1
|
Habib S, Talhami M, Hassanein A, Mahdi E, Al-Ejji M, Hassan MK, Altaee A, Das P, Hawari AH. Advances in functionalization and conjugation mechanisms of dendrimers with iron oxide magnetic nanoparticles. NANOSCALE 2024; 16:13331-13372. [PMID: 38967017 DOI: 10.1039/d4nr01376j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Iron oxide magnetic nanoparticles (MNPs) are crucial in various areas due to their unique magnetic properties. However, their practical use is often limited by instability and aggregation in aqueous solutions. This review explores the advanced technique of dendrimer functionalization to enhance MNP stability and expand their application potential. Dendrimers, with their symmetric and highly branched structure, effectively stabilize MNPs and provide tailored functional sites for specific applications. We summarize key synthetic modifications, focusing on the impacts of dendrimer size, surface chemistry, and the balance of chemical (e.g., coordination, anchoring) and physical (e.g., electrostatic, hydrophobic) interactions on nanocomposite properties. Current challenges such as dendrimer toxicity, control over dendrimer distribution on MNPs, and the need for biocompatibility are discussed, alongside potential solutions involving advanced characterization techniques. This review highlights significant opportunities in environmental, biomedical, and water treatment applications, stressing the necessity for ongoing research to fully leverage dendrimer-functionalized MNPs. Insights offered here aim to guide further development and application of these promising nanocomposites.
Collapse
Affiliation(s)
- Salma Habib
- Department of Mechanical and Industrial Engineering, Qatar University, 2713 Doha, Qatar
- Department of Civil and Environmental Engineering, College of Engineering, Qatar University, PO Box 2713, Doha, Qatar.
| | - Mohammed Talhami
- Department of Civil and Environmental Engineering, College of Engineering, Qatar University, PO Box 2713, Doha, Qatar.
| | - Amani Hassanein
- Department of Civil and Environmental Engineering, College of Engineering, Qatar University, PO Box 2713, Doha, Qatar.
| | - Elsadig Mahdi
- Department of Mechanical and Industrial Engineering, Qatar University, 2713 Doha, Qatar
| | - Maryam Al-Ejji
- Center for Advanced Materials, Qatar University, PO Box 2713, Doha, Qatar
| | - Mohammad K Hassan
- Center for Advanced Materials, Qatar University, PO Box 2713, Doha, Qatar
| | - Ali Altaee
- School of Civil and Environmental Engineering, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Probir Das
- Algal Technologies Program, Center for Sustainable Development, College of Arts and Sciences, Qatar University, 2713, Doha, Qatar
| | - Alaa H Hawari
- Department of Civil and Environmental Engineering, College of Engineering, Qatar University, PO Box 2713, Doha, Qatar.
| |
Collapse
|
2
|
López-Tena M, Winssinger N. Impact of charges on the hybridization kinetics and thermal stability of PNA duplexes. Org Biomol Chem 2024; 22:5759-5767. [PMID: 38920402 PMCID: PMC11253249 DOI: 10.1039/d4ob00887a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024]
Abstract
Peptide nucleic acid (PNA) is a prominent artificial nucleic acid mimetic and modifications at the γ-position of the peptidic backbone are known to further enhance the desirable properties of PNA in terms of duplex stability. Here, we leveraged a propargyl ether modification at this position for late stage functionalization of PNA to obtain positively charged (cationic amino and guanidinium groups), negatively charged (anionic carboxylate and alkyl phosphonate groups) and neutral (PEG) PNAs to assess the impact of these charges on DNA : PNA and PNA : PNA duplex formation. Thermal stability analysis findings concurred with prior studies showing PNA : DNA duplexes are moderately more stable with cationic PNAs than anionic PNAs at physiological salt concentrations. We show that this effect is derived predominantly from differences in the association kinetics. For PNA : PNA duplexes, anionic PNAs were found to form the most stable duplexes, more stable than neutral PNA : PNA duplexes.
Collapse
Affiliation(s)
- Miguel López-Tena
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland.
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland.
| |
Collapse
|
3
|
Giancola JB, Raines RT. Endosomolytic Peptides Enable the Cellular Delivery of Peptide Nucleic Acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599558. [PMID: 38948866 PMCID: PMC11213006 DOI: 10.1101/2024.06.18.599558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Precision genetic medicine enlists antisense oligonucleotides (ASOs) to bind to nucleic acid targets important for human disease. Peptide nucleic acids (PNAs) have many desirable attributes as ASOs but lack cellular permeability. Here, we use an assay based on the corrective splicing of an mRNA to assess the ability of synthetic peptides to deliver a functional PNA into a human cell. We find that the endosomolytic peptides L17E and L17ER 4 are highly efficacious delivery vehicles. Co-treatment of a PNA with low micromolar L17E or L17ER 4 enables robust corrective splicing in nearly all treated cells. Peptide-PNA conjugates are even more effective. These results enhance the utility of PNAs as research tools and potential therapeutic agents.
Collapse
|
4
|
Saini S, Goel K, Ghosh S, Das A, Saraogi I. Effects of PNA Sequence and Target Site Selection on Function of a 4.5S Non-Coding RNA. Chembiochem 2024:e202400029. [PMID: 38595046 DOI: 10.1002/cbic.202400029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/11/2024]
Abstract
Peptide nucleic acid (PNA) based antisense strategy is a promising therapeutic approach to specifically inhibit target gene expression. However, unlike protein coding genes, identification of an ideal PNA binding site for non-coding RNA is not straightforward. Here, we compare the inhibitory activities of PNA molecules that bind a non-coding 4.5S RNA called SRP RNA, a key component of the bacterial signal recognition particle (SRP). A 9-mer PNA (PNA9) complementary to the tetraloop region of the RNA was more potent in inhibiting its interaction with the SRP protein, compared to an 8-mer PNA (PNA8) targeting a stem-loop. PNA9, which contained a homo-pyrimidine sequence could form a triplex with the complementary stretch of RNA in vitro as confirmed using a fluorescent derivative of PNA9 (F-PNA13). The RNA-PNA complex formation resulted in inhibition of SRP function with PNA9 and F-PNA13, but not PNA8 highlighting the importance of target site selection. Surprisingly, F-PNA13 which was more potent in inhibiting SRP function in vitro, showed weaker antibacterial activity compared to PNA9 likely due to poor cell penetration of the longer PNA. Our results underscore the importance of suitable target site selection and optimum PNA length to develop better antisense molecules against non-coding RNA.
