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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: 5] [Impact Index Per Article: 5.0] [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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2
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Pradeep SP, Malik S, Slack FJ, Bahal R. Unlocking the potential of chemically modified peptide nucleic acids for RNA-based therapeutics. RNA (NEW YORK, N.Y.) 2023; 29:434-445. [PMID: 36653113 PMCID: PMC10019372 DOI: 10.1261/rna.079498.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/12/2023] [Indexed: 05/27/2023]
Abstract
RNA therapeutics have emerged as next-generation therapy for the treatment of many diseases. Unlike small molecules, RNA targeted drugs are not limited by the availability of binding pockets on the protein, but rather utilize Watson-Crick (WC) base-pairing rules to recognize the target RNA and modulate gene expression. Antisense oligonucleotides (ASOs) present a powerful therapeutic approach to treat disorders triggered by genetic alterations. ASOs recognize the cognate site on the target RNA to alter gene expression. Nine single-stranded ASOs have been approved for clinical use and several candidates are in late-stage clinical trials for both rare and common diseases. Several chemical modifications, including phosphorothioates, locked nucleic acid, phosphorodiamidate, morpholino, and peptide nucleic acids (PNAs), have been investigated for efficient RNA targeting. PNAs are synthetic DNA mimics where the deoxyribose phosphate backbone is replaced by N-(2-aminoethyl)-glycine units. The neutral pseudopeptide backbone of PNAs contributes to enhanced binding affinity and high biological stability. PNAs hybridize with the complementary site in the target RNA and act by a steric hindrance--based mechanism. In the last three decades, various PNA designs, chemical modifications, and delivery strategies have been explored to demonstrate their potential as an effective and safe RNA-targeting platform. This review covers the advances in PNA-mediated targeting of coding and noncoding RNAs for a myriad of therapeutic applications.
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Affiliation(s)
- Sai Pallavi Pradeep
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Shipra Malik
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Frank J Slack
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
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3
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Sarkar S, Colón-Roura G, Pearse A, Armitage BA. Targeting a KRAS i-motif forming sequence by unmodified and gamma-modified peptide nucleic acid oligomers. Biopolymers 2023; 114:e23529. [PMID: 36573547 PMCID: PMC10078108 DOI: 10.1002/bip.23529] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 12/04/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022]
Abstract
Growing interest in i-motif DNA as a transcriptional regulatory element motivates development of synthetic molecules capable of targeting these structures. In this study, we designed unmodified peptide nucleic acid (PNA) and gamma-modified PNA (γPNA) oligomers complementary to an i-motif forming sequence derived from the promoter of the KRAS oncogene. Biophysical techniques such as circular dichroism (CD) spectroscopy, CD melting, and fluorescence spectroscopy demonstrated the successful invasion of the i-motif by PNA and γPNA. Both PNA and γPNA showed very strong binding to the target sequence with high thermal stability of the resulting heteroduplexes. Interestingly fluorescence and CD experiments indicated formation of an intermolecular i-motif structure via the overhangs of target-probe heteroduplexes formed by PNA/γPNA invasion of the intramolecular i-motif. Targeting promoter i-motif forming sequences with high-affinity oligonucleotide mimics like γPNAs may represent a new approach for inhibiting KRAS transcription, thereby representing a potentially useful anti-cancer strategy.
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Affiliation(s)
- Srijani Sarkar
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Gabriela Colón-Roura
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Alexander Pearse
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Bruce A Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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4
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Kuo C, Nikan M, Yeh ST, Chappell AE, Tanowitz M, Seth PP, Prakash TP, Mullick AE. Targeted Delivery of Antisense Oligonucleotides Through Angiotensin Type 1 Receptor. Nucleic Acid Ther 2022; 32:300-311. [PMID: 35612431 DOI: 10.1089/nat.2021.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We evaluated the potential of AGTR1, the principal receptor for angiotensin II (Ang II) and a member of the G protein-coupled receptor family, for targeted delivery of antisense oligonucleotides (ASOs) in cells and tissues with abundant AGTR1 expression. Ang II peptide ASO conjugates maintained robust AGTR1 signaling and receptor internalization when ASO was placed at the N-terminus of the peptide, but not at C-terminus. Conjugation of Ang II peptide improved ASO potency up to 12- to 17-fold in AGTR1-expressing cells. Additionally, evaluation of Ang II conjugates in cells lacking AGTR1 revealed no enhancement of ASO potency. Ang II peptide conjugation improves potency of ASO in mouse heart, adrenal, and adipose tissues. The data presented in this report add to a growing list of approaches for improving ASO potency in extrahepatic tissues.
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Affiliation(s)
- Carol Kuo
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Mehran Nikan
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Steve T Yeh
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | | | | | - Punit P Seth
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
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5
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Bhingardeve P, Jain P, Ganesh KN. Molecular Assembly of Triplex of Duplexes from Homothyminyl-Homocytosinyl Cγ( S/ R)-Bimodal Peptide Nucleic Acids with dA 8/dG 6 and the Cell Permeability of Bimodal Peptide Nucleic Acids. ACS OMEGA 2021; 6:19757-19770. [PMID: 34368563 PMCID: PMC8340421 DOI: 10.1021/acsomega.1c02451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/05/2021] [Indexed: 05/08/2023]
Abstract
Peptide nucleic acids (PNAs) are analogues of DNA with a neutral acyclic polyamide backbone containing nucleobases attached through a t-amide link on repeating units of aminoethylglycine (aeg). They bind to complementary DNA or RNA in a sequence-specific manner to form duplexes with higher stablity than DNA:DNA and DNA:RNA hybrids. We have recently explored a new type of PNA termed bimodal PNA (bm-PNA) designed with two nucleobases per aeg repeating unit of PNA oligomer and attached at Cα or Cγ of each aeg unit through a spacer sidechain. We demonstrated that Cγ-bimodal PNA oligomers with mixed nucleobase sequences bind concurrently two different complementary DNAs, forming double duplexes, one from each t-amide and Cγ face, sharing a common PNA backbone. In such bm-PNA:DNA ternary complexes, the two duplexes show higher thermal stability than individual duplexes. Herein, we show that Cγ(S/R)-bimodal PNAs with homothymines (T8) on a t-amide face and homocytosine (C6) on a Cγ-face form a conjoined pentameric complex consisting of a triplex (bm-PNA-T8)2:dA8 and two duplexes of bm-PNA-C6:dG6. The pentameric complex [dG6:Cγ(S/R)-bm-PNA:dA8:Cγ(S/R)-bm-PNA:dG6] exhibits higher thermal stability than the individual triplex and duplex, with Cγ(S)-bm-PNA complexes being more stable than Cγ(R)-bm-PNA complexes. The conjoined duplexes of Cγ-bimodal PNAs can be used to generate novel higher-order assemblies with DNA and RNA. The Cγ(S/R)-bimodal PNAs are shown to enter MCF7 and NIH 3T3 cells and exhibit low toxicity to cells.
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Affiliation(s)
- Pramod Bhingardeve
- Indian
Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
| | - Prashant Jain
- Indian
Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
| | - Krishna N. Ganesh
- Indian
Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
- Indian
Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Mangalam, Tirupati 517507, India
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6
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Brodyagin N, Katkevics M, Kotikam V, Ryan CA, Rozners E. Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications. Beilstein J Org Chem 2021; 17:1641-1688. [PMID: 34367346 PMCID: PMC8313981 DOI: 10.3762/bjoc.17.116] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/28/2021] [Indexed: 12/23/2022] Open
Abstract
Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA's chemistry, optimization of structure and function, applications as probes and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA's binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA therapeutics. While many modifications have improved on PNA's binding affinity and specificity, solubility and other biophysical properties, the original PNA is still most frequently used in diagnostic and other in vitro applications. Development of therapeutics and other in vivo applications of PNA has notably lagged behind and is still limited by insufficient bioavailability and difficulties with tissue specific delivery. Relatively high doses are required to overcome poor cellular uptake and endosomal entrapment, which increases the risk of toxicity. These limitations remain unsolved problems waiting for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Venubabu Kotikam
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Christopher A Ryan
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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7
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Shiraishi T, Ghavami M, Nielsen PE. In Vitro Cellular Delivery of Peptide Nucleic Acid (PNA). Methods Mol Biol 2021; 2105:173-185. [PMID: 32088870 DOI: 10.1007/978-1-0716-0243-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Cellular delivery methods are a prerequisite for cellular studies with PNA. This chapter describes PNA cellular delivery using cell-penetrating peptide (CPP)-PNA conjugates and transfection of PNA-ligand conjugates mediated by cationic lipids. Furthermore, two endosomolytic procedures employing chloroquine treatment or photochemical internalization (PCI) for significantly improving PNA delivery efficacy are described.
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Affiliation(s)
- Takehiko Shiraishi
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Mahdi Ghavami
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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8
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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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9
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Volpi S, Cancelli U, Neri M, Corradini R. Multifunctional Delivery Systems for Peptide Nucleic Acids. Pharmaceuticals (Basel) 2020; 14:14. [PMID: 33375595 PMCID: PMC7823687 DOI: 10.3390/ph14010014] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023] Open
Abstract
The number of applications of peptide nucleic acids (PNAs)-oligonucleotide analogs with a polyamide backbone-is continuously increasing in both in vitro and cellular systems and, parallel to this, delivery systems able to bring PNAs to their targets have been developed. This review is intended to give to the readers an overview on the available carriers for these oligonucleotide mimics, with a particular emphasis on newly developed multi-component- and multifunctional vehicles which boosted PNA research in recent years. The following approaches will be discussed: (a) conjugation with carrier molecules and peptides; (b) liposome formulations; (c) polymer nanoparticles; (d) inorganic porous nanoparticles; (e) carbon based nanocarriers; and (f) self-assembled and supramolecular systems. New therapeutic strategies enabled by the combination of PNA and proper delivery systems are discussed.
