic diseases are comprehensively summarized. Moreover, we illustrate the selection of administration routes for targeted mRNA delivery. Finally, challenges in the field and potential solutions to tackle them are proposed, offering insights for future development toward mRNA targeted therapy.
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Affiliation(s)
- Yuchen Zhang
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Zhifei Gao
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Xiao Yang
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Qinglong Xu
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Yao Lu
- Department of Joint and Orthopedics, Orthopedic Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
- Clinical Research Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
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5
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Tor Y. Isomorphic Fluorescent Nucleosides. Acc Chem Res 2024; 57:1325-1335. [PMID: 38613490 PMCID: PMC11079976 DOI: 10.1021/acs.accounts.4c00042] [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: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/15/2024]
Abstract
In 1960, Weber prophesied that "There are many ways in which the properties of the excited state can be utilized to study points of ignorance of the structure and function of proteins". This has been realized, illustrating that an intrinsic and highly responsive fluorophore such as tryptophan can alter the course of an entire scientific discipline. But what about RNA and DNA? Adapting Weber's protein photophysics prophecy to nucleic acids requires the development of intrinsically emissive nucleoside surrogates as, unlike Trp, the canonical nucleobases display unusually low emission quantum yields, which render nucleosides, nucleotides, and oligonucleotides practically dark for most fluorescence-based applications.Over the past decades, we have developed emissive nucleoside surrogates that facilitate the monitoring of nucleoside-, nucleotide-, and nucleic acid-based transformations at a nucleobase resolution in real time. The premise underlying our approach is the identification of minimal atomic/structural perturbations that endow the synthetic analogs with favorable photophysical features while maintaining native conformations and pairing. As illuminating probes, the photophysical parameters of such isomorphic nucleosides display sensitivity to microenvironmental factors. Responsive isomorphic analogs that function similarly to their native counterparts in biochemical contexts are defined as isofunctional.Early analogs included pyrimidines substituted with five-membered aromatic heterocycles at their 5 position and have been used to assess the polarity of the major groove in duplexes. Polarized quinazolines have proven useful in assembling FRET pairs with established fluorophores and have been used to study RNA-protein and RNA-small-molecule binding. Completing a fluorescent ribonucleoside alphabet, composed of visibly emissive purine (thA, thG) and pyrimidine (thU, thC) analogs, all derived from thieno[3,4-d]pyrimidine as the heterocyclic nucleus, was a major breakthrough. To further augment functionality, a second-generation emissive RNA alphabet based on an isothiazolo[4,3-d]pyrimidine core (thA, tzG, tzU, and tzC) was fabricated. This single-atom "mutagenesis" restored the basic/coordinating nitrogen corresponding to N7 in the purine skeleton and elevated biological recognition.The isomorphic emissive nucleosides and nucleotides, particularly the purine analogs, serve as substrates for diverse enzymes. Beyond polymerases, we have challenged the emissive analogs with metabolic and catabolic enzymes, opening optical windows into the biochemistry of nucleosides and nucleotides as metabolites as well as coenzymes and second messengers. Real-time fluorescence-based assays for adenosine deaminase, guanine deaminase, and cytidine deaminase have been fabricated and used for inhibitor discovery. Emissive cofactors (e.g., SthAM), coenzymes (e.g., NtzAD+), and second messengers (e.g., c-di-tzGMP) have been enzymatically synthesized, using xyNTPs and native enzymes. Both their biosynthesis and their transformations can be fluorescently monitored in real time.Highly isomorphic and isofunctional emissive surrogates can therefore be fabricated and judiciously implemented. Beyond their utility, side-by-side comparison to established analogs, particularly to 2-aminopurine, the workhorse of nucleic acid biophysics over 5 decades, has proven prudent as they refined the scope and limitations of both the new analogs and their predecessors. Challenges, however, remain. Associated with such small heterocycles are relatively short emission wavelengths and limited brightness. Recent advances in multiphoton spectroscopy and further structural modifications have shown promise for overcoming such barriers.