Collapse
Affiliation(s)
- Snehlata Saini
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Khushboo Goel
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Sudipta Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Anirban Das
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Ishu Saraogi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| |
Collapse
|
5
|
Oyaghire SN, Quijano E, Perera JDR, Mandl HK, Saltzman WM, Bahal R, Glazer PM. DNA recognition and induced genome modification by a hydroxymethyl-γ tail-clamp peptide nucleic acid. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101635. [PMID: 37920723 PMCID: PMC10621889 DOI: 10.1016/j.xcrp.2023.101635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Peptide nucleic acids (PNAs) can target and stimulate recombination reactions in genomic DNA. We have reported that γPNA oligomers possessing the diethylene glycol γ-substituent show improved efficacy over unmodified PNAs in stimulating recombination-induced gene modification. However, this structural modification poses a challenge because of the inherent racemization risk in O-alkylation of the precursory serine side chain. To circumvent this risk and improve γPNA accessibility, we explore the utility of γPNA oligomers possessing the hydroxymethyl-γ moiety for gene-editing applications. We demonstrate that a γPNA oligomer possessing the hydroxymethyl modification, despite weaker preorganization, retains the ability to form a hybrid with the double-stranded DNA target of comparable stability and with higher affinity than that of the diethylene glycol-γPNA. When formulated into poly(lactic-co-glycolic acid) nanoparticles, the hydroxymethyl-γPNA stimulates higher frequencies (≥ 1.5-fold) of gene modification than the diethylene glycol γPNA in mouse bone marrow cells.
Collapse
Affiliation(s)
- Stanley N. Oyaghire
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- These authors contributed equally
| | - Elias Quijano
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- These authors contributed equally
| | - J. Dinithi R. Perera
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hanna K. Mandl
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - W. Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Department of Chemical & Environmental Engineering, Yale University, New Haven, CT 06511, USA
- Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Peter M. Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
- Lead contact
| |
Collapse
|
6
|
Kakar A, Sastré-Velásquez LE, Hess M, Galgóczy L, Papp C, Holzknecht J, Romanelli A, Váradi G, Malanovic N, Marx F. The Membrane Activity of the Amphibian Temporin B Peptide Analog TB_KKG6K Sheds Light on the Mechanism That Kills Candida albicans. mSphere 2022; 7:e0029022. [PMID: 35972132 PMCID: PMC9599520 DOI: 10.1128/msphere.00290-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
Temporin B (TB) is a 13-amino-acid-long, cationic peptide secreted by the granular glands of the European frog Rana temporaria. We recently showed that the modified TB peptide analog TB_KKG6K rapidly killed planktonic and sessile Candida albicans at low micromolar concentrations and was neither hemolytic nor cytotoxic to mammalian cells in vitro. The present study aimed to shed light into its mechanism of action, with a focus on its fungal cell membrane activity. We utilized different fluorescent dyes to prove that it rapidly induces membrane depolarization and permeabilization. Studies on model membrane systems revealed that the TB analog undergoes hydrophobic and electrostatic membrane interactions, showing a preference for anionic lipids, and identified phosphatidylinositol and cardiolipin as possible peptide targets. Fluorescence microscopy using fluorescein isothiocyanate-labeled TB_KKG6K in the presence of the lipophilic dye FM4-64 indicated that the peptide compromises membrane integrity and rapidly enters C. albicans cells in an energy-independent manner. Peptide-treated cells analyzed by cryo-based electron microscopy exhibited no signs of cell lysis; however, subcellular structures had disintegrated, suggesting that intracellular activity may form part of the killing mechanism of the peptide. Taken together, this study proved that TB_KKG6K compromises C. albicans membrane function, which explains the previously observed rapid, fungicidal mode of action and supports its great potential as a future anti-Candida therapeutic. IMPORTANCE Fungal infections with the opportunistic human pathogen C. albicans are associated with high mortality rates in immunocompromised patients. This is partly due to the yeast's ability to rapidly develop resistance toward currently available antifungals. Small, cationic, membrane-active peptides are promising compounds to fight against resistance development, as many of them effectuate rapid fungal cell death. This fast killing is believed to hamper the development of resistance, as the fungi do not have sufficient time to adapt to the antifungal compound. We previously reported that the synthetic variant of the amphibian TB peptide, TB_KKG6K, rapidly kills C. albicans. In the current study, the mechanism of action of the TB analog was investigated. We show that this TB analog is membrane-active and impairs cell membrane function, highlighting its potential to be developed as an attractive alternative anti-C. albicans therapeutic that may hinder the development of resistance.
Collapse
Affiliation(s)
- Anant Kakar
- Biocenter, Institute of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Michael Hess
- Institute for Histology and Embryology, Medical University of Innsbruck, Innsbruck, Austria
| | - László Galgóczy
- Department of Biotechnology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Csaba Papp
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Jeanett Holzknecht
- Biocenter, Institute of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Györgyi Váradi
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Nermina Malanovic
- Institute of Molecular Biosciences, Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Florentine Marx
- Biocenter, Institute of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
| |
Collapse
|
7
|
Tomassi S, Ieranò C, Del Bene A, D’Aniello A, Napolitano M, Rea G, Auletta F, Portella L, Capiluongo A, Mazzarella V, Russo R, Chambery A, Scala S, Di Maro S, Messere A. Tailoring the Structure of Cell Penetrating DNA and RNA Binding Nucleopeptides. Int J Mol Sci 2022; 23:ijms23158504. [PMID: 35955638 PMCID: PMC9369335 DOI: 10.3390/ijms23158504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Synthetic nucleic acid interactors represent an exciting research field due to their biotechnological and potential therapeutic applications. The translation of these molecules into drugs is a long and difficult process that justifies the continuous research of new chemotypes endowed with favorable binding, pharmacokinetic and pharmacodynamic properties. In this scenario, we describe the synthesis of two sets of homo-thymine nucleopeptides, in which nucleobases are inserted in a peptide structure, to investigate the role of the underivatized amino acid residue and the distance of the nucleobase from the peptide backbone on the nucleic acid recognition process. It is worth noting that the CD spectroscopy investigation showed that two of the reported nucleopeptides, consisting of alternation of thymine functionalized L-Orn and L-Dab and L-Arg as underivatized amino acids, were able to efficiently bind DNA and RNA targets and cross both cell and nuclear membranes.
Collapse
Affiliation(s)
- Stefano Tomassi
- Department of Pharmacy, University of Naples “Federico” II, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Caterina Ieranò
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Alessandra Del Bene
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Antonia D’Aniello
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Maria Napolitano
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Giuseppina Rea
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Federica Auletta
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Luigi Portella
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Anna Capiluongo
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Vincenzo Mazzarella
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Stefania Scala
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Salvatore Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
- Correspondence: (S.D.M.); (A.M.)
| | - Anna Messere
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
- Correspondence: (S.D.M.); (A.M.)
| |
Collapse
|
8
|
Suparpprom C, Vilaivan T. Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications. RSC Chem Biol 2022; 3:648-697. [PMID: 35755191 PMCID: PMC9175113 DOI: 10.1039/d2cb00017b] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022] Open
Abstract
Peptide nucleic acid or PNA is a synthetic DNA mimic that contains a sequence of nucleobases attached to a peptide-like backbone derived from N-2-aminoethylglycine. The semi-rigid PNA backbone acts as a scaffold that arranges the nucleobases in a proper orientation and spacing so that they can pair with their complementary bases on another DNA, RNA, or even PNA strand perfectly well through the standard Watson-Crick base-pairing. The electrostatically neutral backbone of PNA contributes to its many unique properties that make PNA an outstanding member of the xeno-nucleic acid family. Not only PNA can recognize its complementary nucleic acid strand with high affinity, but it does so with excellent specificity that surpasses the specificity of natural nucleic acids and their analogs. Nevertheless, there is still room for further improvements of the original PNA in terms of stability and specificity of base-pairing, direction of binding, and selectivity for different types of nucleic acids, among others. This review focuses on attempts towards the rational design of new generation PNAs with superior performance by introducing conformational constraints such as a ring or a chiral substituent in the PNA backbone. A large collection of conformationally rigid PNAs developed during the past three decades are analyzed and compared in terms of molecular design and properties in relation to structural data if available. Applications of selected modified PNA in various areas such as targeting of structured nucleic acid targets, supramolecular scaffold, biosensing and bioimaging, and gene regulation will be highlighted to demonstrate how the conformation constraint can improve the performance of the PNA. Challenges and future of the research in the area of constrained PNA will also be discussed.