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Affiliation(s)
| | | | | | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.V.); (U.C.); (M.N.)
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10
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Transcriptome-based design of antisense inhibitors potentiates carbapenem efficacy in CRE Escherichia coli. Proc Natl Acad Sci U S A 2020; 117:30699-30709. [PMID: 33199638 DOI: 10.1073/pnas.1922187117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In recent years, the prevalence of carbapenem-resistant Enterobacteriaceae (CRE) has risen substantially, and the study of CRE resistance mechanisms has become increasingly important for antibiotic development. Although much research has focused on genomic resistance factors, relatively few studies have examined CRE pathogens through changes in gene expression. In this study, we examined the gene expression profile of a CRE Escherichia coli clinical isolate that is sensitive to meropenem but resistant to ertapenem to explore transcriptomic contributions to resistance and to identify gene knockdown targets for carbapenem potentiation. We sequenced total and short RNA to analyze the gene expression response to ertapenem or meropenem treatment and found significant expression changes in genes related to motility, maltodextrin metabolism, the formate hydrogenlyase complex, and the general stress response. To validate these findings, we used our laboratory's Facile Accelerated Specific Therapeutic (FAST) platform to create antisense peptide nucleic acids (PNAs), gene-specific molecules designed to inhibit protein translation. PNAs were designed to inhibit the pathways identified in our transcriptomic analysis, and each PNA was then tested in combination with each carbapenem to assess its effect on the antibiotics' minimum inhibitory concentrations. We observed significant PNA-antibiotic interaction with five different PNAs across six combinations. Inhibition of the genes hycA, dsrB, and bolA potentiated carbapenem efficacy in CRE E. coli, whereas inhibition of the genes flhC and ygaC conferred added resistance. Our results identify resistance factors and demonstrate that transcriptomic analysis is a potent tool for designing antibiotic PNA.
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11
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Yang L, Toh DFK, Krishna MS, Zhong Z, Liu Y, Wang S, Gong Y, Chen G. Tertiary Base Triple Formation in the SRV-1 Frameshifting Pseudoknot Stabilizes Secondary Structure Components. Biochemistry 2020; 59:4429-4438. [PMID: 33166472 DOI: 10.1021/acs.biochem.0c00611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Minor-groove base triples formed between stem 1 and loop 2 of the simian retrovirus type 1 (SRV-1) mRNA frameshifting pseudoknot are essential in stimulating -1 ribosomal frameshifting. How tertiary base triple formation affects the local stabilities of secondary structures (stem 1 and stem 2) and thus ribosomal frameshifting efficiency is not well understood. We made a short peptide nucleic acid (PNA) that is expected to invade stem 1 of the SRV-1 pseudoknot by PNA-RNA duplex formation to mimic the stem 1 unwinding process by a translating ribosome. In addition, we used a PNA for invading stem 2 in the SRV-1 pseudoknot. Our nondenaturing polyacrylamide gel electrophoresis data for the binding of PNA to the SRV-1 pseudoknot and mutants reveal that mutations in loop 2 disrupting base triple formation between loop 2 and stem 1 in the SRV-1 pseudoknot result in enhanced invasion by both PNAs. Our data suggest that tertiary stem 1-loop 2 base triple interactions in the SRV-1 pseudoknot can stabilize both of the secondary structural components, stem 1 and stem 2. Stem 2 stability is thus coupled to the structural stability of stem 1-loop 2 base triples, mediated through a long-range effect. The apparent dissociation constants of both PNAs are positively correlated with the pseudoknot mechanical stabilities and frameshifting efficiencies. The relatively simple PNA local invasion experiment may be used to characterize the energetic contribution of tertiary interactions and ligand binding in many other RNA and DNA structures.
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Affiliation(s)
- Lixia Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, Sichuan 610054, P. R. China.,School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), No. 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P. R. China.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Zhensheng Zhong
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Physics and Engineering, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Yiyao Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, Sichuan 610054, P. R. China
| | - Shaomeng Wang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, Sichuan 610054, P. R. China
| | - Yubin Gong
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, Sichuan 610054, P. R. China
| | - Gang Chen
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), No. 2001 Longxiang Boulevard, Longgang District, Shenzhen, Guangdong 518172, P. R. China.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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12
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Bhingardeve P, Madhanagopal BR, Ganesh KN. Cγ( S/ R)-Bimodal Peptide Nucleic Acids (Cγ- bm-PNA) Form Coupled Double Duplexes by Synchronous Binding to Two Complementary DNA Strands. J Org Chem 2020; 85:13680-13693. [PMID: 32985197 DOI: 10.1021/acs.joc.0c01853] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Peptide nucleic acids (PNAs) are linear equivalents of DNA with a neutral acyclic polyamide backbone that has nucleobases attached via tert-amide link on repeating units of aminoethylglycine. They bind complementary DNA or RNA with sequence specificity to form hybrids that are more stable than the corresponding DNA/RNA self-duplexes. A new type of PNA termed bimodal PNA [Cγ(S/R)-bm-PNA] is designed to have a second nucleobase attached via amide spacer to a side chain at Cγ on the repeating aeg units of PNA oligomer. Cγ-bimodal PNA oligomers that have two nucleobases per aeg unit are demonstrated to concurrently bind two different complementary DNAs, to form duplexes from both tert-amide side and Cγ side. In such PNA:DNA ternary complexes, the two duplexes share a common PNA backbone. The ternary DNA 1:Cγ(S/R)-bm-PNA:DNA 2 complexes exhibit better thermal stability than the isolated duplexes, and the Cγ(S)-bm-PNA duplexes are more stable than Cγ(R)-bm-PNA duplexes. Bimodal PNAs are first examples of PNA analogues that can form DNA2:PNA:DNA1 double duplexes via recognition through natural bases. The conjoined duplexes of Cγ-bimodal PNAs can be used to generate novel higher-level assemblies.
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Affiliation(s)
- Pramod Bhingardeve
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Bharath Raj Madhanagopal
- Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Mangalam, Tirupati 517507, India
| | - Krishna N Ganesh
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, India.,Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Mangalam, Tirupati 517507, India
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13
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Lu Z, Paolella BR, Truex NL, Loftis AR, Liao X, Rabideau AE, Brown MS, Busanovich J, Beroukhim R, Pentelute BL. Targeting Cancer Gene Dependencies with Anthrax-Mediated Delivery of Peptide Nucleic Acids. ACS Chem Biol 2020; 15:1358-1369. [PMID: 32348107 PMCID: PMC7521945 DOI: 10.1021/acschembio.9b01027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Antisense oligonucleotide therapies are important cancer treatments, which can suppress genes in cancer cells that are critical for cell survival. SF3B1 has recently emerged as a promising gene target that encodes a key splicing factor in the SF3B protein complex. Over 10% of cancers have lost one or more copies of the SF3B1 gene, rendering these cancers vulnerable after further suppression. SF3B1 is just one example of a CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) gene, but over 120 additional candidate CYCLOPS genes are known. Antisense oligonucleotide therapies for cancer offer the promise of effective suppression for CYCLOPS genes, but developing these treatments is difficult due to their limited permeability into cells and poor cytosolic stability. Here, we develop an effective approach to suppress CYCLOPS genes by delivering antisense peptide nucleic acids (PNAs) into the cytosol of cancer cells. We achieve efficient cytosolic PNA delivery with the two main nontoxic components of the anthrax toxin: protective antigen (PA) and the 263-residue N-terminal domain of lethal factor (LFN). Sortase-mediated ligation readily enables the conjugation of PNAs to the C terminus of the LFN protein. LFN and PA work together in concert to translocate PNAs into the cytosol of mammalian cells. Antisense SF3B1 PNAs delivered with the LFN/PA system suppress the SF3B1 gene and decrease cell viability, particularly of cancer cells with partial copy-number loss of SF3B1. Moreover, antisense SF3B1 PNAs delivered with a HER2-binding PA variant selectively target cancer cells that overexpress the HER2 cell receptor, demonstrating receptor-specific targeting of cancer cells. Taken together, our efforts illustrate how PA-mediated delivery of PNAs provides an effective and general approach for delivering antisense PNA therapeutics and for targeting gene dependencies in cancer.
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Affiliation(s)
- Zeyu Lu
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Brenton R. Paolella
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02139, USA
| | - Nicholas L. Truex
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Alexander R. Loftis
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Xiaoli Liao
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Amy E. Rabideau
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Meredith S. Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02139, USA
| | - John Busanovich
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02139, USA
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02139, USA
| | - Bradley L. Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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14
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Gupta MK, Madhanagopal BR, Datta D, Ganesh KN. Structural Design and Synthesis of Bimodal PNA That Simultaneously Binds Two Complementary DNAs To Form Fused Double Duplexes. Org Lett 2020; 22:5255-5260. [PMID: 32551691 DOI: 10.1021/acs.orglett.0c01950] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bimodal PNAs are new PNA constructs designed to bind two different cDNA sequences synchronously to form double duplexes. They are synthesized on solid phase using sequential coupling and click reaction to introduce a second base in each monomer at Cα via alkyltriazole linker. The ternary bimodal PNA:DNA complexes show stability higher than that of individual duplexes. Bimodal PNAs are appropriate to create higher-order fused nucleic acid assemblies.