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Affiliation(s)
- Yitzhak Tor
- Department of Chemistry and
Biochemistry, University of California,
San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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6
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Mir B, Serrano-Chacón I, Medina P, Macaluso V, Terrazas M, Gandioso A, Garavís M, Orozco M, Escaja N, González C. Site-specific incorporation of a fluorescent nucleobase analog enhances i-motif stability and allows monitoring of i-motif folding inside cells. Nucleic Acids Res 2024; 52:3375-3389. [PMID: 38366792 PMCID: PMC11014255 DOI: 10.1093/nar/gkae106] [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: 04/28/2023] [Revised: 01/17/2024] [Accepted: 02/09/2024] [Indexed: 02/18/2024] Open
Abstract
The i-motif is an intriguing non-canonical DNA structure, whose role in the cell is still controversial. Development of methods to study i-motif formation under physiological conditions in living cells is necessary to study its potential biological functions. The cytosine analog 1,3-diaza-2-oxophenoxazine (tCO) is a fluorescent nucleobase able to form either hemiprotonated base pairs with cytosine residues, or neutral base pairs with guanines. We show here that when tCO is incorporated in the proximity of a G:C:G:C minor groove tetrad, it induces a strong thermal and pH stabilization, resulting in i-motifs with Tm of 39ºC at neutral pH. The structural determination by NMR methods reveals that the enhanced stability is due to a large stacking interaction between the guanines of the tetrad with the tCO nucleobase, which forms a tCO:C+ in the folded structure at unusually-high pHs, leading to an increased quenching in its fluorescence at neutral conditions. This quenching is much lower when tCO is base-paired to guanines and totally disappears when the oligonucleotide is unfolded. By taking profit of this property, we have been able to monitor i-motif folding in cells.
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Affiliation(s)
- Bartomeu Mir
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. Spain
- Inorganic and Organic Chemistry Department. Organic Chemistry Section and IBUB. University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona. Spain
| | - Israel Serrano-Chacón
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. Spain
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
| | - Pedro Medina
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
- Departament de Bioquímica i Biomedicina. Facultat de Biologia. Universitat de Barcelona. 08028 Barcelona. Spain
| | - Veronica Macaluso
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
| | - Montserrat Terrazas
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
- Inorganic and Organic Chemistry Department. Organic Chemistry Section and IBUB. University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona. Spain
| | - Albert Gandioso
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
| | - Miguel Garavís
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
- Departament de Bioquímica i Biomedicina. Facultat de Biologia. Universitat de Barcelona. 08028 Barcelona. Spain
| | - Núria Escaja
- Inorganic and Organic Chemistry Department. Organic Chemistry Section and IBUB. University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona. Spain
| | - Carlos González
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. Spain
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7
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Zhou F, Huang L, Li S, Yang W, Chen F, Cai Z, Liu X, Xu W, Lehto V, Lächelt U, Huang R, Shi Y, Lammers T, Tao W, Xu ZP, Wagner E, Xu Z, Yu H. From structural design to delivery: mRNA therapeutics for cancer immunotherapy. EXPLORATION (BEIJING, CHINA) 2024; 4:20210146. [PMID: 38855617 PMCID: PMC11022630 DOI: 10.1002/exp.20210146] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/15/2023] [Indexed: 06/11/2024]
Abstract
mRNA therapeutics have emerged as powerful tools for cancer immunotherapy in accordance with their superiority in expressing all sequence-known proteins in vivo. In particular, with a small dosage of delivered mRNA, antigen-presenting cells (APCs) can synthesize mutant neo-antigens and multi-antigens and present epitopes to T lymphocytes to elicit antitumor effects. In addition, expressing receptors like chimeric antigen receptor (CAR), T-cell receptor (TCR), CD134, and immune-modulating factors including cytokines, interferons, and antibodies in specific cells can enhance immunological response against tumors. With the maturation of in vitro transcription (IVT) technology, large-scale and pure mRNA encoding specific proteins can be synthesized quickly. However, the clinical translation of mRNA-based anticancer strategies is restricted by delivering mRNA into target organs or cells and the inadequate endosomal escape efficiency of mRNA. Recently, there have been some advances in mRNA-based cancer immunotherapy, which can be roughly classified as modifications of the mRNA structure and the development of delivery systems, especially the lipid nanoparticle platforms. In this review, the latest strategies for overcoming the limitations of mRNA-based cancer immunotherapies and the recent advances in delivering mRNA into specific organs and cells are summarized. Challenges and opportunities for clinical applications of mRNA-based cancer immunotherapy are also discussed.