Collapse
Affiliation(s)
- Chaturong Suparpprom
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
| | - Tirayut Vilaivan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
| |
Collapse
|
9
|
Periyalagan A, Kim Y, Hong IS. Synthesis and Characterization of Optically Pure Gamma‐
PNA
Backbones by
SIBX
‐Mediated Reductive Amination. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Alagarsamy Periyalagan
- Department of Chemistry College of Natural Science, Konju National University 56, Gongjudaehak‐ro, Gongju‐si Chungnam 32588 Republic of Korea
| | - Yong‐Tae Kim
- Material Division of Research Institute SEASUN BIOMATERIALS Inc N317, 11‐3, Techno 1‐ro, Yuseong‐gu Daejeon 34015 Republic of Korea
| | - In Seok Hong
- Department of Chemistry College of Natural Science, Konju National University 56, Gongjudaehak‐ro, Gongju‐si Chungnam 32588 Republic of Korea
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Perera JDR, Carufe KEW, Glazer PM. Peptide nucleic acids and their role in gene regulation and editing. Biopolymers 2021; 112:e23460. [PMID: 34129732 DOI: 10.1002/bip.23460] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/19/2022]
Abstract
The unique properties of peptide nucleic acid (PNA) makes it a desirable candidate to be used in therapeutic and biotechnological interventions. It has been broadly utilized for numerous applications, with a major focus in regulation of gene expression, and more recently in gene editing. While the classic PNA design has mainly been employed to date, chemical modifications of the PNA backbone and nucleobases provide an avenue to advance the technology further. This review aims to discuss the recent developments in PNA based gene manipulation techniques and the use of novel chemical modifications to improve the current state of PNA mediated gene targeting.
Collapse
Affiliation(s)
- J Dinithi R Perera
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kelly E W Carufe
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| |
Collapse
|
12
|
Das A, Pradhan B. Evolution of peptide nucleic acid with modifications of its backbone and application in biotechnology. Chem Biol Drug Des 2020; 97:865-892. [PMID: 33314595 DOI: 10.1111/cbdd.13815] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/17/2020] [Accepted: 12/05/2020] [Indexed: 01/23/2023]
Abstract
Peptide nucleic acids (PNAs) are getting prodigious interest currently in the biomedical and diagnostic field as an extremely powerful tool because of their potentiality to hybridize with natural nucleic acids. Although PNA has strong affinity and sequence specificity to DNA/RNA, there is a considerable ongoing effort to further enhance their special chemical and biological properties for potential application in numerous fields, notably in the field of therapeutics. The toolbox for backbone modified PNAs synthesis has been extended substantially in recent decades, providing a more efficient synthesis of peptides with numerous scaffolds and modifications. This paper reviews the various strategies that have been developed so far for the modification of the PNA backbone, challenging the search for new PNA systems with improved chemical and physical properties lacking in the original aegPNA backbone. The various practical issues and limitations of different PNA systems are also summarized. The focus of this review is on the evolution of PNA by its backbone modification to improve the cellular uptake, sequence specificity, and compatibility of PNA to bind to DNA/RNA. Finally, an insight was also gained into major applications of backbone modified PNAs for the development of biosensors.
Collapse
Affiliation(s)
- Anuradha Das
- National Institute of Science Education and Research Bhubaneswar (HBNI), Bhubaneswar, India
| | - Biswaranjan Pradhan
- S. K. Dash Center of Excellence of Biosciences and Engineering & Technology, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| |
Collapse
|
13
|
Moccia M, Mercurio FA, Langella E, Piacenti V, Leone M, Adamo MFA, Saviano M. Structural Insights on Tiny Peptide Nucleic Acid (PNA) Analogues of miRNA-34a: An in silico and Experimental Integrated Approach. Front Chem 2020; 8:568575. [PMID: 33330358 PMCID: PMC7719796 DOI: 10.3389/fchem.2020.568575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/02/2020] [Indexed: 11/17/2022] Open
Abstract
In the present work, structural features of the interaction between peptide nucleic acid (PNA)-based analogs of the tumor-suppressor microRNA-34a with both its binding sites on MYCN mRNA were investigated. In particular, the region from base 1 to 8 ("seed" region) of miR-34a was reproduced in the form of an 8-mer PNA fragment (tiny PNA), and binding to target 3'UTR MYCN mRNA, was studied by a seldom reported and detailed NMR characterization, providing evidence for the formation of anti-parallel duplexes with a well-organized structural core. The formation of PNA-3'UTR duplexes was also confirmed by Circular Dichroism, and their melting curves were measured by UV spectroscopy. Nevertheless, this study offered a valuable comparison between molecular dynamics predictions and experimental evidence, which showed great correlation. Preliminary uptake assays were carried out in Neuroblastoma Kelly cells, using short peptide conjugates as carriers and FITC fluorescent tag for subcellular localization. Moderate internalization was observed without the use of transfecting agents. The reported results corroborate the interest toward the design and development of chimeric PNA/RNA sequences as effective RNA-targeting agents.
Collapse
Affiliation(s)
- Maria Moccia
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technologies, Bari, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy
| | - Emma Langella
- Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy
| | - Valerio Piacenti
- Royal College of Surgeons in Ireland, Department of Pharmaceutical and Medicinal Chemistry, Dublin, Ireland
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy
| | - Mauro F. A. Adamo
- Royal College of Surgeons in Ireland, Department of Pharmaceutical and Medicinal Chemistry, Dublin, Ireland
| | - Michele Saviano
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technologies, Bari, Italy
| |
Collapse
|
14
|
Synthesis, Antiproliferative Activity, and DNA Binding Studies of Nucleoamino Acid-Containing Pt(II) Complexes. Pharmaceuticals (Basel) 2020; 13:ph13100284. [PMID: 33007911 PMCID: PMC7600948 DOI: 10.3390/ph13100284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 11/17/2022] Open
Abstract
We here report our studies on the reaction with the platinum(II) ion of a nucleoamino acid constituted by the l-2,3-diaminopropanoic acid linked to the thymine nucleobase through a methylenecarbonyl linker. The obtained new platinum complexes, characterized by spectroscopic and mass spectrometric techniques, were envisaged to exploit synergistic effects due to the presence of both the platinum center and the nucleoamino acid moiety. The latter can be potentially useful to protect the complexes from early deactivation, as well as to facilitate their cell internalization. The biological activity of the complexes in terms of antiproliferative effects was evaluated in vitro on different cancer cell lines and healthy cells, showing the best results on human cervical adenocarcinoma (HeLa) cells along with good selectivity for cancer over normal cells. In contrast, the metal-free nucleoamino acid did not show any cytotoxicity on both normal and cancer cell lines. Finally, the ability of the novel Pt(II) complexes to bind various DNA model systems was investigated by circular dichroism (CD) spectroscopy and polyacrylamide gel electrophoresis analyses proving that the newly obtained compounds can potentially target DNA, similarly to other well-known anticancer Pt complexes, with a peculiar G-quadruplex vs. duplex selectivity.