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Affiliation(s)
- Manoj Kumar Gupta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
| | - Bharath Raj Madhanagopal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
| | - Dhrubajyoti Datta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
| | - Krishna N Ganesh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India.,Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
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15
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Lundin KE, Gissberg O, Smith CIE, Zain R. Chemical Development of Therapeutic Oligonucleotides. Methods Mol Biol 2020; 2036:3-16. [PMID: 31410788 DOI: 10.1007/978-1-4939-9670-4_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of several different chemical modifications of nucleic acids, with improved base-pairing affinity and specificity as well as increased resistance against nucleases, has been described. These new chemistries have allowed the synthesis of different types of therapeutic oligonucleotides. Here we discuss selected chemistries used in antisense oligonucleotide (ASO) applications (e.g., small interfering RNA (siRNA), RNase H activation, translational block, splice-switching, and also as aptamers). Recently approved oligonucleotide-based drugs are also presented briefly.
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Affiliation(s)
- Karin E Lundin
- Department of Laboratory Medicine, Center for Advanced Therapies, Karolinska Institutet, Stockholm, Sweden.
| | - Olof Gissberg
- Department of Laboratory Medicine, Center for Advanced Therapies, Karolinska Institutet, Stockholm, Sweden
| | - C I Edvard Smith
- Department of Laboratory Medicine, Center for Advanced Therapies, Karolinska University Hospital Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Center for Advanced Therapies, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Center for Rare Diseases, Karolinska University Hospital, Stockholm, Sweden
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16
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Indumathi K, Abiram A, Praveena G. Effect of peptidic backbone on the nucleic acid dimeric strands. Mol Phys 2020. [DOI: 10.1080/00268976.2019.1584682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- K. Indumathi
- Department of Physics, PSGR Krishnammal College for Women, Coimbatore, India
| | - A. Abiram
- Department of Physics, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - G. Praveena
- Department of Physics, PSGR Krishnammal College for Women, Coimbatore, India
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17
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Malik S, Asmara B, Moscato Z, Mukker JK, Bahal R. Advances in Nanoparticle-based Delivery of Next Generation Peptide Nucleic Acids. Curr Pharm Des 2019; 24:5164-5174. [PMID: 30657037 DOI: 10.2174/1381612825666190117164901] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 01/11/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND Peptide nucleic acids (PNAs) belong to the next generation of synthetic nucleic acid analogues. Their high binding affinity and specificity towards the target DNA or RNA make them the reagent of choice for gene therapy-based applications. OBJECTIVE To review important gene therapy based applications of regular and chemically modified peptide nucleic acids in combination with nanotechnology. METHOD Selective research of the literature. RESULTS Poor intracellular delivery of PNAs has been a significant challenge. Among several delivery strategies explored till date, nanotechnology-based strategies hold immense potential. Recent studies have shown that advances in nanotechnology can be used to broaden the range of therapeutic applications of PNAs. In this review, we discussed significant advances made in nanoparticle-based on PLGA polymer, silicon, oxidized carbon and graphene oxide for the delivery of PNAs. CONCLUSION Nanoparticles delivered PNAs can be implied in diverse gene therapy based applications including gene editing as well as gene targeting (antisense) based strategies.
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Affiliation(s)
- Shipra Malik
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
| | - Brenda Asmara
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
| | - Zoe Moscato
- Biomedical Engineering Department, University of Connecticut, Storrs, CT, United States
| | - Jatinder Kaur Mukker
- Translational Medicine & Clinical Pharmacology, Boehringer-Ingelheim Pharmaceutical, Inc. Ridgefield, CT, United States
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
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18
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Cooperative Cellular Uptake and Activity of Octaarginine Antisense Peptide Nucleic acid (PNA) Conjugates. Biomolecules 2019; 9:biom9100554. [PMID: 31581514 PMCID: PMC6843268 DOI: 10.3390/biom9100554] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/07/2019] [Accepted: 09/23/2019] [Indexed: 12/21/2022] Open
Abstract
Cellular uptake and antisense activity of d-octaarginine conjugated peptide nucleic acids (PNAs) is shown to exhibit pronounced cooperativity in serum-containing medium, in particular by being enhanced by analogous mis-match PNA–cell-penetrating peptide (PNA–CPP) conjugates without inherent antisense activity. This cooperativity does not show cell or PNA sequence dependency, suggesting that it is a common effect in cationic CPP conjugated PNA delivery. Interestingly, our results also indicate that Deca-r8-PNA and r8-PNA could assist each other and even other non-CPP PNAs as an uptake enhancer agent. However, the peptide itself (without being attached to the PNA) failed to enhance uptake and antisense activity. These results are compatible with an endosomal uptake mechanism in which the endocytosis event is induced by multiple CPP–PNA binding to the cell surface requiring a certain CPP density, possibly in terms of nanoparticle number and/or size, to be triggered. In particular the finding that the number of endosomal events is dependent on the total CPP–PNA concentration supports such a model. It is not possible from the present results to conclude whether endosomal escape is also cooperatively induced by CPP–PNA.
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19
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Montazersaheb S, Kazemi M, Nabat E, Nielsen PE, Hejazi MS. Downregulation of TdT Expression through Splicing Modulation by Antisense Peptide Nucleic Acid (PNA). Curr Pharm Biotechnol 2019; 20:168-178. [PMID: 30727883 DOI: 10.2174/1389201020666190206202650] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/29/2018] [Accepted: 01/30/2019] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND OBJECTIVE Antisense oligonucleotides are able to modulate splicing patterns and offer therapeutic intervention for cancer and other diseases. Considering TdT potential as a target in cancer therapy, the present study aimed to investigate splicing alteration of TdT pre-mRNA in Molt-4 cells using peptide nucleic acid (PNA) octaarginine and cholic acid conjugates. METHOD We examined 16 mer PNAs targeting 5' and 3' junctions of intron 7 and addressed their mRNA splicing modulation effects using RT-PCR analysis. We also tested corresponding 2-base mismatch PNAs to confirm the sequence specificity. In addition, protien level of TdT, apoptosis induction and cell viability rate were analysed. RESULTS PCR analysis showed that full match PNAs could modulate the splicing process, thereby producing a longer mRNA still including intron 7. PCR results also implied exon 7 skipping. In addition, reduced level of TdT protein in Molt-4 cells was observed. Downregulation of TdT level in PNA treated cells was accompanied by an increased rate of apoptosis and decreased the level of cell survival. CONCLUSION PNA-mediated splicing modulation can specifically downregulate TdT expression. TdT dowregulation results in apoptosis induction and reduced cell survival in Molt-4 cells. These observations could draw more attentions to develop PNA based strategies for TdT suppression and consequent apoptosis induction in acute lymphoblastic leukemia.
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Affiliation(s)
- Soheila Montazersaheb
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoumeh Kazemi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elahe Nabat
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Faculty of Health and Medical Science, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Mohammad S Hejazi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
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20
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Patil KM, Toh DFK, Yuan Z, Meng Z, Shu Z, Zhang H, Ong A, Krishna MS, Lu L, Lu Y, Chen G. Incorporating uracil and 5-halouracils into short peptide nucleic acids for enhanced recognition of A-U pairs in dsRNAs. Nucleic Acids Res 2018; 46:7506-7521. [PMID: 30011039 PMCID: PMC6125629 DOI: 10.1093/nar/gky631] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 06/09/2018] [Accepted: 07/03/2018] [Indexed: 01/16/2023] Open
Abstract
Double-stranded RNA (dsRNA) structures form triplexes and RNA-protein complexes through binding to single-stranded RNA (ssRNA) regions and proteins, respectively, for diverse biological functions. Hence, targeting dsRNAs through major-groove triplex formation is a promising strategy for the development of chemical probes and potential therapeutics. Short (e.g., 6-10 mer) chemically-modified Peptide Nucleic Acids (PNAs) have been developed that bind to dsRNAs sequence specifically at physiological conditions. For example, a PNA incorporating a modified base thio-pseudoisocytosine (L) has an enhanced recognition of a G-C pair in an RNA duplex through major-groove L·G-C base triple formation at physiological pH, with reduced pH dependence as observed for C+·G-C base triple formation. Currently, an unmodified T base is often incorporated into PNAs to recognize a Watson-Crick A-U pair through major-groove T·A-U base triple formation. A substitution of the 5-methyl group in T by hydrogen and halogen atoms (F, Cl, Br, and I) causes a decrease of the pKa of N3 nitrogen atom, which may result in improved hydrogen bonding in addition to enhanced base stacking interactions. Here, we synthesized a series of PNAs incorporating uracil and halouracils, followed by binding studies by non-denaturing polyacrylamide gel electrophoresis, circular dichroism, and thermal melting. Our results suggest that replacing T with uracil and halouracils may enhance the recognition of an A-U pair by PNA·RNA2 triplex formation in a sequence-dependent manner, underscoring the importance of local stacking interactions. Incorporating bromouracils and chlorouracils into a PNA results in a significantly reduced pH dependence of triplex formation even for PNAs containing C bases, likely due to an upshift of the apparent pKa of N3 atoms of C bases. Thus, halogenation and other chemical modifications may be utilized to enhance hydrogen bonding of the adjacent base triples and thus triplex formation. Furthermore, our experimental and computational modelling data suggest that PNA·RNA2 triplexes may be stabilized by incorporating a BrUL step but not an LBrU step, in dsRNA-binding PNAs.