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Affiliation(s)
- Feng Zhou
- State Key Laboratory of Chemical Biology and Center of Pharmaceutics, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lujia Huang
- State Key Laboratory of Chemical Biology and Center of Pharmaceutics, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Shiqin Li
- State Key Laboratory of Chemical Biology and Center of Pharmaceutics, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | - Wenfang Yang
- State Key Laboratory of Chemical Biology and Center of Pharmaceutics, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | - Fangmin Chen
- State Key Laboratory of Chemical Biology and Center of Pharmaceutics, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhixiong Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian ProvinceMengchao Hepatobiliary Hospital of Fujian Medical UniversityFuzhouChina
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian ProvinceMengchao Hepatobiliary Hospital of Fujian Medical UniversityFuzhouChina
| | - Wujun Xu
- Department of Applied PhysicsUniversity of Eastern FinlandKuopioFinland
| | - Vesa‐Pekka Lehto
- Department of Applied PhysicsUniversity of Eastern FinlandKuopioFinland
| | - Ulrich Lächelt
- Department of Pharmaceutical SciencesUniversity of ViennaViennaAustria
| | - Rongqin Huang
- Department of Pharmaceutics, School of Pharmacy, Key Laboratory of Smart Drug DeliveryMinistry of Education, Fudan UniversityShanghaiChina
| | - Yang Shi
- Department of Nanomedicine and Theranostics, Institute for Experimental Molecular ImagingRWTH Aachen University ClinicAachenGermany
| | - Twan Lammers
- Department of Nanomedicine and Theranostics, Institute for Experimental Molecular ImagingRWTH Aachen University ClinicAachenGermany
| | - Wei Tao
- Center for Nanomedicine and Department of Anaesthesiology, Brigham and Women's HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Zhi Ping Xu
- Institute of Biomedical Health Technology and Engineering and Institute of Systems and Physical BiologyShenzhen Bay LaboratoryShenzhenChina
| | - Ernst Wagner
- Pharmaceutical Biotechnology, Center for NanoscienceLudwig‐Maximilians‐UniversitätMunichGermany
| | - Zhiai Xu
- School of Chemistry and Molecular EngineeringEast China Normal UniversityShanghaiChina
| | - Haijun Yu
- State Key Laboratory of Chemical Biology and Center of Pharmaceutics, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
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8
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Khatik SY, Roy S, Srivatsan SG. Synthesis and Enzymatic Incorporation of a Dual-App Nucleotide Probe That Reports Antibiotics-Induced Conformational Change in the Bacterial Ribosomal Decoding Site RNA. ACS Chem Biol 2024; 19:687-695. [PMID: 38407057 DOI: 10.1021/acschembio.3c00676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Natural nucleosides are nonfluorescent and do not have intrinsic labels that can be readily utilized for analyzing nucleic acid structure and recognition. In this regard, researchers typically use the so-called "one-label, one-technique" approach to study nucleic acids. However, we envisioned that a responsive dual-app nucleoside system that harnesses the power of two complementing biophysical techniques namely, fluorescence and 19F NMR, will allow the investigation of nucleic acid conformations more comprehensively than before. We recently introduced a nucleoside analogue by tagging trifluoromethyl-benzofuran at the C5 position of 2'-deoxyuridine, which serves as an excellent fluorescent and 19F NMR probe to study G-quadruplex and i-motif structures. Taking forward, here, we report the development of a ribonucleotide version of the dual-app probe to monitor antibiotics-induced conformational changes in RNA. The ribonucleotide analog is derived by conjugating trifluoromethyl-benzofuran at the C5 position of uridine (TFBF-UTP). The analog is efficiently incorporated by T7 RNA polymerase to produce functionalized RNA transcripts. Detailed photophysical and 19F NMR of the nucleoside and nucleotide incorporated into RNA oligonucleotides revealed that the analog is structurally minimally invasive and can be used for probing RNA conformations by fluorescence and 19F NMR techniques. Using the probe, we monitored and estimated aminoglycoside antibiotics binding to the bacterial ribosomal decoding site RNA (A-site, a very important RNA target). While 2-aminopurine, a famous fluorescent nucleic acid probe, fails to detect structurally similar aminoglycoside antibiotics binding to the A-site, our probe reports the binding of different aminoglycosides to the A-site. Taken together, our results demonstrate that TFBF-UTP is a very useful addition to the nucleic acid analysis toolbox and could be used to devise discovery platforms to identify new RNA binders of therapeutic potential.