Collapse
|
15
|
Muangkaew P, Vilaivan T. Modulation of DNA and RNA by PNA. Bioorg Med Chem Lett 2020; 30:127064. [PMID: 32147357 DOI: 10.1016/j.bmcl.2020.127064] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 02/08/2023]
Abstract
Peptide nucleic acid (PNA), a synthetic DNA mimic that is devoid of the (deoxy)ribose-phosphate backbone yet still perfectly retains the ability to recognize natural nucleic acids in a sequence-specific fashion, can be employed as a tool to modulate gene expressions via several different mechanisms. The unique strength of PNA compared to other oligonucleotide analogs is its ability to bind to nucleic acid targets with secondary structures such as double-stranded and quadruplex DNA as well as RNA. This digest aims to introduce general readers to the advancement in the area of modulation of DNA/RNA functions by PNA, its current status and future research opportunities, with emphasis on recent progress in new targeting modes of structured DNA/RNA by PNA and PNA-mediated gene editing.
Collapse
Affiliation(s)
- Penthip Muangkaew
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
| |
Collapse
|
16
|
Swenson CS, Heemstra JM. Peptide nucleic acids harness dual information codes in a single molecule. Chem Commun (Camb) 2020; 56:1926-1935. [PMID: 32009137 DOI: 10.1039/c9cc09905k] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nature encodes the information required for life in two fundamental biopolymers: nucleic acids and proteins. Peptide nucleic acid (PNA), a synthetic analog comprised of nucleobases arrayed along a pseudopeptide backbone, has the ability to combine the power of nucleic acids to encode information with the versatility of amino acids to encode structure and function. Historically, PNA has been perceived as a simple nucleic acid mimic having desirable properties such as high biostability and strong affinity for complementary nucleic acids. In this feature article, we aim to adjust this perception by highlighting the ability of PNA to act as a peptide mimic and showing the largely untapped potential to encode information in the amino acid sequence. First, we provide an introduction to PNA and discuss the use of conjugation to impart tunable properties to the biopolymer. Next, we describe the integration of functional groups directly into the PNA backbone to impart specific physical properties. Lastly, we highlight the use of these integrated amino acid side chains to encode peptide-like sequences in the PNA backbone, imparting novel activity and function and demonstrating the ability of PNA to simultaneously mimic both a peptide and a nucleic acid.
Collapse
Affiliation(s)
- Colin S Swenson
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA.
| | | |
Collapse
|
17
|
Antibacterial Peptide Nucleic Acids-Facts and Perspectives. Molecules 2020; 25:molecules25030559. [PMID: 32012929 PMCID: PMC7038079 DOI: 10.3390/molecules25030559] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance is an escalating, worldwide problem. Due to excessive use of antibiotics, multidrug-resistant bacteria have become a serious threat and a major global healthcare problem of the 21st century. This fact creates an urgent need for new and effective antimicrobials. The common strategies for antibiotic discovery are based on either modifying existing antibiotics or screening compound libraries, but these strategies have not been successful in recent decades. An alternative approach could be to use gene-specific oligonucleotides, such as peptide nucleic acid (PNA) oligomers, that can specifically target any single pathogen. This approach broadens the range of potential targets to any gene with a known sequence in any bacterium, and could significantly reduce the time required to discover new antimicrobials or their redesign, if resistance arises. We review the potential of PNA as an antibacterial molecule. First, we describe the physicochemical properties of PNA and modifications of the PNA backbone and nucleobases. Second, we review the carriers used to transport PNA to bacterial cells. Furthermore, we discuss the PNA targets in antibacterial studies focusing on antisense PNA targeting bacterial mRNA and rRNA.
Collapse
|
18
|
Galli V, Sadhu KK, Masi D, Saarbach J, Roux A, Winssinger N. Caprin‐1 Promotes Cellular Uptake of Nucleic Acids with Backbone and Sequence Discrimination. Helv Chim Acta 2019. [DOI: 10.1002/hlca.201900255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Valentina Galli
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Kalyan K. Sadhu
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Daniela Masi
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Jacques Saarbach
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Aurélien Roux
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| | - Nicolas Winssinger
- School of Chemistry and BiochemistryFaculty of Science and National Centre of Competence in Research (NCCR) Chemical BiologyUniversity of Geneva CH-1211 Geneva Switzerland
| |
Collapse
|
19
|
Avitabile C, Diaferia C, Roviello V, Altamura D, Giannini C, Vitagliano L, Accardo A, Romanelli A. Fluorescence and Morphology of Self-Assembled Nucleobases and Their Diphenylalanine Hybrid Aggregates. Chemistry 2019; 25:14850-14857. [PMID: 31566814 DOI: 10.1002/chem.201902709] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/18/2019] [Indexed: 12/12/2022]
Abstract
Studies carried out in recent decades have revealed that the ability to self-assemble is a widespread property among biomolecules. Small nucleic acid moieties or very short peptides are able to generate intricate assemblies endowed with remarkable structural and spectroscopic properties. Herein, the structural/spectroscopic characterization of aggregates formed by nucleobases and peptide nucleic acid (PNA)-peptide conjugates are reported. At high concentration, all studied nucleobases form aggregates characterized by previously unreported fluorescence properties. The conjugation of these bases, as PNA derivatives, to the dipeptide Phe-Phe leads to the formation of novel hybrid assemblies, which are characterized by an amyloid-like association of the monomers. Although these compounds share the same basic cross-β motif, the nature and number of PNA units have an important impact on both the level of structural order and the intrinsic fluorescence of the self-assembled nanostructure.
Collapse
Affiliation(s)
- Concetta Avitabile
- Institute of Biostructures and Bioimaging (CNR), via Mezzocannone 16, 80134, Naples, Italy
| | - Carlo Diaferia
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134, Naples, Italy
| | - Valentina Roviello
- Advanced Metrologic Service Center (CeSMA), University of Naples "Federico II", Corso N. Protopisani, 80146, Naples, Italy
| | - Davide Altamura
- Institute of Crystallography (CNR), via Amendola 122, 70126, Bari, Italy
| | - Cinzia Giannini
- Institute of Crystallography (CNR), via Amendola 122, 70126, Bari, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (CNR), via Mezzocannone 16, 80134, Naples, Italy
| | - Antonella Accardo
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134, Naples, Italy
| | - Alessandra Romanelli
- Department of Pharmaceutical Sciences, University of Milan, via Venezian 21, 20133, Milan, Italy
| |
Collapse
|
20
|
Saarbach J, Sabale PM, Winssinger N. Peptide nucleic acid (PNA) and its applications in chemical biology, diagnostics, and therapeutics. Curr Opin Chem Biol 2019; 52:112-124. [PMID: 31541865 DOI: 10.1016/j.cbpa.2019.06.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/07/2019] [Accepted: 06/06/2019] [Indexed: 12/11/2022]
Abstract
Peptide nucleic acid (PNA) stands as one of the most successful artificial oligonucleotide mimetics. Salient features include the stability of hybridization complexes (either as duplexes or triplexes), metabolic stability, and ease of chemical modifications. These features have enabled important applications such as antisense agents, gene editing, nucleic acid sensing and as a platform to program the assembly of PNA-tagged molecules. Here, we review recent advances in these areas.