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Affiliation(s)
- Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Zhen Yuan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Zhenyu Meng
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Zhiyu Shu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Haiping Zhang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Alan Ann Lerk Ong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Yunpeng Lu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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21
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Sabale PM, Ambi UB, Srivatsan SG. A Lucifer-Based Environment-Sensitive Fluorescent PNA Probe for Imaging Poly(A) RNAs. Chembiochem 2018; 19:826-835. [PMID: 29396904 PMCID: PMC5972818 DOI: 10.1002/cbic.201700661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 12/14/2022]
Abstract
Fluorescence‐based oligonucleotide (ON) hybridization probes greatly aid the detection and profiling of RNA sequences in cells. However, certain limitations such as target accessibility and hybridization efficiency in cellular environments hamper their broad application because RNAs can form complex and stable structures. In this context, we have developed a robust hybridization probe suitable for imaging RNA in cells by combining the properties of 1) a new microenvironment‐sensitive fluorescent nucleobase analogue, obtained by attaching the Lucifer chromophore (1,8‐naphthalimide) at the 5‐position of uracil, and 2) a peptide nucleic acid (PNA) capable of forming stable hybrids with RNA. The fluorescence of the PNA base analogue labeled with the Lucifer chromophore, when incorporated into PNA oligomers and hybridized to complementary and mismatched ONs, is highly responsive to its neighboring base environment. Notably, the PNA base reports the presence of an adenine repeat in an RNA ON with reasonable enhancement in fluorescence. This feature of the emissive analogue enabled the construction of a poly(T) PNA probe for the efficient visualization of polyadenylated [poly(A)] RNAs in cells—poly(A) being an important motif that plays vital roles in the lifecycle of many types of RNA. Our results demonstrate that such responsive fluorescent nucleobase analogues, when judiciously placed in PNA oligomers, could generate useful hybridization probes to detect nucleic acid sequences in cells and also to image them.
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Affiliation(s)
- Pramod M Sabale
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
| | - Uddhav B Ambi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
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22
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Hegarty JP, Stewart DB. Advances in therapeutic bacterial antisense biotechnology. Appl Microbiol Biotechnol 2017; 102:1055-1065. [PMID: 29209794 DOI: 10.1007/s00253-017-8671-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 12/15/2022]
Abstract
Antisense therapeutics are a biotechnological form of antibiotic therapy using chemical analogues of short single-stranded nucleic acid sequences modified to form stable oligomers. These molecules are termed antisense oligonucleotides (ASOs) because their sequence is complementary, via Watson-Crick specific base pairing, to their target messenger RNA (mRNA). ASOs modify gene expression in this sequence-dependent manner by binding to its complementary mRNA and inhibiting its translation into protein through steric blockage and/or through RNase degradation of the ASO/RNA duplex. The widespread use of conventional antibiotics has led to the increasing emergence of multiple drug-resistant pathogenic bacteria. There is an urgent need to develop alternative therapeutic strategies to reduce the morbidity and mortality associated with bacterial infections, and until recently, the use of ASOs as therapeutic agents has been essentially limited to eukaryotic cells, with ASOs as antibacterials having been largely unexplored primarily due to the poor uptake efficiency of antisense molecules by bacteria. There are conceptual advantages to bacterial antisense antibiotic therapies, including a sequence-dependent approach that allows for a rational design to multiple specific molecular targets. This review summarizes the current knowledge of antisense bacterial biotechnology and highlights the recent progress and the current obstacles in their development for therapeutic applications.
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Affiliation(s)
- John P Hegarty
- College of Medicine, Department of Surgery, The Pennsylvania State University, 500 University Drive, H137, P.O. Box 850, Hershey, PA, 17033-0850, USA
| | - David B Stewart
- College of Medicine, Department of Surgery, The Pennsylvania State University, 500 University Drive, H137, P.O. Box 850, Hershey, PA, 17033-0850, USA.
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23
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Tools for attenuation of gene expression in malaria parasites. Int J Parasitol 2017; 47:385-398. [PMID: 28153780 DOI: 10.1016/j.ijpara.2016.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/15/2016] [Accepted: 11/28/2016] [Indexed: 12/30/2022]
Abstract
An understanding of the biology of Plasmodium parasites, which are the causative agents of the disease malaria, requires study of gene function. Various reverse genetic tools have been described for determining gene function. These tools can be broadly grouped as trans- and cis-acting. Trans-acting tools control gene functions through synthetic nucleic acid probe molecules matching the sequence of the gene of interest. Once delivered to the parasite, the probe engages with the mRNA of the target gene and attenuates its function. Cis-acting tools control gene function through elements introduced into the gene of interest by DNA transfection. The expression of the modified gene can be controlled using external agents, typically small molecule ligands. In this review, we discuss the strengths and weaknesses of these tools to guide researchers in selecting the appropriate tool for studies of gene function, and for guiding future refinements of these tools.
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24
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Abstract
Oligonucleotide-based therapeutics have made rapid progress in the clinic for treatment of a variety of disease indications. Unmodified oligonucleotides are polyanionic macromolecules with poor drug-like properties. Over the past two decades, medicinal chemists have identified a number of chemical modification and conjugation strategies which can improve the nuclease stability, RNA-binding affinity, and pharmacokinetic properties of oligonucleotides for therapeutic applications. In this perspective, we present a summary of the most commonly used nucleobase, sugar and backbone modification, and conjugation strategies used in oligonucleotide medicinal chemistry.
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Affiliation(s)
- W Brad Wan
- Department of Medicinal Chemistry, Ionis Pharmaceuticals , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P Seth
- Department of Medicinal Chemistry, Ionis Pharmaceuticals , 2855 Gazelle Court, Carlsbad, California 92010, United States
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25
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Oyaghire SN, Cherubim CJ, Telmer CA, Martinez JA, Bruchez MP, Armitage BA. RNA G-Quadruplex Invasion and Translation Inhibition by Antisense γ-Peptide Nucleic Acid Oligomers. Biochemistry 2016; 55:1977-88. [PMID: 26959335 DOI: 10.1021/acs.biochem.6b00055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have examined the abilities of three complementary γ-peptide nucleic acid (γPNA) oligomers to invade an RNA G-quadruplex and potently inhibit translation of a luciferase reporter transcript containing the quadruplex-forming sequence (QFS) within its 5'-untranslated region. All three γPNA oligomers bind with low nanomolar affinities to an RNA oligonucleotide containing the QFS. However, while all probes inhibit translation with low to midnanomolar IC50 values, the γPNA designed to hybridize to the first two G-tracts of the QFS and adjacent 5'-overhanging nucleotides was 5-6 times more potent than probes directed to either the 3'-end or internal regions of the target at 37 °C. This position-dependent effect was eliminated after the probes and target were preincubated at an elevated temperature prior to translation, demonstrating that kinetic effects exert significant control over quadruplex invasion and translation inhibition. We also found that antisense γPNAs exhibited similarly potent effects against luciferase reporter transcripts bearing QFS motifs having G2, G3, or G4 tracts. Finally, our results indicate that γPNA oligomers exhibit selectivity and/or potency higher than those of other antisense molecules such as standard PNA and 2'-OMe RNA previously reported to target G-quadruplexes in RNA.
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Affiliation(s)
- Stanley N Oyaghire
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Collin J Cherubim
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Cheryl A Telmer
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Joe A Martinez
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Marcel P Bruchez
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Bruce A Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
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26
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Gupta A, Bahal R, Gupta M, Glazer PM, Saltzman WM. Nanotechnology for delivery of peptide nucleic acids (PNAs). J Control Release 2016; 240:302-311. [PMID: 26776051 DOI: 10.1016/j.jconrel.2016.01.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 12/10/2015] [Accepted: 01/04/2016] [Indexed: 12/22/2022]
Abstract
Over the past three decades, peptide nucleic acids have been employed in numerous chemical and biological applications. Peptide nucleic acids possess enormous potential because of their superior biophysical properties, compared to other oligonucleotide chemistries. However, for therapeutic applications, intracellular delivery of peptide nucleic acids remains a challenge. In this review, we summarize the progress that has been made in delivering peptide nucleic acids to intracellular targets. In addition, we emphasize recent nanoparticle-based strategies for efficient delivery of conventional and chemically-modified peptides nucleic acids.