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Affiliation(s)
- Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Sarupa Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
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9
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Le HN, Kuchlyan J, Baladi T, Albinsson B, Dahlén A, Wilhelmsson LM. Synthesis and photophysical characterization of a pH-sensitive quadracyclic uridine (qU) analogue. Chemistry 2024:e202303539. [PMID: 38230625 DOI: 10.1002/chem.202303539] [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: 10/26/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/18/2024]
Abstract
Fluorescent base analogues (FBAs) have become useful tools for applications in biophysical chemistry, chemical biology, live-cell imaging, and RNA therapeutics. Herein, two synthetic routes towards a novel FBA of uracil named qU (quadracyclic uracil/uridine) are described. The qU nucleobase bears a tetracyclic fused ring system and is designed to allow for specific Watson-Crick base pairing with adenine. We find that qU absorbs light in the visible region of the spectrum and emits brightly with a quantum yield of 27 % and a dual-band character in a wide pH range. With evidence, among other things, from fluorescence lifetime measurements we suggest that this dual emission feature results from an excited-state proton transfer (ESPT) process. Furthermore, we find that both absorption and emission of qU are highly sensitive to pH. The high brightness in combination with excitation in the visible and pH responsiveness makes qU an interesting native-like nucleic acid label in spectroscopy and microscopy applications in, for example, the field of mRNA and antisense oligonucleotide (ASO) therapeutics.
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Affiliation(s)
- Hoang-Ngoan Le
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
- Cell Gene and RNA Therapy, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50, Gothenburg, Sweden
| | - Jagannath Kuchlyan
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
| | - Tom Baladi
- Cell Gene and RNA Therapy, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50, Gothenburg, Sweden
| | - Bo Albinsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
| | - Anders Dahlén
- Cell Gene and RNA Therapy, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
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10
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Poveda C, Chen YL, Strych U. Generation and Characterization of In Vitro Transcribed mRNA. Methods Mol Biol 2024; 2786:147-165. [PMID: 38814393 DOI: 10.1007/978-1-0716-3770-8_6] [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: 05/31/2024]
Abstract
Here we describe the in vitro preparation of mRNA from DNA templates, including setting up the transcription reaction, mRNA capping, and mRNA labeling. We then describe methods used for mRNA characterization, including UV and fluorescence spectrophotometry, as well as gel electrophoresis. Moreover, characterization of the in vitro transcribed RNA using the Bioanalyzer instrument is described, allowing a higher resolution analysis of the target molecules. For the in vitro testing of the mRNA molecules, we include protocols for the transfection of various primary cell cultures and the confirmation of translation by intracellular staining and western blotting.
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Affiliation(s)
- Cristina Poveda
- Baylor College of Medicine, Department of Pediatrics, Division of Pediatric Tropical Medicine, Houston, TX, USA
- Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA
| | - Yi-Lin Chen
- Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA
| | - Ulrich Strych
- Baylor College of Medicine, Department of Pediatrics, Division of Pediatric Tropical Medicine, Houston, TX, USA.
- Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA.
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11
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Bassi T, Hirlinger A, Grayson L, Vantourout J, Toor N. Fluorescent labeling of RNA and DNA on the Hoogsteen edge using sulfinate chemistry. RNA (NEW YORK, N.Y.) 2023; 29:1437-1451. [PMID: 37277186 PMCID: PMC10573292 DOI: 10.1261/rna.079679.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/12/2023] [Indexed: 06/07/2023]
Abstract
We have devised a single pot, low-cost method to add azide groups to unmodified nucleic acids without the need for enzymes or chemically modified nucleoside triphosphates. This involves reacting an azide-containing sulfinate salt with the nucleic acid, leading to replacement of C-H bonds on the nucleobase aromatic rings with C-R, where R is the azide-containing linker derived from the original sulfinate salt. With the addition of azide functional groups, the modified nucleic acid can easily be reacted with any alkyne-labeled compound of interest, including fluorescent dyes as shown in this work. This methodology enables the fluorescent labeling of a wide variety of nucleic acids, including natively folded RNAs, under mild conditions with minimal effects upon biochemical function and ribozyme catalysis. To demonstrate this, we show that a pair of labeled complementary ssDNA oligonucleotides (oligos) can hybridize to form dsDNA, even when labeled with multiple fluorophores per oligo. In addition, we also demonstrate that two different group II introns can splice when prelabeled internally with fluorophores, using our method. Broadly, this demonstrates that sulfinate modification of RNA is compatible with ribozyme function and Watson-Crick pairing, while preserving the labile backbone.