Collapse
Affiliation(s)
- Jacques Saarbach
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Pramod M Sabale
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland.
| |
Collapse
|
21
|
Hsieh WC, Shaikh AY, Perera JDR, Thadke SA, Ly DH. Synthesis of ( R)- and ( S)-Fmoc-Protected Diethylene Glycol Gamma PNA Monomers with High Optical Purity. J Org Chem 2019; 84:1276-1287. [PMID: 30608165 PMCID: PMC11104511 DOI: 10.1021/acs.joc.8b02714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A robust synthetic route has been developed for preparing optically pure, Fmoc-protected diethylene glycol-containing ( R)- and ( S)-γPNA monomers. The strategy involves the application of 9-(4-bromophenyl)-9-fluorenyl as a temporary, safety-catch protecting group for the suppression of epimerization in the O-alkylation and reductive amination steps. The optical purities of the final monomers were determined to be greater than 99.5% ee, as assessed by 19F-NMR and HPLC. The new synthetic methodology is well-suited for large-scale monomer production, with most synthetic steps providing excellent chemical yields without the need for chromatographic purification other than a simple workup and precipitation.
Collapse
Affiliation(s)
- Wei-Che Hsieh
- Institute for Biomolecular Design and Discovery (IBD) and Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Ashif Y. Shaikh
- Institute for Biomolecular Design and Discovery (IBD) and Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - J. Dinithi R. Perera
- Institute for Biomolecular Design and Discovery (IBD) and Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Shivaji A. Thadke
- Institute for Biomolecular Design and Discovery (IBD) and Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Danith H. Ly
- Institute for Biomolecular Design and Discovery (IBD) and Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| |
Collapse
|
22
|
Zhang Y, Rana A, Stratton Y, Czyzyk-Krzeska MF, Esfandiari L. Sequence-Specific Detection of MicroRNAs Related to Clear Cell Renal Cell Carcinoma at fM Concentration by an Electroosmotically Driven Nanopore-Based Device. Anal Chem 2017; 89:9201-9208. [PMID: 28832110 DOI: 10.1021/acs.analchem.7b01944] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRs) are small noncoding RNAs that play a critical role in gene regulation. Recently, traces of cancer-related miRs have been identified in body fluids, which make them remarkable noninvasive biomarkers. In this study, a new nanopore-based detection scheme utilizing a borosilicate micropipette and an assay of complementary γ-peptide nucleic acid (γ-PNA) probes conjugated to polystyrene beads have been reported for the detection of miR-204 and miR-210 related to the clear cell Renal Cell Carcinoma (ccRCC). Electroosmotic flow (EOF) is induced as the driving force to transport PNA-beads harboring target miRs to the tip of the pore (sensing zone), which results in pore blockades with unique and easily distinguishable serrated shape electrical signals. The concentration detection limit is investigated to be 1 and 10 fM for miR-204 and miR-210, respectively. The EOF transport mechanism enables highly sensitive detection of molecules with low surface charge density with 97.6% detection accuracy compared to the conventional electrophoretically driven methods. Furthermore, resistive-pulse experiments are conducted to study the correlation of the particles' surface charge density with their translocation time and verify the detection principle.
Collapse
Affiliation(s)
- Yuqian Zhang
- Department of Electrical Engineering and Computing Systems, University of Cincinnati , Cincinnati, Ohio 45221, United States
| | - Ankit Rana
- Department of Electrical Engineering and Computing Systems, University of Cincinnati , Cincinnati, Ohio 45221, United States
| | - Yiwen Stratton
- Department of Cancer Biology, University of Cincinnati , Cincinnati, Ohio 45267, United States
| | - Maria F Czyzyk-Krzeska
- Department of Cancer Biology, University of Cincinnati , Cincinnati, Ohio 45267, United States.,Department of Veterans Affairs, VA Research Service , Cincinnati, Ohio 45220, United States
| | - Leyla Esfandiari
- Department of Electrical Engineering and Computing Systems, University of Cincinnati , Cincinnati, Ohio 45221, United States.,Department of Biomedical Chemical and Environmental Engineering, University of Cincinnati , Cincinnati, Ohio 45221, United States
| |
Collapse
|
23
|
Roviello GN, Musumeci D. Synthetic approaches to nucleopeptides containing all four nucleobases, and nucleic acid-binding studies on a mixed-sequence nucleo-oligolysine. RSC Adv 2016; 6:63578-63585. [PMID: 28496969 PMCID: PMC5361140 DOI: 10.1039/c6ra08765e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/27/2016] [Indexed: 11/21/2022] Open
Abstract
In this article we describe two solid-phase synthetic routes to obtain a nucleo-oligolysine α-peptide containing all four natural nucleobases.
In this article we describe two solid-phase synthetic routes to obtain a nucleo-oligolysine α-peptide containing all four natural nucleobases. The first one is based on the oligomerization of the nucleobase-containing monomers, easily synthesized as herein described. The second strategy has the advantage of avoiding the solution synthesis of the monomeric building blocks, leading to the final nucleopeptide by direct solid-phase couplings of the suitably protected nucleobases with the free amino groups on the growing peptide chain still anchored to the resin. Both strategies are general and can be applied to the synthesis of nucleopeptides having backbones formed by any other diamino acid moiety decorated with the four nucleobases. We also report the CD and UV studies on the hybridization properties of the obtained nucleopeptide, containing all four nucleobases on alternate lysines in the sequence, towards complementary DNA and RNA strands. The nucleo-oligolysine with a mixed-base sequence did not prove to bind complementary DNA, but was able to recognize the complementary RNA forming a complex with a higher melting temperature than that of the corresponding RNA/RNA natural duplex and comparable with that of the analogous PNA/RNA system.