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Affiliation(s)
- Anisha Gupta
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Raman Bahal
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Meera Gupta
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Department of Chemical Engineering, Indian Institute of Technology-Delhi, New Delhi, India
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA; Department of Genetics, Yale University, New Haven, CT, USA.
| | - W Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
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27
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Canady TD, Telmer CA, Oyaghire SN, Armitage BA, Bruchez MP. In Vitro Reversible Translation Control Using γPNA Probes. J Am Chem Soc 2015; 137:10268-75. [PMID: 26241615 DOI: 10.1021/jacs.5b05351] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
On-demand regulation of gene expression in living cells is a central goal of chemical biology and antisense therapeutic development. While significant advances have allowed regulatory modulation through inserted genetic elements, on-demand control of the expression/translation state of a given native gene by complementary sequence interactions remains a technical challenge. Toward this objective, we demonstrate the reversible suppression of a luciferase gene in cell-free translation using Watson-Crick base pairing between the mRNA and a complementary γ-modified peptide nucleic acid (γPNA) sequence with a noncomplementary toehold. Exploiting the favorable thermodynamics of γPNA-γPNA interactions, the antisense sequence can be removed by hybridization of a second, fully complementary γPNA, through a strand displacement reaction, allowing translation to proceed. Complementary RNA is also shown to displace the bound antisense γPNA, opening up possibilities of in vivo regulation by native gene expression.
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Affiliation(s)
- Taylor D Canady
- †Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Cheryl A Telmer
- †Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Stanley N Oyaghire
- †Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Bruce A Armitage
- †Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Marcel P Bruchez
- †Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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28
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Jia F, Balaji BS, Gallazzi F, Lewis MR. Copper-64-labeled anti-bcl-2 PNA-peptide conjugates selectively localize to bcl-2-positive tumors in mouse models of B-cell lymphoma. Nucl Med Biol 2015; 42:809-15. [PMID: 26239085 DOI: 10.1016/j.nucmedbio.2015.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 05/06/2015] [Accepted: 06/03/2015] [Indexed: 10/23/2022]
Abstract
INTRODUCTION The bcl-2 gene is overexpressed in non-Hodgkin's lymphoma (NHL). We have reported micro-SPECT/CT imaging of Mec-1 human lymphoma xenografts in SCID mice, using [(111)In]DOTA-anti-bcl-2-PNA-Tyr(3)-octreotate. In order to reduce normal organ accumulation and improve imaging contrast, modified monomers with neutral hydrophilic (serine, TS) or negatively charged (aspartic acid, TD) residues were synthesized as substitutes for glycine at T(14) in the PNA sequence. The parent and modified PNA-peptide conjugates were labeled with (64)Cu and evaluated in biodistribution studies and high resolution PET/CT imaging of SCID mice bearing bcl-2-positive Mec-1 xenografts as well as bcl-2-negative Ramos xenografts. METHODS Mice were administered the (64)Cu-labeled conjugates for biodistribution and imaging studies. Biodistributions were obtained from 1 to 48 h post-injection. Mice were imaged from 1 to 48 h post-injection. RESULTS The parent glycine conjugate and two modified conjugates all showed selective tumor uptake in Mec-1 xenografts. The liver uptake of the serine conjugate was significantly reduced compared to the two other PNA conjugates. Its kidney uptake was highest of the three at 47.1% ID/g at 1h and dropped to 20.6% ID/g at 24h. [Copper-64]DOTA-anti-bcl-2-TS-PNA-Tyr(3)-octreotate showed tumor uptake of 1.38% ID/g at 1h and 1.06% ID/g at 24h. The tumor-to-blood ratio was increased by factor of 2 from 1h to 24h. This compound detected Mec-1 tumors by micro-PET/CT as early as 1h post-injection and at time points out to 48 h. However, the negative control Ramos tumor could not be detected. CONCLUSIONS These (64)Cu-labeled, amino acid-modified PNA conjugates showed selective tumor targeting in vivo, and tumor xenografts were detected by micro-PET/CT as early as 1h post-injection, suggesting that bcl-2 expression at the mRNA level can detected by PET in mouse models of NHL. Advances in knowledge and implications for patient care Down-regulating bcl-2, an anti-apoptotic proto-oncogene, is a mechanism to reverse chemotherapy resistance in humans with NHL. Thus, bcl-2 overexpression might be considered a new independent prognostic parameter in NHL, aiding in the identification of patients at risk for treatment failure. We have developed [(64)Cu]DOTA-anti-bcl-2-PNA-Tyr(3)-octreotate conjugates for targeted antisense PET imaging. Our preclinical studies identified an effective combination of antisense and radionuclide imaging, with the goal of future clinical trials in patients. This imaging modality may improve clinical care by identifying patients who might respond better to conventional chemotherapy.
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Affiliation(s)
- Fang Jia
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, 65211
| | - Baghavathy S Balaji
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, 65211
| | - Fabio Gallazzi
- Molecular Biology Program, University of Missouri, Columbia, MO, 65211
| | - Michael R Lewis
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, 65211; Nuclear Science and Engineering Institute, University of Missouri, Columbia, MO, 65211; Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201.
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Jain HV, Verthelyi D, Beaucage SL. Amphipathic trans-acting phosphorothioate DNA elements mediate the delivery of uncharged nucleic acid sequences in mammalian cells. RSC Adv 2015. [DOI: 10.1039/c5ra12038a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Amphipathic trans-acting phosphorothioate DNA elements deliver PNA and PMO oligomers in mammalian cells.
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Affiliation(s)
- H. V. Jain
- Division of Biotechnology Review and Research IV
- CDER
- FDA
- Maryland 20933
- USA
| | - D. Verthelyi
- Division of Biotechnology Review and Research III
- CDER
- FDA
- Maryland 20933
- USA
| | - S. L. Beaucage
- Division of Biotechnology Review and Research IV
- CDER
- FDA
- Maryland 20933
- USA
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Shiraishi T, Nielsen PE. Cellular delivery of peptide nucleic acids (PNAs). Methods Mol Biol 2014; 1050:193-205. [PMID: 24297361 DOI: 10.1007/978-1-62703-553-8_16] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cellular delivery methods are a prerequisite for cellular studies with PNA. This chapter describes PNA cellular delivery using cell-penetrating peptide (CPP)-PNA conjugates and transfection of PNA-ligand conjugates mediated by cationic lipids. Furthermore, two endosomolytic procedures employing chloroquine treatment or photochemical internalization (PCI) for significantly improving PNA delivery efficacy are described.
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Affiliation(s)
- Takehiko Shiraishi
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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Towheed A, Markantone DM, Crain AT, Celotto AM, Palladino MJ. Small mitochondrial-targeted RNAs modulate endogenous mitochondrial protein expression in vivo. Neurobiol Dis 2014; 69:15-22. [PMID: 24807207 DOI: 10.1016/j.nbd.2014.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 04/04/2014] [Accepted: 04/27/2014] [Indexed: 11/26/2022] Open
Abstract
Endogenous mitochondrial genes encode critical oxidative phosphorylation components and their mutation results in a set of disorders known collectively as mitochondrial encephalomyopathies. There is intensive interest in modulating mitochondrial function as organelle dysfunction has been associated with numerous disease states. Proteins encoded by the mitochondrial genome cannot be genetically manipulated by current techniques. Here we report the development of a mitochondrial-targeted RNA expression system (mtTRES) utilizing distinct non-coding leader sequences (NCLs) and enabling in vivo expression of small mitochondrial-targeted RNAs. mtTRES expressing small chimeric antisense RNAs was used as translational inhibitors (TLIs) to target endogenous mitochondrial protein expression in vivo. By utilizing chimeric antisense RNA we successfully modulate expression of two mitochondrially-encoded proteins, ATP6 and COXII, and demonstrate the utility of this system in vivo and in human cells. This technique has important and obvious research and clinical implications.
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Affiliation(s)
- Atif Towheed
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Desiree M Markantone
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Aaron T Crain
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Alicia M Celotto
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Michael J Palladino
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
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Zhao X, Wang N, Ren X, Zhang J, Wang J, Han J, Jia L, Liu Y, Zhang Z. Preparation and Evaluation of (99m)Tc-Epidermal Growth Factor Receptor (EGFR)-Peptide Nucleic Acid for Visualization of EGFR Messenger RNA Expression in Malignant Tumors. J Nucl Med 2014; 55:1008-16. [PMID: 24744447 DOI: 10.2967/jnumed.113.136101] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 03/11/2014] [Indexed: 01/29/2023] Open
Abstract
UNLABELLED Epidermal growth factor receptor (EGFR) is overexpressed in many carcinomas and remains a prime target for diagnostic and therapeutic applications. There is a need to develop noninvasive methods to identify the subset of patients that is most likely to benefit from EGFR-targeted treatment. Noninvasive imaging of EGFR messenger RNA (mRNA) expression may be a useful approach. The aim of this study was to develop a method for preparation of single-photon-emitting probes, (99m)Tc-labeled EGFR mRNA antisense peptide nucleic acid (PNA) ((99m)Tc-EGFR-PNA), and nontargeting control ((99m)Tc-CTL-PNA) and to evaluate their feasibility for imaging EGFR mRNA overexpression in malignant tumors in vivo. METHODS On the 5' terminus of synthesized single-stranded 17-mer antisense EGFR mRNA antisense PNA and mismatched PNA, a 4-amino-acid (Gly-(D)-Ala-Gly-Gly) linker forming an N4 structure was used for coupling (99m)Tc. Probes were labeled with (99m)Tc by ligand exchange. The radiochemical purity of these (99m)Tc-labeled probes was determined by reversed-phase high-performance liquid chromatography. Cellular uptake, retention, binding specificity, and stability of the probes were studied either in vitro or in vivo. Biodistribution and radionuclide imaging were performed in BALB/c nude mice bearing SKOV3 (EGFR-positive) or MDA-MB-435S (EGFR-negative) carcinoma xenografts, respectively. RESULTS The average labeling efficiencies of (99m)Tc-EGFR-PNA and (99m)Tc-CTL-PNA were 98.80% ± 1.14% and 98.63% ± 1.36% (mean ± SD, n = 6), respectively, within 6 h at room temperature, and the radiochemical purity of the probes was higher than 95%. (99m)Tc-EGFR-PNA was highly stable in normal saline and fresh human serum at 37°C in vitro and in urine and plasma samples of nude mice after 2-3 h of injection. Cellular uptake and retention ratios of (99m)Tc-EGFR-PNA in SKOV3 cells were higher than those of (99m)Tc-CTL-PNA and the EGFR-negative control. Meanwhile, EGFR mRNA binding (99m)Tc-EGFR-PNA was blocked with an excess of unlabeled EGFR-PNA in SKOV3 cell lines. The biodistribution study demonstrated accumulation of (99m)Tc-EGFR-PNA primarily in the SKOV3 xenografts and in EGFR-expressing organs. Radionuclide imaging demonstrated clear localization of (99m)Tc-EGFR-PNA in the SKOV3 xenografts shortly after injection but not in (99m)Tc-CTL-PNA and the EGFR-negative control. CONCLUSION (99m)Tc-EGFR-PNA has the potential for imaging EGFR mRNA overexpression in tumors.