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Affiliation(s)
- Tiziano Bassi
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Anastassia Hirlinger
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Leah Grayson
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Julien Vantourout
- Department of Chemistry, Scripps Research, La Jolla, California 92037, USA
| | - Navtej Toor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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12
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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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13
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Lang F, Rönicke F, Wagenknecht HA. Aminophthalimide as a mimetic of purines and a fluorescent RNA base surrogate for RNA imaging. Org Biomol Chem 2023; 21:3079-3082. [PMID: 36943317 DOI: 10.1039/d3ob00302g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Aminophthalimide and N,N-dimethylaminophthalimide are used as fluorescent mimetics of purines due to their similar size and their possibility for hydrogen bonding. Their C-nucleotides were synthetically incorporated into RNA by means of phosphoramidite chemistry, behave as nonspecific fluorescent base analogs with flexible hydrogen bonding capabilities, and show solvatochromic fluorescence that is suitable for RNA imaging in live cells.
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Affiliation(s)
- Fabian Lang
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
| | - Franziska Rönicke
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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14
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Ashley J, Potts IG, Olorunniji FJ. Applications of Terminal Deoxynucleotidyl Transferase Enzyme in Biotechnology. Chembiochem 2023; 24:e202200510. [PMID: 36342345 DOI: 10.1002/cbic.202200510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Indexed: 11/09/2022]
Abstract
The use of polymerase enzymes in biotechnology has allowed us to gain unprecedented control over the manipulation of DNA, opening up new and exciting applications in areas such as biosensing, polynucleotide synthesis, and DNA storage, aptamer development and DNA-nanotechnology. One of the most intriguing enzymes which has gained prominence in the last decade is terminal deoxynucleotidyl transferase (TdT), which is one of the only polymerase enzymes capable of catalysing the template independent stepwise addition of nucleotides onto an oligonucleotide chain. This unique enzyme has seen a significant increase in a variety of different applications. In this review, we give a comprehensive discussion of the unique properties and applications of TdT as a biotechnology tool, and the application in the enzymatic synthesis of poly/oligonucleotides. Finally, we look at the increasing role of TdT enzyme in biosensing, DNA storage, synthesis of DNA nanostructures and aptamer development, and give a future outlook for this technology.
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Affiliation(s)
- Jon Ashley
- School of Pharmaceutical and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, 3 Byrom St, Liverpool, L3 3AF, UK
| | - Indiia G Potts
- School of Pharmaceutical and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, 3 Byrom St, Liverpool, L3 3AF, UK
| | - Femi J Olorunniji
- School of Pharmaceutical and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, 3 Byrom St, Liverpool, L3 3AF, UK
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15
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Graczyk A, Radzikowska-Cieciura E, Kaczmarek R, Pawlowska R, Chworos A. Modified Nucleotides for Chemical and Enzymatic Synthesis of Therapeutic RNA. Curr Med Chem 2023; 30:1320-1347. [PMID: 36239720 DOI: 10.2174/0929867330666221014111403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022]
Abstract
In recent years, RNA has emerged as a medium with a broad spectrum of therapeutic potential, however, for years, a group of short RNA fragments was studied and considered therapeutic molecules. In nature, RNA plays both functions, with coding and non-coding potential. For RNA, like any other therapeutic, to be used clinically, certain barriers must be crossed. Among them, there are biocompatibility, relatively low toxicity, bioavailability, increased stability, target efficiency and low off-target effects. In the case of RNA, most of these obstacles can be overcome by incorporating modified nucleotides into its structure. This may be achieved by both, in vitro and in vivo biosynthetic methods, as well as chemical synthesis. Some advantages and disadvantages of each approach are summarized here. The wide range of nucleotide analogues has been tested for their utility as monomers for RNA synthesis. Many of them have been successfully implemented, and a lot of pre-clinical and clinical studies involving modified RNA have been carried out. Some of these medications have already been introduced into clinics. After the huge success of RNA-based vaccines that were introduced into widespread use in 2020, and the introduction to the market of some RNA-based drugs, RNA therapeutics containing modified nucleotides appear to be the future of medicine.