Collapse
Affiliation(s)
- Giovanni N Roviello
- CNR , Istituto di Biostrutture e Bioimmagini , Via Mezzocannone 16 , 80134 Napoli , Italy . ; ; Tel: +39-81-2534585
| | - Domenica Musumeci
- CNR , Istituto di Biostrutture e Bioimmagini , Via Mezzocannone 16 , 80134 Napoli , Italy . ; ; Tel: +39-81-2534585.,Università di Napoli "Federico II" , Dipartimento di Scienze Chimiche , 80126 Napoli , Italy . ; Tel: +39-81-674143
| |
Collapse
|
24
|
Ringhieri P, Avitabile C, Saviano M, Morelli G, Romanelli A, Accardo A. The influence of liposomal formulation on the incorporation and retention of PNA oligomers. Colloids Surf B Biointerfaces 2016; 145:462-469. [PMID: 27236097 DOI: 10.1016/j.colsurfb.2016.05.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/04/2016] [Accepted: 05/11/2016] [Indexed: 11/28/2022]
Abstract
Liposomal formulations composed of phospholipids with different unsaturation degrees, head groups and at different cholesterol content have been tested for the encapsulation of Peptide Nucleic Acid (PNA) oligomers. The best loading capability (177μg, ER%=87.2) was obtained for pure liposomes of phosphatidylglycerol (DOPG) with negatively charged head group. The insertion of a 10-20% of cholesterol in DOPG based liposomes provides a slight decrease (∼160μg) of the PNA loading. On the other hand, the cholesterol addition (20-30%) slows down the PNA's release (∼27%) in fetal bovine serum from the liposomal formulation. Based on the encapsulation and the release properties, PEGylated DOPG liposomes with a percentage of cholesterol of 10-20% are the optimal formulation for the loading of PNA-a210.
Collapse
Affiliation(s)
- Paola Ringhieri
- Department of Pharmacy, University of Naples "Federico II", via Mezzocannone 16, 80134 Napoli, Italy; Interuniversity Research Centre on Bioactive Peptides (CIRPeB), via Mezzocannone 16, 80134 Napoli, Italy
| | - Concetta Avitabile
- Institute of Biostructure and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Michele Saviano
- Institute of Crystallography (IC), CNR, Via Amendola 122, 70126 Bari, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, University of Naples "Federico II", via Mezzocannone 16, 80134 Napoli, Italy; Interuniversity Research Centre on Bioactive Peptides (CIRPeB), via Mezzocannone 16, 80134 Napoli, Italy
| | - Alessandra Romanelli
- Department of Pharmacy, University of Naples "Federico II", via Mezzocannone 16, 80134 Napoli, Italy; Interuniversity Research Centre on Bioactive Peptides (CIRPeB), via Mezzocannone 16, 80134 Napoli, Italy.
| | - Antonella Accardo
- Department of Pharmacy, University of Naples "Federico II", via Mezzocannone 16, 80134 Napoli, Italy; Interuniversity Research Centre on Bioactive Peptides (CIRPeB), via Mezzocannone 16, 80134 Napoli, Italy.
| |
Collapse
|
25
|
Roviello GN, Vicidomini C, Di Gaetano S, Capasso D, Musumeci D, Roviello V. Solid phase synthesis and RNA-binding activity of an arginine-containing nucleopeptide. RSC Adv 2016; 6:14140-14148. [PMID: 29057071 PMCID: PMC5635565 DOI: 10.1039/c5ra25809j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 01/15/2016] [Indexed: 01/22/2023] Open
Abstract
Here we report the solid phase synthesis and characterization (LC-ESIMS, CD) of a cationic nucleobase-containing α-peptide, composed of both l-arginine residues and l-lysine-based nucleoamino acids sequentially present in the structure. The binding properties of this novel basic nucleopeptide towards nucleic acids were investigated by CD spectroscopy which revealed the ability of the thymine-containing oligomer to bind both adenine-containing DNA (dA12) and RNA (poly rA) molecules inducing high conformational variations in the nucleic acid structures. Moreover, the artificial oligonucleotide inhibited the enzymatic activity of HIV reverse transcriptase, opening the door to the exploitation of novel antiviral strategies inspired to this molecular tool.
Collapse
Affiliation(s)
- G N Roviello
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
| | - C Vicidomini
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
| | - S Di Gaetano
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
| | - D Capasso
- Università di Napoli "Federico II" , Dipartimento di Farmacia , 80134 Napoli , Italy
| | - D Musumeci
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
- Università di Napoli "Federico II" , Dipartimento di Scienze Chimiche , 80126 Napoli , Italy
| | - V Roviello
- Università di Napoli "Federico II" , Dipartimento di Ingegneria Chimica , dei Materiali e della Produzione Industriale (DICMaPI) , 80125 Napoli , Italy
| |
Collapse
|
26
|
Zhao XL, Chen BC, Han JC, Wei L, Pan XB. Delivery of cell-penetrating peptide-peptide nucleic acid conjugates by assembly on an oligonucleotide scaffold. Sci Rep 2015; 5:17640. [PMID: 26612536 PMCID: PMC4661726 DOI: 10.1038/srep17640] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 11/03/2015] [Indexed: 01/01/2023] Open
Abstract
Delivery to intracellular target sites is still one of the main obstacles in the development of peptide nucleic acids (PNAs) as antisense-antigene therapeutics. Here, we designed a self-assembled oligonucleotide scaffold that included a central complementary region for self-assembly and lateral regions complementing the PNAs. Assembly of cell-penetrating peptide (CPP)-PNAs on the scaffold significantly promoted endocytosis of PNAs by at least 10-fold in cell cultures, particularly for scaffolds in which the central complementary region was assembled by poly(guanine) and poly(cytosine). The antisense activity of CPP-PNAs increased by assembly on the scaffold and was further enhanced after co-assembly with endosomolytic peptide (EP)-PNA. This synergistic effect was also observed following the assembly of antigene CPP-PNAs\EP-PNAs on the scaffold. However, antigene activity was only observed by targeting episomal viral DNA or transfected plasmids, but not the chromosome in the cell cultures. In conclusion, assembly on oligonucleotide scaffolds significantly enhanced the antisense-antigene activity of PNAs by promoting endocytosis and endosomal escape. This oligonucleotide scaffold provided a simple strategy for assembly of multiple functional peptide-PNA conjugates, expanding the applications of PNAs and demonstrating the potential of PNAs as antiviral therapeutics.
Collapse
Affiliation(s)
- Xing-Liang Zhao
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases; Beijing 100044, P.R. China
| | - Bi-Cheng Chen
- Zhejiang Provincial Top Key Discipline in Surgery, Wenzhou Key Laboratory of Surgery; Department of Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325200, P.R. China
| | - Jin-Chao Han
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases; Beijing 100044, P.R. China
| | - Lai Wei
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases; Beijing 100044, P.R. China
| | - Xiao-Ben Pan
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases; Beijing 100044, P.R. China
| |
Collapse
|
27
|
Kirillova Y, Boyarskaya N, Dezhenkov A, Tankevich M, Prokhorov I, Varizhuk A, Eremin S, Esipov D, Smirnov I, Pozmogova G. Polyanionic Carboxyethyl Peptide Nucleic Acids (ce-PNAs): Synthesis and DNA Binding. PLoS One 2015; 10:e0140468. [PMID: 26469337 PMCID: PMC4607454 DOI: 10.1371/journal.pone.0140468] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/25/2015] [Indexed: 11/29/2022] Open
Abstract
New polyanionic modifications of polyamide nucleic acid mimics were obtained. Thymine decamers were synthesized from respective chiral α- and γ-monomers, and their enantiomeric purity was assessed. Here, we present the decamer synthesis, purification and characterization by MALDI-TOF mass spectrometry and an investigation of the hybridization properties of the decamers. We show that the modified γ-S-carboxyethyl-T10 PNA forms a stable triplex with polyadenine DNA.