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Affiliation(s)
- Xinming Zhao
- Department of Nuclear Medicine, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Na Wang
- Department of Nuclear Medicine, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xiuchun Ren
- Department of Nuclear Medicine, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jingmian Zhang
- Department of Nuclear Medicine, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jianfang Wang
- Department of Nuclear Medicine, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jingya Han
- Department of Nuclear Medicine, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lizhuo Jia
- Department of Nuclear Medicine, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yunuan Liu
- Department of Nuclear Medicine, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhaoqi Zhang
- Department of Nuclear Medicine, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
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Bahal R, McNeer NA, Ly DH, Saltzman WM, Glazer PM. Nanoparticle for delivery of antisense γPNA oligomers targeting CCR5. ARTIFICIAL DNA, PNA & XNA 2014; 4:49-57. [PMID: 23954968 DOI: 10.4161/adna.25628] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The development of a new class of peptide nucleic acids (PNAs), i.e., gamma PNAs (γPNAs), creates the need for a general and effective method for its delivery into cells for regulating gene expression in mammalian cells. Here we report the antisense activity of a recently developed hydrophilic and biocompatible diethylene glycol (miniPEG)-based gamma peptide nucleic acid called MPγPNAs via its delivery by poly(lactide-co-glycolide) (PLGA)-based nanoparticle system. We show that MPγPNA oligomers designed to bind to the selective region of chemokine receptor 5 (CC R5) transcript, induce potent and sequence-specific antisense effects as compared with regular PNA oligomers. In addition, PLGA nanoparticle delivery of MPγPNAs is not toxic to the cells. The findings reported in this study provide a combination of γPNA technology and PLGA-based nanoparticle delivery method for regulating gene expression in live cells via the antisense mechanism.
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Gambari R. Peptide nucleic acids: a review on recent patents and technology transfer. Expert Opin Ther Pat 2014; 24:267-94. [PMID: 24405414 DOI: 10.1517/13543776.2014.863874] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION DNA/RNA-based drugs are considered of major interest in molecular diagnosis and nonviral gene therapy. In this field, peptide nucleic acids (PNAs, DNA analogs in which the sugar-phosphate backbone is replaced by N-(2-aminoethyl)glycine units or similar building blocks) have been demonstrated to be excellent candidates as diagnostic reagents and biodrugs. AREAS COVERED Recent (2002 - 2013) patents based on studies on development of PNA analogs, delivery systems for PNAs, applications of PNAs in molecular diagnosis, and use of PNA for innovative therapeutic protocols. EXPERT OPINION PNAs are unique reagents in molecular diagnosis and have been proven to be very active and specific for alteration of gene expression, despite the fact that solubility and uptake by target cells can be limiting factors. Accordingly, patents on PNAs have taken in great consideration delivery strategies. PNAs have been proven stable and effective in vivo, despite the fact that possible long-term toxicity should be considered. For possible clinical applications, the use of PNA molecules in combination with drugs already employed in therapy has been suggested. Considering the patents available and the results on in vivo testing on animal models, we expect in the near future relevant PNA-based clinical trials.
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Affiliation(s)
- Roberto Gambari
- University of Ferrara, Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section , Via Fossato di Mortara n.74, 44100 Ferrara , Italy +39 532 974443 ; +39 532 974500 ;
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Bae YM, Kim MH, Yu GS, Um BH, Park HK, Lee HI, Lee KT, Suh YD, Choi JS. Enhanced splicing correction effect by an oligo-aspartic acid-PNA conjugate and cationic carrier complexes. J Control Release 2013; 175:54-62. [PMID: 24369124 DOI: 10.1016/j.jconrel.2013.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 12/09/2013] [Accepted: 12/17/2013] [Indexed: 10/25/2022]
Abstract
Peptide nucleic acids (PNAs) are synthetic structural analogues of DNA and RNA. They recognize specific cellular nucleic acid sequences and form stable complexes with complementary DNA or RNA. Here, we designed an oligo-aspartic acid-PNA conjugate and showed its enhanced delivery into cells with high gene correction efficiency using conventional cationic carriers, such as polyethylenimine (PEI) and Lipofectamine 2000. The negatively charged oligo-aspartic acid-PNA (Asp(n)-PNA) formed complexes with PEI and Lipofectamine, and the resulting Asp(n)-PNA/PEI and Asp(n)-PNA/Lipofectamine complexes were introduced into cells. We observed significantly enhanced cellular uptake of Asp(n)-PNA by cationic carriers and detected an active splicing correction effect even at nanomolar concentrations. We found that the splicing correction efficiency of the complex depended on the kind of the cationic carriers and on the number of repeating aspartic acid units. By enhancing the cellular uptake efficiency of PNAs, these results may provide a novel platform technology of PNAs as bioactive substances for their biological and therapeutic applications.
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Affiliation(s)
- Yun Mi Bae
- Department of Biochemistry, Chungnam National University, Daejeon 305-764, Republic of Korea; Laboratory for Advanced Molecular Probing, Research Center for Convergence Nanotechnology, Korea Research Institute of Chemical Technology, Daejeon 305-600, Republic of Korea
| | - Myung Hee Kim
- Department of Biochemistry, Chungnam National University, Daejeon 305-764, Republic of Korea; Catholic Research Institutes of Medical Science, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul 137-701, Republic of Korea
| | - Gwang Sig Yu
- Department of Biochemistry, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Bong Ho Um
- PANAGENE Inc., 816 Tamnip-dong, Yuseong-gu, Daejeon 305-510, Republic of Korea
| | - Hee Kyung Park
- PANAGENE Inc., 816 Tamnip-dong, Yuseong-gu, Daejeon 305-510, Republic of Korea
| | - Hyun-il Lee
- PANAGENE Inc., 816 Tamnip-dong, Yuseong-gu, Daejeon 305-510, Republic of Korea
| | - Kang Taek Lee
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 500-712, Republic of Korea
| | - Yung Doug Suh
- Laboratory for Advanced Molecular Probing, Research Center for Convergence Nanotechnology, Korea Research Institute of Chemical Technology, Daejeon 305-600, Republic of Korea; School of Chemical Engineering, Sungkyunkwan University, Suwon 440-746, Republic of Korea.
| | - Joon Sig Choi
- Department of Biochemistry, Chungnam National University, Daejeon 305-764, Republic of Korea.
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Abstract
Photochemical internalization (PCI) is a method for releasing macromolecules from endosomal and lysosomal compartments. The PCI approach uses a photosensitizer that localizes to endosomal and lysosomal compartments, and a light source with appropriate light spectra for excitation of the photosensitizer. Upon photosensitizer excitation, endosomal and lysosomal membranes are destroyed, due to the formation of reactive oxygen species, followed by release of the endocytosed material. PCI has been demonstrated to enhance and control (site- and time-specific) delivery of various macromolecules such as viruses, proteins, chemotherapeutics, nucleic acid, and so on. In this Review we present past and current studies of PCI-controlled delivery of natural and artificial nucleic acids, such as peptide nucleic acids, siRNA molecules, mRNA molecules and plasmids. We also discuss critical aspects to further the possibilities for successful gene targeting in space and time.
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Sugiyama T, Kittaka A. Chiral peptide nucleic acids with a substituent in the N-(2-aminoethy)glycine backbone. Molecules 2012; 18:287-310. [PMID: 23271467 PMCID: PMC6269907 DOI: 10.3390/molecules18010287] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 12/19/2012] [Accepted: 12/19/2012] [Indexed: 11/16/2022] Open
Abstract
A peptide nucleic acid (PNA) is a synthetic nucleic acid mimic in which the sugar-phosphate backbone is replaced by a peptide backbone. PNAs hybridize to complementary DNA and RNA with higher affinity and superior sequence selectivity compared to DNA. PNAs are resistant to nucleases and proteases and have a low affinity for proteins. These properties make PNAs an attractive agent for biological and medical applications. To improve the antisense and antigene properties of PNAs, many backbone modifications of PNAs have been explored under the concept of preorganization. This review focuses on chiral PNAs bearing a substituent in the N-(2-aminoethyl)glycine backbone. Syntheses, properties, and applications of chiral PNAs are described.