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Affiliation(s)
- Anna Graczyk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Renata Kaczmarek
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Roza Pawlowska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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16
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Yamaji R, Nakagawa O, Kishimoto Y, Fujii A, Matsumura T, Nakayama T, Kamada H, Osawa T, Yamaguchi T, Obika S. Synthesis and physical and biological properties of 1,3-diaza-2-oxophenoxazine-conjugated oligonucleotides. Bioorg Med Chem 2022; 72:116972. [DOI: 10.1016/j.bmc.2022.116972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/26/2022]
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17
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Gebhard J, Hirsch L, Schwechheimer C, Wagenknecht HA. Hybridization-Sensitive Fluorescent Probes for DNA and RNA by a Modular "Click" Approach. Bioconjug Chem 2022; 33:1634-1642. [PMID: 35995426 PMCID: PMC9501807 DOI: 10.1021/acs.bioconjchem.2c00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Fluorescent DNA probes were prepared in a modular approach
using
the “click” post-synthetic modification strategy. The
new glycol-based module and DNA building block place just two carbons
between the phosphodiester bridges and anchor the dye by an additional
alkyne group. This creates a stereocenter in the middle of this artificial
nucleoside substitute. Both enantiomers and a variety of photostable
cyanine–styryl dyes as well as thiazole orange derivatives
were screened as “clicked” conjugates in different surrounding
DNA sequences. The combination of the (S)-configured
DNA anchor and the cyanylated cyanine–styryl dye shows the
highest fluorescence light-up effect of 9.2 and a brightness of approximately
11,000 M–1 cm–1. This hybridization
sensitivity and fluorescence readout were further developed utilizing
electron transfer and energy transfer processes. The combination of
the hybridization-sensitive DNA building block with the nucleotide
of 5-nitroindole as an electron acceptor and a quencher increases
the light-up effect to 20 with the DNA target and to 15 with the RNA
target. The fluorescence readout could significantly be enhanced to
values between 50 and 360 by the use of energy transfer to a second
DNA probe with commercially available dyes, like Cy3.5, Cy5, and Atto590,
as energy acceptors at the 5′-end. The latter binary probes
shift the fluorescent readout from the range of 500–550 nm
to the range of 610–670 nm. The optical properties make these
fluorescent DNA probes potentially useful for RNA imaging. Due to
the strong light-up effect, they will not require washing procedures
and will thus be suitable for live-cell imaging.
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Affiliation(s)
- Julian Gebhard
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
| | - Lara Hirsch
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
| | - Christian Schwechheimer
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
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18
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Wang D, Shalamberidze A, Arguello AE, Purse BW, Kleiner RE. Live-Cell RNA Imaging with Metabolically Incorporated Fluorescent Nucleosides. J Am Chem Soc 2022; 144:14647-14656. [PMID: 35930766 PMCID: PMC9940818 DOI: 10.1021/jacs.2c04142] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescence imaging is a powerful method for probing macromolecular dynamics in biological systems; however, approaches for cellular RNA imaging are limited to the investigation of individual RNA constructs or bulk RNA labeling methods compatible primarily with fixed samples. Here, we develop a platform for fluorescence imaging of bulk RNA dynamics in living cells. We show that fluorescent bicyclic and tricyclic cytidine analogues can be metabolically incorporated into cellular RNA by overexpression of uridine-cytidine kinase 2. In particular, metabolic feeding with the tricyclic cytidine-derived nucleoside tC combined with confocal imaging enables the investigation of RNA synthesis, degradation, and trafficking at single-cell resolution. We apply our imaging modality to study RNA metabolism and localization during the oxidative stress response and find that bulk RNA turnover is greatly accelerated upon NaAsO2 treatment. Furthermore, we identify cytoplasmic RNA granules containing RNA transcripts generated during oxidative stress that are distinct from canonical stress granules and P-bodies and co-localize with the RNA helicase DDX6. Taken together, our work provides a powerful approach for live-cell RNA imaging and reveals how cells reshape RNA transcriptome dynamics in response to oxidative stress.
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Affiliation(s)
- Danyang Wang
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Ana Shalamberidze
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | | | - Byron W. Purse
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Ralph E. Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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19
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Vervaeke P, Borgos SE, Sanders NN, Combes F. Regulatory guidelines and preclinical tools to study the biodistribution of RNA therapeutics. Adv Drug Deliv Rev 2022; 184:114236. [PMID: 35351470 PMCID: PMC8957368 DOI: 10.1016/j.addr.2022.114236] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/09/2022] [Accepted: 03/23/2022] [Indexed: 12/27/2022]
Abstract
The success of the messenger RNA-based COVID-19 vaccines of Moderna and Pfizer/BioNTech marks the beginning of a new chapter in modern medicine. However, the rapid rise of mRNA therapeutics has resulted in a regulatory framework that is somewhat lagging. The current guidelines either do not apply, do not mention RNA therapeutics, or do not have widely accepted definitions. This review describes the guidelines for preclinical biodistribution studies of mRNA/siRNA therapeutics and highlights the relevant differences for mRNA vaccines. We also discuss the role of in vivo RNA imaging techniques and other assays to fulfill and/or complement the regulatory requirements. Specifically, quantitative whole-body autoradiography, microautoradiography, mass spectrometry-based assays, hybridization techniques (FISH, bDNA), PCR-based methods, in vivo fluorescence imaging, and in vivo bioluminescence imaging, are discussed. We conclude that this new and rapidly evolving class of medicines demands a multi-layered approach to fully understand its biodistribution and in vivo characteristics.