Collapse
Affiliation(s)
- Yuliya Kirillova
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
- * E-mail:
| | - Nataliya Boyarskaya
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Andrey Dezhenkov
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Mariya Tankevich
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
| | - Ivan Prokhorov
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Anna Varizhuk
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
- Department of Structure-Functional Analysis of Biopolymers, Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - Sergei Eremin
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Dmitry Esipov
- Department of Bioorganic Chemistry, Biology Faculty, Moscow State University, Moscow, Russia
| | - Igor Smirnov
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
| | - Galina Pozmogova
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
| |
Collapse
|
28
|
Ovadia R, Lebrun A, Barvik I, Vasseur JJ, Baraguey C, Alvarez K. Synthesis and structural characterization of monomeric and dimeric peptide nucleic acids prepared by using microwave-promoted multicomponent reactions. Org Biomol Chem 2015; 13:11052-71. [PMID: 26394794 DOI: 10.1039/c5ob01604e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A solution phase synthesis of peptide nucleic acid monomers and dimers was developed by using microwave-promoted Ugi multicomponent reactions. A mixture of a functionalized amine, a carboxymethyl nucleobase, paraformaldehyde and an isocyanide as building blocks generates PNA monomers which are then partially deprotected and used in a second Ugi 4CC reaction, leading to PNA dimers. Conformational rotamers were identified by using NMR and MD simulations.
Collapse
Affiliation(s)
- Reuben Ovadia
- Laboratoire d'Architecture et Fonction des Macromolécules Biologiques, Université Aix-Marseille UMR CNRS 7257, Equipe "Antiviral Medicinal Chemistry", Parc scientifique de Luminy, 163 av. de Luminy, 13288 Marseille Cedex 9, France.
| | | | | | | | | | | |
Collapse
|
29
|
Viéville JMP, Barluenga S, Winssinger N, Delsuc MA. Duplex formation and secondary structure of γ-PNA observed by NMR and CD. Biophys Chem 2015; 210:9-13. [PMID: 26493008 DOI: 10.1016/j.bpc.2015.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 08/13/2015] [Accepted: 09/07/2015] [Indexed: 10/23/2022]
Abstract
Peptide nucleic acids (PNAs) are non-natural oligonucleotides mimics, wherein the phosphoribose backbone has been replaced by a peptidic moiety (N-(2-aminoethyl)glycine). This peptidic backbone lends itself to substitution and the γ-position has proven to yield oligomers with enhanced hybridization properties. In this study, we use Nuclear Magnetic Resonance (NMR) and Circular Dichroism (CD) to explore the properties of the supramolecular duplexes formed by these species. We show that standard Watson-Crick base pair as well as non-standard ones are formed in solution. The duplexes thus formed present marked melting transition temperatures substantially higher than their nucleic acid homologs. Moreover, the presence of a chiral group on the γ-peptidic backbone increases further this transition temperature, leading to very stable duplexes. PNA duplexes with a chiral backbone present a marked chiral secondary structure, observed by CD, and showing a common folding pattern for all studied structures. Nevertheless small differences are observed depending on the details of the nucleobase sequence.
Collapse
Affiliation(s)
- J M P Viéville
- Strasbourg University, Plateforme d'Analyse Chimique de Strasbourg Illkirch, 74 route du Rhin 67401 Illkirch, France
| | - S Barluenga
- Department of Organic Chemistry, University of Geneva, Geneva CH1211, Switzerland
| | - N Winssinger
- Department of Organic Chemistry, University of Geneva, Geneva CH1211, Switzerland
| | - M A Delsuc
- IGBMC, CNRS UMR 7104, 1 rue Laurent Fries BP10142, 67404 Illkirch France.
| |
Collapse
|
30
|
Banerjee A, Bagmare S, Varada M, Kumar VA. Glycine-Linked Nucleoside-β-Amino Acids: Polyamide Analogues of Nucleic Acids. Bioconjug Chem 2015; 26:1737-42. [PMID: 26076350 DOI: 10.1021/acs.bioconjchem.5b00296] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
3'-5'-Deoxyribose-sugar-phoshate backbone in DNA is completely replaced by 2'-deoxyribonucleoside-based β-amino acids interlinked by glycine to create uncharged polyamide DNA with 3'-5'-directionality. These oligomers as conjugates of α-amino acids and nucleoside-β-amino acids bind strongly and sequence-specifically only to the antiparallel complementary RNA and DNA.
Collapse
Affiliation(s)
- Anjan Banerjee
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India 411008
| | - Seema Bagmare
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India 411008
| | - Manojkumar Varada
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India 411008
| | - Vaijayanti A Kumar
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India 411008
| |
Collapse
|
31
|
Sacui I, Hsieh WC, Manna A, Sahu B, Ly DH. Gamma Peptide Nucleic Acids: As Orthogonal Nucleic Acid Recognition Codes for Organizing Molecular Self-Assembly. J Am Chem Soc 2015; 137:8603-10. [PMID: 26079820 DOI: 10.1021/jacs.5b04566] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nucleic acids are an attractive platform for organizing molecular self-assembly because of their specific nucleobase interactions and defined length scale. Routinely employed in the organization and assembly of materials in vitro, however, they have rarely been exploited in vivo, due to the concerns for enzymatic degradation and cross-hybridization with the host's genetic materials. Herein we report the development of a tight-binding, orthogonal, synthetically versatile, and informationally interfaced nucleic acid platform for programming molecular interactions, with implications for in vivo molecular assembly and computing. The system consists of three molecular entities: the right-handed and left-handed conformers and a nonhelical domain. The first two are orthogonal to each other in recognition, while the third is capable of binding to both, providing a means for interfacing the two conformers as well as the natural nucleic acid biopolymers (i.e., DNA and RNA). The three molecular entities are prepared from the same monomeric chemical scaffold, with the exception of the stereochemistry or lack thereof at the γ-backbone that determines if the corresponding oligo adopts a right-handed or left-handed helix, or a nonhelical motif. These conformers hybridize to each other with exquisite affinity, sequence selectivity, and level of orthogonality. Recognition modules as short as five nucleotides in length are capable of organizing molecular assembly.
Collapse
Affiliation(s)
- Iulia Sacui
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Wei-Che Hsieh
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Arunava Manna
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Bichismita Sahu
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Danith H Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| |
Collapse
|
32
|
Roviello GN, Musumeci D, Roviello V, Pirtskhalava M, Egoyan A, Mirtskhulava M. Natural and artificial binders of polyriboadenylic acid and their effect on RNA structure. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2015; 6:1338-1347. [PMID: 26199837 PMCID: PMC4505092 DOI: 10.3762/bjnano.6.138] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/22/2015] [Indexed: 06/10/2023]
Abstract
The employment of molecular tools with nucleic acid binding ability to specifically control crucial cellular functions represents an important scientific area at the border between biochemistry and pharmaceutical chemistry. In this review we describe several molecular systems of natural or artificial origin, which are able to bind polyriboadenylic acid (poly(rA)) both in its single-stranded or structured forms. Due to the fundamental role played by the poly(rA) tail in the maturation and stability of mRNA, as well as in the initiation of the translation process, compounds able to bind this RNA tract, influencing the mRNA fate, are of special interest for developing innovative biomedical strategies mainly in the field of anticancer therapy.