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Affiliation(s)
- Toru Sugiyama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
- Author to whom correspondence should be addressed; E-Mail: ; Tel./Fax: +81-3-5465-8743
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Kaga, Itabashi-ku, Tokyo 173-8605, Japan; E-Mail:
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Shiraishi T, Nielsen PE. Peptide nucleic acid (PNA) cell penetrating peptide (CPP) conjugates as carriers for cellular delivery of antisense oligomers. ARTIFICIAL DNA, PNA & XNA 2012; 2:90-9. [PMID: 22567192 DOI: 10.4161/adna.18739] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have explored the merits of a novel delivery strategy for the antisense oligomers based on cell penetrating peptide (CPP) conjugated to a carrier PNA with sequence complementary to part of the antisense oligomer. The effect of these carrier CPP-PNAs was evaluated by using antisense PNA targeting splicing correction of the mutated luciferase gene in the HeLa pLuc705 cell line, reporting cellular (nuclear) uptake of the antisense PNA via luciferase activity measurement. Carrier CPP-PNA constructs were studied in terms of construct modification (with octaarginine and/or decanoic acid) and carrier PNA length (to adjust binding affinity). In general, the carrier CPP-PNA constructs including the ones with decanoyl modification provided significant increase of the activity of unmodified antisense PNA as well as of antisense octaarginine-PNA conjugates. Antisense activity, and by inference cellular delivery, of unmodified antisense PNA was enhanced at least 20-fold at 6 μM upon the complexation with an equimolar amount of nonamer carrier decanoyl-CPP-PNA (Deca-cPNA1(9)-(D-Arg)8). The antisense activity of a CPP-PNA ((D-Arg)8-asPNA) (at 2 μM) was improved 6-fold and 8-fold by a heptamer carrier CPP-PNA (cPNA1(7)-(D-Arg)8) and hexamer carrier decanoyl-CPP-PNA (Deca-cPNA1(6)-(D-Arg)8), respectively, without showing significant additional cellular toxicity. Most interestingly, the activity reached the same level obtained by enhancement with endosomolytic chloroquine (CQ) treatment, suggesting that the carrier might facilitate endosomal escape. Furthermore, 50% downregulation of luciferase expression at 60 nM siRNA was obtained using this carrier CPP-PNA delivery strategy (with CQ co-treatment) for a single stranded antisense RNA targeting normal luciferase mRNA. These results indicated that CPP-PNA carriers may be used as effective cellular delivery vectors for different types of antisense oligomers and also allows use of combinations of (at least two) different CPP ligands.
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Affiliation(s)
- Takehiko Shiraishi
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, The Panum Institute, University of Copenhagen, Copenhagen N, Denmark.
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Dorn S, Aghaallaei N, Jung G, Bajoghli B, Werner B, Bock H, Lindhorst T, Czerny T. Side chain modified peptide nucleic acids (PNA) for knock-down of six3 in medaka embryos. BMC Biotechnol 2012; 12:50. [PMID: 22901024 PMCID: PMC3469332 DOI: 10.1186/1472-6750-12-50] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 07/31/2012] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Synthetic antisense molecules have an enormous potential for therapeutic applications in humans. The major aim of such strategies is to specifically interfere with gene function, thus modulating cellular pathways according to the therapeutic demands. Among the molecules which can block mRNA function in a sequence specific manner are peptide nucleic acids (PNA). They are highly stable and efficiently and selectively interact with RNA. However, some properties of non-modified aminoethyl glycine PNAs (aegPNA) hamper their in vivo applications. RESULTS We generated new backbone modifications of PNAs, which exhibit more hydrophilic properties. When we examined the activity and specificity of these novel phosphonic ester PNAs (pePNA) molecules in medaka (Oryzias latipes) embryos, high solubility and selective binding to mRNA was observed. In particular, mixing of the novel components with aegPNA components resulted in mixed PNAs with superior properties. Injection of mixed PNAs directed against the medaka six3 gene, which is important for eye and brain development, resulted in specific six3 phenotypes. CONCLUSIONS PNAs are well established as powerful antisense molecules. Modification of the backbone with phosphonic ester side chains further improves their properties and allows the efficient knock down of a single gene in fish embryos.
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Affiliation(s)
- Sebastian Dorn
- Department for Biomedical Sciences, University of Veterinary Medicine, Veterinärplatz 1, A-1210, Vienna, Austria
| | - Narges Aghaallaei
- Department for Biomedical Sciences, University of Veterinary Medicine, Veterinärplatz 1, A-1210, Vienna, Austria
| | - Gerlinde Jung
- Department for Applied Life Sciences, University of Applied Sciences, FH Campus Wien, Helmut-Qualtinger-Gasse 2, A-1030, Vienna, Austria
| | - Baubak Bajoghli
- Department for Biomedical Sciences, University of Veterinary Medicine, Veterinärplatz 1, A-1210, Vienna, Austria
- Current address: Director’s Research Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Birgit Werner
- Ugichem GmbH, Mitterweg 24, A-6020, Innsbruck, Austria
| | - Holger Bock
- Ugichem GmbH, Mitterweg 24, A-6020, Innsbruck, Austria
| | | | - Thomas Czerny
- Department for Biomedical Sciences, University of Veterinary Medicine, Veterinärplatz 1, A-1210, Vienna, Austria
- Department for Applied Life Sciences, University of Applied Sciences, FH Campus Wien, Helmut-Qualtinger-Gasse 2, A-1030, Vienna, Austria
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Avitabile C, Moggio L, Malgieri G, Capasso D, Di Gaetano S, Saviano M, Pedone C, Romanelli A. γ Sulphate PNA (PNA S): highly selective DNA binding molecule showing promising antigene activity. PLoS One 2012; 7:e35774. [PMID: 22586450 PMCID: PMC3346730 DOI: 10.1371/journal.pone.0035774] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 03/21/2012] [Indexed: 11/18/2022] Open
Abstract
Peptide Nucleic Acids (PNAs), nucleic acid analogues showing high stability to enzyme degradation and strong affinity and specificity of binding toward DNA and RNA are widely investigated as tools to interfere in gene expression. Several studies have been focused on PNA analogues with modifications on the backbone and bases in the attempt to overcome solubility, uptake and aggregation issues. γ PNAs, PNA derivatives having a substituent in the γ position of the backbone show interesting properties in terms of secondary structure and affinity of binding toward complementary nucleic acids. In this paper we illustrate our results obtained on new analogues, bearing a sulphate in the γ position of the backbone, developed to be more DNA-like in terms of polarity and charge. The synthesis of monomers and oligomers is described. NMR studies on the conformational properties of monomers and studies on the secondary structure of single strands and triplexes are reported. Furthermore the hybrid stability and the effect of mismatches on the stability have also been investigated. Finally, the ability of the new analogue to work as antigene, interfering with the transcription of the ErbB2 gene on a human cell line overexpressing ErbB2 (SKBR3), assessed by FACS and qPCR, is described.
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Affiliation(s)
- Concetta Avitabile
- Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Università di Napoli “Federico II”, Napoli, Italy
| | - Loredana Moggio
- Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Università di Napoli “Federico II”, Napoli, Italy
| | - Gaetano Malgieri
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli, Caserta, Italy
| | - Domenica Capasso
- Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Università di Napoli “Federico II”, Napoli, Italy
| | | | | | - Carlo Pedone
- Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Università di Napoli “Federico II”, Napoli, Italy
- Istituto di Biostrutture e Bioimmagini (CNR), Napoli, Italy
| | - Alessandra Romanelli
- Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Università di Napoli “Federico II”, Napoli, Italy
- Istituto di Biostrutture e Bioimmagini (CNR), Napoli, Italy
- * E-mail:
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Kam Y, Rubinstein A, Nissan A, Halle D, Yavin E. Detection of endogenous K-ras mRNA in living cells at a single base resolution by a PNA molecular beacon. Mol Pharm 2012; 9:685-93. [PMID: 22289057 DOI: 10.1021/mp200505k] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Detection of mRNA alterations is a promising approach for identifying biomarkers as means of differentiating benign from malignant lesions. By choosing the KRAS oncogene as a target gene, two types of molecular beacons (MBs) based on either phosphothioated DNA (PS-DNA-MB) or peptide nucleic acid (TO-PNA-MB, where TO = thiazole orange) were synthesized and compared in vitro and in vivo. Their specificity was examined in wild-type KRAS (HT29) or codon 12 point mutation (Panc-1, SW480) cells. Incubation of both beacons with total RNA extracted from the Panc-1 cell line (fully complementary sequence) showed a fluorescent signal for both beacons. Major differences were observed, however, for single mismatch mRNA transcripts in cell lines HT29 and SW480. PS-DNA-MB weakly discriminated such single mismatches in comparison to TO-PNA-MB, which was profoundly more sensitive. Cell transfection of TO-PNA-MB with the aid of PEI resulted in fluorescence in cells expressing the fully complementary RNA transcript (Panc-1) but undetectable fluorescence in cells expressing the K-ras mRNA that has a single mismatch to the designed TO-PNA-MB (HT29). A weaker fluorescent signal was also detected in SW480 cells; however, these cells express approximately one-fifth of the target mRNA of the designed TO-PNA-MB. In contrast, PS-DNA-MB showed no fluorescence in all cell lines tested post PEI transfection. Based on the fast hybridization kinetics and on the single mismatch discrimination found for TO-PNA-MB we believe that such molecular beacons are promising for in vivo real-time imaging of endogenous mRNA with single nucleotide polymorphism (SNP) resolution.