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Affiliation(s)
- P Vervaeke
- Laboratory of Gene Therapy, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
| | - S E Borgos
- SINTEF Industry, Dept. of Biotechnology and Nanomedicine, Research Group Mass Spectrometry, Sem Sælands v. 2A, N-7034 Trondheim, Norway
| | - N N Sanders
- Laboratory of Gene Therapy, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium.
| | - F Combes
- SINTEF Industry, Dept. of Biotechnology and Nanomedicine, Research Group Mass Spectrometry, Sem Sælands v. 2A, N-7034 Trondheim, Norway.
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20
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Choi H, Kim H, Kim KT. Fluorescent nucleobase analogs constructed by
aldol‐type
condensation: Design, properties, and synthetic optimization for fluorogenic labeling of
5‐formyluracil. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hayeon Choi
- Department of Chemistry Chungbuk National University Cheongju Republic of Korea
| | - Hokyung Kim
- Department of Chemistry Chungbuk National University Cheongju Republic of Korea
| | - Ki Tae Kim
- Department of Chemistry Chungbuk National University Cheongju Republic of Korea
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21
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Nising CF, Nussbaum F. Industrial Organic Synthesis in Life Sciences – Today and Tomorrow. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Carl F. Nising
- Corporate R&D and Science Engagement Bayer AG Kaiser-Wilhelm Allee 1 51368 Leverkusen Germany
| | - Franz Nussbaum
- Life Science Chemistry Nuvisan ICB GmbH Muellerstrasse 178 13353 Berlin Germany
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22
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Xiao L, Jun YW, Kool ET. DNA Tiling Enables Precise Acylation‐Based Labeling and Control of mRNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202112106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lu Xiao
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Yong Woong Jun
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Eric T. Kool
- Department of Chemistry Stanford University Stanford CA 94305 USA
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23
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Xiao L, Jun YW, Kool ET. DNA Tiling Enables Precise Acylation-Based Labeling and Control of mRNA. Angew Chem Int Ed Engl 2021; 60:26798-26805. [PMID: 34624169 PMCID: PMC8649056 DOI: 10.1002/anie.202112106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/04/2021] [Indexed: 12/15/2022]
Abstract
Methods for the site-selective labeling of long, native RNAs are needed for studying mRNA biology and future therapies. Current approaches involve engineering RNA sequences, which may alter folding, or are limited to specific sequences or bases. Here, we describe a versatile strategy for mRNA conjugation via a novel DNA-tiling approach. The method, TRAIL, exploits a pool of "protector" oligodeoxynucleotides to hybridize and block the mRNA, combined with an "inducer" DNA that extrudes a reactive RNA loop for acylation at a predetermined site. Using TRAIL, an azido-acylimidazole reagent was employed for labeling and controlling RNA for multiple applications in vitro and in cells, including analysis of RNA-binding proteins, imaging mRNA in cells, and analysis and control of translation. The TRAIL approach offers an efficient and accessible way to label and manipulate RNAs of virtually any length or origin without altering native sequence.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Yong Woong Jun
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
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24
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Kleiner RE. Interrogating the transcriptome with metabolically incorporated ribonucleosides. Mol Omics 2021; 17:833-841. [PMID: 34635895 DOI: 10.1039/d1mo00334h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
RNA is a central player in biological processes, but there remain major gaps in our understanding of transcriptomic processes and the underlying biochemical mechanisms regulating RNA in cells. A powerful strategy to facilitate molecular analysis of cellular RNA is the metabolic incorporation of chemical probes. In this review, we discuss current approaches for RNA metabolic labeling with modified ribonucleosides and their integration with Next-Generation Sequencing, mass spectrometry-based proteomics, and fluorescence microscopy in order to interrogate RNA behavior in its native context.
