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Carson LM, Watson EE. Peptide Nucleic Acids: From Origami to Editing. Chempluschem 2024; 89:e202400305. [PMID: 38972843 DOI: 10.1002/cplu.202400305] [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: 04/30/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/09/2024]
Abstract
Peptide nucleic acids (PNAs) combine the programmability of native nucleic acids with the robustness and ease of synthesis of a peptide backbone. These designer biomolecules have demonstrated tremendous utility across a broad range of applications, from the formation of bespoke biosupramolecular architectures to biosensing and gene regulation. Herein, we explore some of the key developments in the application of PNA in chemical biology and biotechnology in the last 5 years and present anticipated key areas of future development.
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Affiliation(s)
- Liam M Carson
- Department of Chemistry, The University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
| | - Emma E Watson
- Department of Chemistry, The University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
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2
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López-Tena M, Winssinger N. Impact of charges on the hybridization kinetics and thermal stability of PNA duplexes. Org Biomol Chem 2024; 22:5759-5767. [PMID: 38920402 PMCID: PMC11253249 DOI: 10.1039/d4ob00887a] [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: 05/27/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024]
Abstract
Peptide nucleic acid (PNA) is a prominent artificial nucleic acid mimetic and modifications at the γ-position of the peptidic backbone are known to further enhance the desirable properties of PNA in terms of duplex stability. Here, we leveraged a propargyl ether modification at this position for late stage functionalization of PNA to obtain positively charged (cationic amino and guanidinium groups), negatively charged (anionic carboxylate and alkyl phosphonate groups) and neutral (PEG) PNAs to assess the impact of these charges on DNA : PNA and PNA : PNA duplex formation. Thermal stability analysis findings concurred with prior studies showing PNA : DNA duplexes are moderately more stable with cationic PNAs than anionic PNAs at physiological salt concentrations. We show that this effect is derived predominantly from differences in the association kinetics. For PNA : PNA duplexes, anionic PNAs were found to form the most stable duplexes, more stable than neutral PNA : PNA duplexes.
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Affiliation(s)
- Miguel López-Tena
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland.
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland.
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3
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Jeong J, Hu X, Yin R, Fantin M, Das SR, Matyjaszewski K. Nucleic Acid-Binding Dyes as Versatile Photocatalysts for Atom-Transfer Radical Polymerization. J Am Chem Soc 2024; 146:13598-13606. [PMID: 38691811 PMCID: PMC11100002 DOI: 10.1021/jacs.4c03513] [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: 03/11/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/03/2024]
Abstract
Nucleic acid-binding dyes (NuABDs) are fluorogenic probes that light up after binding to nucleic acids. Taking advantage of their fluorogenicity, NuABDs have been widely utilized in the fields of nanotechnology and biotechnology for diagnostic and analytical applications. We demonstrate the potential of NuABDs together with an appropriate nucleic acid scaffold as an intriguing photocatalyst for precisely controlled atom-transfer radical polymerization (ATRP). Additionally, we systematically investigated the thermodynamic and electrochemical properties of the dyes, providing insights into the mechanism that drives the photopolymerization. The versatility of the NuABD-based platform was also demonstrated through successful polymerizations using several NuABDs in conjunction with diverse nucleic acid scaffolds, such as G-quadruplex DNA or DNA nanoflowers. This study not only extends the horizons of controlled photopolymerization but also broadens opportunities for nucleic acid-based materials and technologies, including nucleic acid-polymer biohybrids and stimuli-responsive ATRP platforms.
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Affiliation(s)
- Jaepil Jeong
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Center
for Nucleic Acids Science & Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Xiaolei Hu
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Rongguan Yin
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Marco Fantin
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, Padova 35131, Italy
| | - Subha R. Das
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Center
for Nucleic Acids Science & Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Krzysztof Matyjaszewski
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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4
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Qi Q, Shen Q, Geng J, An W, Wu Q, Wang N, Zhang Y, Li X, Wang W, Yu C, Li L. Stimuli-responsive biodegradable silica nanoparticles: From native structure designs to biological applications. Adv Colloid Interface Sci 2024; 324:103087. [PMID: 38278083 DOI: 10.1016/j.cis.2024.103087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/24/2023] [Accepted: 01/05/2024] [Indexed: 01/28/2024]
Abstract
Due to their inherent advantages, silica nanoparticles (SiNPs) have greatly potential applications as bioactive materials in biosensors/biomedicine. However, the long-term and nonspecific accumulation in healthy tissues may give rise to toxicity, thereby impeding their widespread clinical application. Hence, it is imperative and noteworthy to develop biodegradable and clearable SiNPs for biomedical purposes. Recently, the design of multi-stimuli responsive SiNPs to improve degradation efficiency under specific pathological conditions has increased their clinical trial potential as theranostic nanoplatform. This review comprehensively summaries the rational design and recent progress of biodegradable SiNPs under various internal and external stimuli for rapid in vivo degradation and clearance. In addition, the factors that affect the biodegradation of SiNPs are also discussed. We believe that this systematic review will offer profound stimulus and timely guide for further research in the field of SiNP-based nanosensors/nanomedicine.
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Affiliation(s)
- Qianhui Qi
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China; Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
| | - Qian Shen
- Key Laboratory of Flexible Electronics (KLOFE) and School of Flexible Electronics (Future Technologies), Nanjing Tech University, Nanjing 211800, China
| | - Jiaying Geng
- Key Laboratory of Flexible Electronics (KLOFE) and School of Flexible Electronics (Future Technologies), Nanjing Tech University, Nanjing 211800, China
| | - Weizhen An
- Key Laboratory of Flexible Electronics (KLOFE) and School of Flexible Electronics (Future Technologies), Nanjing Tech University, Nanjing 211800, China
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE) and School of Flexible Electronics (Future Technologies), Nanjing Tech University, Nanjing 211800, China
| | - Nan Wang
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China
| | - Yu Zhang
- Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xue Li
- Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wei Wang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China.
| | - Changmin Yu
- Key Laboratory of Flexible Electronics (KLOFE) and School of Flexible Electronics (Future Technologies), Nanjing Tech University, Nanjing 211800, China; State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210023, China.
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
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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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