Collapse
Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Domenica Musumeci
- Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, 80134 Napoli, Italy
- Dipartimento di Scienze Chimiche, Università di Napoli “Federico II”, 80126 Napoli, Italy
| | - Valentina Roviello
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale (DICMaPI), Università di Napoli “Federico II”, 80125 Napoli, Italy
| | | | | | | |
Collapse
|
33
|
Dezhenkov AV, Tankevich MV, Nikolskaya ED, Smirnov IP, Pozmogova GE, Shvets VI, Kirillova YG. Synthesis of anionic peptide nucleic acid oligomers including γ-carboxyethyl thymine monomers. MENDELEEV COMMUNICATIONS 2015. [DOI: 10.1016/j.mencom.2015.01.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
34
|
Moccia M, Adamo MFA, Saviano M. Insights on chiral, backbone modified peptide nucleic acids: Properties and biological activity. ARTIFICIAL DNA, PNA & XNA 2014; 5:e1107176. [PMID: 26752710 PMCID: PMC5329900 DOI: 10.1080/1949095x.2015.1107176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 10/02/2015] [Accepted: 10/07/2015] [Indexed: 12/14/2022]
Abstract
PNAs are emerging as useful synthetic devices targeting natural miRNAs. In particular 3 classes of structurally modified PNAs analogs are herein described, namely α, β and γ, which differ by their backbone modification. Their mode and binding affinity for natural nucleic acids and their use in medicinal chemistry as potential miRNA binders is discussed.
Collapse
Affiliation(s)
- Maria Moccia
- Consiglio Nazionale delle Ricerche-Institute of Cristallography; Bari, Italy
| | - Mauro F A Adamo
- Centre for Synthesis and Chemical Biology (CSCB); Department of Pharmaceutical & Medicinal Chemistry; Royal College of Surgeons in Ireland; Dublin, Ireland
| | - Michele Saviano
- Consiglio Nazionale delle Ricerche-Institute of Cristallography; Bari, Italy
| |
Collapse
|
35
|
Avitabile C, Cimmino A, Romanelli A. Oligonucleotide analogues as modulators of the expression and function of noncoding RNAs (ncRNAs): emerging therapeutics applications. J Med Chem 2014; 57:10220-40. [PMID: 25280271 DOI: 10.1021/jm5006594] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
ncRNAs are emerging as key regulators of physiological and pathological processes and therefore have been identified as pharmacological targets and as markers for some diseases. Oligonucleotide analogues represent so far the most widely employed tool for the modulation of the expression of ncRNAs. In this perspective we briefly describe most of the known classes of ncRNAs and then we discuss the design and the applications of oligonucleotide analogues for their targeting. The effects of modifications of the chemical structure of the oligonucleotides on properties such as the binding affinity toward targets and off targets, and the stability to degradation and their biological effects (when known) are discussed. Examples of molecules currently used in clinical trials are also reported.
Collapse
Affiliation(s)
- Concetta Avitabile
- Università di Napoli "Federico II" , Dipartimento di Farmacia, via Mezzocannone 16, 80134 Napoli, Italy
| | | | | |
Collapse
|
36
|
Amato F, Tomaiuolo R, Borbone N, Elce A, Amato J, D'Errico S, De Rosa G, Mayol L, Piccialli G, Oliviero G, Castaldo G. Design, synthesis and biochemical investigation, by in vitro luciferase reporter system, of peptide nucleic acids as new inhibitors of miR-509-3p involved in the regulation of cystic fibrosis disease-gene expression. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00257h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
37
|
Synthesis and biological properties of caffeic acid-PNA dimers containing guanine. Molecules 2013; 18:9147-62. [PMID: 23912270 PMCID: PMC6270098 DOI: 10.3390/molecules18089147] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 07/18/2013] [Accepted: 07/29/2013] [Indexed: 11/17/2022] Open
Abstract
Caffeic acid (CA; 3,4-dihydroxycinnamic acid) is endowed with high antioxidant activity. CA derivatives (such as amides) have gained a lot of attention due to their antioxidative, antitumor and antimicrobial properties as well as stable characteristics. Caffeoyl-peptide derivatives showed different antioxidant activity depending on the type and the sequence of amino acid used. For these reasons, we decided to combine CA with Peptide Nucleic Acid (PNA) to test whether the new PNA-CA amide derivatives would result in an improvement or gain of CA's biological (i.e., antioxidant, cytotoxic, cytoprotective) properties. We performed the synthesis and characterization of seven dimer conjugates with various combinations of nucleic acid bases and focused NMR studies on the model compound ga-CA dimer. We demonstrate that PNA dimers containing guanine conjugated to CA exhibited different biological activities depending on composition and sequence of the nucleobases. The dimer ag-CA protected HepG2, SK-B-NE(2), and C6 cells from a cytotoxic dose of hydrogen peroxide (H₂O₂).
Collapse
|
38
|
De Costa NTS, Heemstra JM. Evaluating the effect of ionic strength on duplex stability for PNA having negatively or positively charged side chains. PLoS One 2013; 8:e58670. [PMID: 23484047 PMCID: PMC3590165 DOI: 10.1371/journal.pone.0058670] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 02/06/2013] [Indexed: 11/19/2022] Open
Abstract
The enhanced thermodynamic stability of PNA:DNA and PNA:RNA duplexes compared with DNA:DNA and DNA:RNA duplexes has been attributed in part to the lack of electrostatic repulsion between the uncharged PNA backbone and negatively charged DNA or RNA backbone. However, there are no previously reported studies that systematically evaluate the effect of ionic strength on duplex stability for PNA having a charged backbone. Here we investigate the role of charge repulsion in PNA binding by synthesizing PNA strands having negatively or positively charged side chains, then measuring their duplex stability with DNA or RNA at varying salt concentrations. At low salt concentrations, positively charged PNA binds more strongly to DNA and RNA than does negatively charged PNA. However, at medium to high salt concentrations, this trend is reversed, and negatively charged PNA shows higher affinity for DNA and RNA than does positively charged PNA. These results show that charge screening by counterions in solution enables negatively charged side chains to be incorporated into the PNA backbone without reducing duplex stability with DNA and RNA. This research provides new insight into the role of electrostatics in PNA binding, and demonstrates that introduction of negatively charged side chains is not significantly detrimental to PNA binding affinity at physiological ionic strength. The ability to incorporate negative charge without sacrificing binding affinity is anticipated to enable the development of PNA therapeutics that take advantage of both the inherent benefits of PNA and the multitude of charge-based delivery technologies currently being developed for DNA and RNA.
Collapse
Affiliation(s)
- N. Tilani S. De Costa
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, United States of America
| | - Jennifer M. Heemstra
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, United States of America
| |
Collapse
|
39
|
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.
Collapse
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:
| |
Collapse
|