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Affiliation(s)
- Ralph E Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.
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25
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Mamot A, Sikorski PJ, Siekierska A, de Witte P, Kowalska J, Jemielity J. Ethylenediamine derivatives efficiently react with oxidized RNA 3' ends providing access to mono and dually labelled RNA probes for enzymatic assays and in vivo translation. Nucleic Acids Res 2021; 50:e3. [PMID: 34591964 PMCID: PMC8755103 DOI: 10.1093/nar/gkab867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/31/2021] [Accepted: 09/15/2021] [Indexed: 01/01/2023] Open
Abstract
Development of RNA-based technologies relies on the ability to detect, manipulate, and modify RNA. Efficient, selective and scalable covalent modification of long RNA molecules remains a challenge. We report a chemical method for modification of RNA 3′-end based on previously unrecognized superior reactivity of N-substituted ethylenediamines in reductive amination of periodate-oxidized RNA. Using this method, we obtained fluorescently labelled or biotinylated RNAs varying in length (from 3 to 2000 nt) and carrying different 5′ ends (including m7G cap) in high yields (70–100% by HPLC). The method is scalable (up to sub-milligrams of mRNA) and combined with label-facilitated HPLC purification yields highly homogeneous products. The combination of 3′-end labelling with 5′-end labelling by strain-promoted azide-alkyne cycloaddition (SPAAC) afforded a one-pot protocol for site-specific RNA bifunctionalization, providing access to two-colour fluorescent RNA probes. These probes exhibited fluorescence resonance energy transfer (FRET), which enabled real-time monitoring of several RNA hydrolase activities (RNase A, RNase T1, RNase R, Dcp1/2, and RNase H). Dually labelled mRNAs were efficiently translated in cultured cells and in zebrafish embryos, which combined with their detectability by fluorescent methods and scalability of the synthesis, opens new avenues for the investigation of mRNA metabolism and the fate of mRNA-based therapeutics.
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Affiliation(s)
- Adam Mamot
- Centre of New Technologies, University of Warsaw, Banacha 2c Street, 02-097 Warsaw, Poland.,Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5 Street, 02-093 Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, Banacha 2c Street, 02-097 Warsaw, Poland
| | - Aleksandra Siekierska
- Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg, Herestraat 49, O&N II, 3000 Leuven, Belgium
| | - Peter de Witte
- Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg, Herestraat 49, O&N II, 3000 Leuven, Belgium
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5 Street, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c Street, 02-097 Warsaw, Poland
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26
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Nilsson JR, Baladi T, Gallud A, Baždarević D, Lemurell M, Esbjörner EK, Wilhelmsson LM, Dahlén A. Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics. Sci Rep 2021; 11:11365. [PMID: 34059711 PMCID: PMC8166847 DOI: 10.1038/s41598-021-90629-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/13/2021] [Indexed: 01/28/2023] Open
Abstract
To expand the antisense oligonucleotide (ASO) fluorescence labeling toolbox beyond covalent conjugation of external dyes (e.g. ATTO-, Alexa Fluor-, or cyanine dyes), we herein explore fluorescent base analogues (FBAs) as a novel approach to endow fluorescent properties to ASOs. Both cytosine and adenine analogues (tC, tCO, 2CNqA, and pA) were incorporated into a 16mer ASO sequence with a 3-10-3 cEt-DNA-cEt (cEt = constrained ethyl) gapmer design. In addition to a comprehensive photophysical characterization, we assess the label-induced effects on the gapmers' RNA affinities, RNA-hybridized secondary structures, and knockdown efficiencies. Importantly, we find practically no perturbing effects for gapmers with single FBA incorporations in the biologically critical gap region and, except for pA, the FBAs do not affect the knockdown efficiencies. Incorporating two cytosine FBAs in the gap is equally well tolerated, while two adenine analogues give rise to slightly reduced knockdown efficiencies and what could be perturbed secondary structures. We furthermore show that the FBAs can be used to visualize gapmers inside live cells using fluorescence microscopy and flow cytometry, enabling comparative assessment of their uptake. This altogether shows that FBAs are functional ASO probes that provide a minimally perturbing in-sequence labeling option for this highly relevant drug modality.
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Affiliation(s)
- Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Tom Baladi
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Audrey Gallud
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden.,Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Dženita Baždarević
- Bioscience, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Malin Lemurell
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elin K Esbjörner
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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