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Affiliation(s)
- Yossi Kam
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, PO Box 12065, Jerusalem 91120, Israel
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Shiraishi T, Nielsen PE. Nanomolar cellular antisense activity of peptide nucleic acid (PNA) cholic acid ("umbrella") and cholesterol conjugates delivered by cationic lipids. Bioconjug Chem 2012; 23:196-202. [PMID: 22243634 DOI: 10.1021/bc200460t] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Limited cellular uptake and low bioavailability of peptide nucleic acids (PNAs) have restricted widespread use of PNAs as antisense/antigene agents for cells in culture and not least for in vivo applications. We now report the synthesis and cellular antisense activity in cultured HeLa pLuc705 cells of cholesterol and cholic acid ("umbrella") derivatives of splice correction antisense PNA oligomers. While the conjugates alone were practically inactive up to 1 μM, their activity was dramatically improved when delivered by a cationic lipid transfection agent (LipofectAMINE2000). In particular, PNAs, conjugated to cholesterol through an ester hemisuccinate linker or to cholic acid, exhibited low nanomolar activity (EC(50) ∼ 25 nM). Excellent sequence specificity was retained, as mismatch PNA conjugates did not show any significant antisense activity. Furthermore, we show that increasing the transfection volume improved transfection efficiency, suggesting that accumulation (condensation) of the PNA/lipid complex on the cellular surface is part of the uptake mechanism. These results provide a novel, simple method for very efficient cellular delivery of PNA oligomers, especially using PNA-cholic acid conjugates which, in contrast to PNA-cholesterol conjugates, exhibit sufficient water solubility. The results also question the generality of using cholic acid "umbrella" derivatives as a delivery modality for antisense oligomers.
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Affiliation(s)
- Takehiko Shiraishi
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N, Denmark.
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Su Q, He M, Wu Q, Gao W, Xu H, Ye L, Mu Y. The supramolecular assemblies of 7-amino-2,4-dimethylquinolinium salts and the effect of a variety of anions on their luminescent properties. CrystEngComm 2012. [DOI: 10.1039/c2ce25883h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Dodd DW, Damjanovski S, Hudson RE. Peptide nucleic acid Pt(II) conjugates: a preliminary study of antisense effects in Xenopus laevis. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:257-63. [PMID: 21623539 DOI: 10.1080/15257770.2011.580290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The avid hybridization of peptide nucleic acid (PNA) to DNA and RNA, coupled with the analogue's stability toward enzymatic degradation, has led to its investigation as an antigene/antisense agent. PNA targeted toward the 5'-UTR of an mRNA transcript can effect efficient silencing; however, if targeted to an area within the coding region, the PNA can be displaced by the moving ribosome and be an ineffective antisense agent. Platinum-appended and standard PNAs antisense to an area within the open-reading frame of the gene noggin, were injected into Xenopus laevis embryos. Phenotypic responses were observed and the preliminary results are reported herein.
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Affiliation(s)
- David W Dodd
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
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Ok T, Lee J, Jung C, Lim J, Park CM, Lee JH, Park HG, Lee HS. GNA/aegPNA chimera loaded with RNA binding preference. Chem Asian J 2011; 6:1996-9. [PMID: 21472996 DOI: 10.1002/asia.201100003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Indexed: 11/12/2022]
Affiliation(s)
- Taedong Ok
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea
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46
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Scarfì S, Giovine M, Pintus R, Millo E, Clavarino E, Pozzolini M, Sturla L, Stock RP, Benatti U, Damonte G. Selective inhibition of inducible cyclo-oxygenase-2 expression by antisense peptide nucleic acids in intact murine macrophages. Biotechnol Appl Biochem 2010. [DOI: 10.1111/j.1470-8744.2003.tb01341.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Hatamoto M, Ohashi A, Imachi H. Peptide nucleic acids (PNAs) antisense effect to bacterial growth and their application potentiality in biotechnology. Appl Microbiol Biotechnol 2010; 86:397-402. [PMID: 20135118 DOI: 10.1007/s00253-009-2387-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Revised: 11/26/2009] [Accepted: 11/27/2009] [Indexed: 11/29/2022]
Abstract
Peptide nucleic acids (PNAs) are nucleic acid analogs having attractive properties such as quiet stability against nucleases and proteases, and they form strong complexes with complementary strands of DNA or RNA. Because of this attractive nature, PNA is often used in antisense technology to inhibit gene expression and microbial cell growth with high specificity. Many bacterial antisense or antiribosomal studies using PNA oligomers have been reported so far, and parameters to design effective antisense PNAs and to improve PNA cell entry for efficient inhibition of bacterial growth have been presented. However, there are still several obstacles such as low cellular uptake of PNA while applying antisense PNAs to a complex microbial community. On overcoming these problems, the PNA antisense technique might become a very attractive tool not only for controlling the microbial growth but also for further elucidating microbial ecology in complex microbial consortia. Here, we summarize and present recent studies on the development of antimicrobial PNAs targeting mRNAs and rRNAs. In addition, the application potentiality of antisense techniques in nonclinical biotechnology fields is discussed.
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Affiliation(s)
- Masashi Hatamoto
- Department of Social and Environmental Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8527, Japan.
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Wright DG, Zhang Y, Murphy JR. Effective delivery of antisense peptide nucleic acid oligomers into cells by anthrax protective antigen. Biochem Biophys Res Commun 2008; 376:200-5. [PMID: 18774771 DOI: 10.1016/j.bbrc.2008.08.124] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 08/26/2008] [Indexed: 10/21/2022]
Abstract
Peptide nucleic acid (PNA) is highly stable and binds to complementary RNA and DNA with high affinity, but it resists cellular uptake, thereby limiting its bioavailability. We investigated whether protectiveantigen (PA, a non-toxic component of anthrax toxin) could transport antisense PNA oligomers into reporter cells that contain luciferase transgenes with mutant beta-globin IVS2 intronic inserts, which permit aberrant pre-mRNA splicing and impair luciferase expression. PNA oligomers antisense to mutant splice sites in these IVS2 inserts induced luciferase expression when effectively delivered into the cells. PNA 18-mers with C-terminal poly-lysine tails [PNA(Lys)(8)] demonstrated modest sequence-specific antisense activity by themselves at micromolar concentrations in luc-IVS2 reporter cell cultures. However, this activity was greatly amplified by PA. Antisense PNA(Lys)(8) with but not without PA also corrected the IVS2-654 beta-globin splice defect in cultured erythroid precursor cells from a patient with beta-thalassemia [genotype, IVS2-654(beta(0)/beta(E))], providing further evidence that anthrax PA can effectively transport antisense PNA oligomers into cells.
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Affiliation(s)
- Daniel G Wright
- Molecular Medicine Section, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
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Shiraishi T, Hamzavi R, Nielsen PE. Subnanomolar antisense activity of phosphonate-peptide nucleic acid (PNA) conjugates delivered by cationic lipids to HeLa cells. Nucleic Acids Res 2008; 36:4424-32. [PMID: 18596083 PMCID: PMC2490735 DOI: 10.1093/nar/gkn401] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
In the search of facile and efficient methods for cellular delivery of peptide nucleic acids (PNA), we have synthesized PNAs conjugated to oligophosphonates via phosphonate glutamine and bis-phosphonate lysine amino acid derivatives thereby introducing up to twelve phosphonate moieties into a PNA oligomer. This modification of the PNA does not interfere with the nucleic acid target binding affinity based on thermal stability of the PNA/RNA duplexes. When delivered to cultured HeLa pLuc705 cells by Lipofectamine, the PNAs showed dose-dependent nuclear antisense activity in the nanomolar range as inferred from induced luciferase activity as a consequence of pre-mRNA splicing correction by the antisense-PNA. Antisense activity depended on the number of phosphonate moieties and the most potent hexa-bis-phosphonate-PNA showed at least 20-fold higher activity than that of an optimized PNA/DNA hetero-duplex. These results indicate that conjugation of phosphonate moieties to the PNA can dramatically improve cellular delivery mediated by cationic lipids without affecting on the binding affinity and sequence discrimination ability, exhibiting EC(50) values down to one nanomolar. Thus the intracellular efficacy of PNA oligomers rival that of siRNA and the results therefore emphasize that provided sufficient in vivo bioavailability of PNA can be achieved these molecules may be developed into potent gene therapeutic drugs.
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Affiliation(s)
| | | | - Peter E. Nielsen
- *To whom correspondence should be addressed. +45 353 27762+45 353 96042
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Abstract
Locked nucleic acids (LNAs) are RNA derivatives that have an O-methylene linkage between the 2 and 4 positions of the ribose. This leads to exceptionally high-affinity binding to complementary sequences. They are synthesized using standard DNA/RNA synthesis methods, and have a negatively charged backbone that confers good solubility. This unit describes a method for the introduction of LNA oligomers into cells. A support protocol also describes the determination of melting temperatures for LNA oligomers.
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