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Carson LM, Watson EE. Peptide Nucleic Acids: From Origami to Editing. Chempluschem 2024:e202400305. [PMID: 38972843 DOI: 10.1002/cplu.202400305] [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: 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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Katkevics M, MacKay JA, Rozners E. Triplex-forming peptide nucleic acids as emerging ligands to modulate structure and function of complex RNAs. Chem Commun (Camb) 2024; 60:1999-2008. [PMID: 38259187 PMCID: PMC10922694 DOI: 10.1039/d3cc05409h] [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: 01/24/2024]
Abstract
Over the last three decades, our view of RNA has changed from a simple intermediate supporting protein synthesis to a major regulator of biological processes. In the expanding area of RNA research, peptide nucleic acid (PNA) is emerging as a promising ligand for triple-helical recognition of complex RNAs. As discussed in this feature article, the key advantages of PNAs are high sequence specificity and affinity for RNA (>10 fold higher than for DNA) that are difficult to achieve with small molecule ligands. Emerging studies demonstrate that triple-helical binding of PNAs can modulate biological function and control dynamic conformational equilibria of complex folded RNAs. These results suggest that PNA has a unique potential as a research tool and therapeutic compound targeting RNA. The remaining problems hampering advances in these directions are limitations of sequences that can be recognized by Hoogsteen triplexes (typically purine rich tracts), poor cellular uptake and bioavailability of PNA, and potential off-target effects in biological systems. Recent exciting studies are discussed that illustrate how synthetic nucleic acid chemistry provides innovative solutions for these problems.
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Affiliation(s)
- Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - James A MacKay
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, NY 13902, USA.
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Kumpina I, Loubidi M, Rozners E. Comparison of 2-Aminopyridine and 4-Thiopseudisocytosine PNA Nucleobases for Hoogsteen Recognition of Guanosine in RNA. ACS OMEGA 2024; 9:7249-7254. [PMID: 38371848 PMCID: PMC10870399 DOI: 10.1021/acsomega.3c09775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/20/2024]
Abstract
Peptide nucleic acid (PNA) is emerging as a promising ligand for triple-helical recognition of folded biologically relevant RNA. Chemical modifications are actively being developed to achieve high affinity and sequence specificity under physiological conditions. In this study, we compared two modified PNA nucleobases, 2-aminopyridine (M) and 4-thiopseudisocytosine (L), as alternatives to protonated cytosine (unfavorable under physiological conditions), to form more stable triplets than C+·G-C. Both nucleobases formed M+·G-C and L·G-C triplets of similar stability; however, the L-modified PNAs showed somewhat reduced sequence specificity. In conclusion, M and L represent two alternative solutions to the problem of cytosine protonation in triple-helical recognition of RNA. In M, the pKa is increased to favor partial protonation, which improves solubility and cellular uptake of M-modified PNAs. In L, the sulfur substitution enhances favorable hydrophobic interactions, which may have advantages in avoiding off-target effects that may be caused by cationic modifications. However, our results showed that substituting Ms with Ls did not restore the sequence specificity of a PNA containing cationic groups.
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Affiliation(s)
- Ilze Kumpina
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
| | - Mohammed Loubidi
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
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Nandhini KP, Noki S, Brasil E, Albericio F, de la Torre BG. A safety-catch protecting group strategy compatible with Boc-chemistry for the synthesis of peptide nucleic acids (PNAs). Org Biomol Chem 2023; 21:8125-8135. [PMID: 37772422 DOI: 10.1039/d3ob01348k] [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: 09/30/2023]
Abstract
Peptide Nucleic Acids (PNAs) are an intriguing class of synthetic biomolecules with great potential in medicine. Although PNAs could be considered analogs of oligonucleotides, their synthesis is more like that of peptides. In both cases, a Solid-Phase Synthesis (SPS) approach is used. Herein, the advantage using Boc as a temporal protecting group has been demonstrated to be more favored than Fmoc. In this context, a new PNA SPS strategy has been developed based on a safety-catch protecting group scheme for the exocyclic nitrogen of the side-chain bases and the linker. Sulfinyl (sulfoxide)-containing moieties are fully stable to the trifluoroacetic acid (TFA) used to remove the Boc group, but they can be reduced to the corresponding sulfide derivatives, which are labile in the presence of TFA. The efficiency of this novel synthetic strategy has been demonstrated in the synthesis of the PNA pentamer H-PNA(TATCT)-βAla-OH.
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Affiliation(s)
- K P Nandhini
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa.
| | - Sikabwe Noki
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa.
| | - Edikarlos Brasil
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa.
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa.
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, and Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, 08028 Barcelona, Spain
| | - Beatriz G de la Torre
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
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Gorai A, Chaudhuri R, Mukhopadhyay TK, Datta A, Dash J. Thiazole Containing PNA Mimic Regulates c-MYC Gene Expression through DNA G-Quadruplex. Bioconjug Chem 2022; 33:1145-1155. [PMID: 35537180 DOI: 10.1021/acs.bioconjchem.2c00075] [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
Peptide nucleic acids (PNAs), besides hybridizing to complementary DNA and RNAs, bind and stabilize DNA secondary structures. Herein, we illustrate the design and synthesis of PNA-like scaffolds by incorporating five-membered thiazole rings as modified bases instead of nucleobases and their subsequent effects on gene regulation by biophysical and in vitro assays. A thiazole-modified PNA trimer selectively recognizes c-MYC G-quadruplex (G4) DNA over other G4s and duplex DNA. It displays a high stabilization potential for the c-MYC G4 DNA and shows remarkable fluorescence enhancement with the c-MYC G4. It is flexible enough to bind at 5' and 3' ends as well as in the groove region of c-MYC G4. Furthermore, the PNA trimer easily permeates the cellular membrane and suppresses c-MYC mRNA expression in HeLa cells by targeting the promoter G4. This study illuminates modified PNAs as flexible molecular tools for selective targeting of noncanonical nucleic acids and modulating gene function.
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Affiliation(s)
- Ananta Gorai
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Ritapa Chaudhuri
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Titas Kumar Mukhopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Ayan Datta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
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