1
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Singh G, Monga V. Peptide Nucleic Acids: Recent Developments in the Synthesis and Backbone Modifications. Bioorg Chem 2023; 141:106860. [PMID: 37748328 DOI: 10.1016/j.bioorg.2023.106860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 09/27/2023]
Abstract
Nucleic acid represents the ideal drug candidate for protein targets that are hard to target or against which drug development is not easy. Peptide nucleic acids (PNAs) are synthesized by attaching modified peptide backbones generally derived from repetitive N-2-aminoethyl glycine units in place of the regular phosphodiester backbone and represent synthetic impersonator of nucleic acids that offers an exciting research field due to their fascinating spectrum of biotechnological, diagnostic and potential therapeutic applications. The semi-rigid peptide nucleic acid backbone serves as a nearly-perfect template for attaching complimentary base pairs on DNA or RNA in a sequence-dependent manner as described by Watson-Crick models. PNAs and their analogues are endowed with exceptionally high affinity and specificity for receptor sites, essentially due to their polyamide backbone's uncharged and flexible nature. The present review compiled various strategies to modify the polypeptide backbone for improving the target selectivity and stability of the PNAs in the body. The investigated biological activities carried out on PNAs have also been summarized in the present review.
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Affiliation(s)
- Gurpreet Singh
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Vikramdeep Monga
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, VPO-Ghudda, Bathinda 151401, Punjab, India.
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2
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Chowdhury M, Hudson RHE. Exploring Nucleobase Modifications in Oligonucleotide Analogues for Use as Environmentally Responsive Fluorophores and Beyond. CHEM REC 2023; 23:e202200218. [PMID: 36344432 DOI: 10.1002/tcr.202200218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/07/2022] [Indexed: 11/09/2022]
Abstract
Over the past two decades, it has become abundantly clear that nucleic acid biochemistry, especially with respect to RNA, is more convoluted and complex than previously appreciated. Indeed, the application and exploitation of nucleic acids beyond their predestined role as the medium for storage and transmission of genetic information to the treatment and study of diseases has been achieved. In other areas of endeavor, utilization of nucleic acids as a probe molecule requires that they possess a reporter group. The reporter group of choice is often a luminophore because fluorescence spectroscopy has emerged as an indispensable tool to probe the structural and functional properties of modified nucleic acids. The scope of this review spans research done in the Hudson lab at The University of Western Ontario and is focused on modified pyrimidine nucleobases and their applications as environmentally sensitive fluorophores, base discriminating fluorophores, and in service of antisense applications as well as tantalizing new results as G-quadruplex destabilizing agents. While this review is a focused personal account, particularly influential work of colleagues in the chemistry community will be highlighted. The intention is not to make a comprehensive review, citations to the existing excellent reviews are given, any omission of the wonderful and impactful work being done by others globally is not intentional. Thus, this review will briefly introduce the context of our work, summarize what has been accomplished and finish with the prospects of future developments.
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Affiliation(s)
- Mria Chowdhury
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, N6A 5B7
| | - Robert H E Hudson
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, N6A 5B7
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3
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Bizzarri BM, Fanelli A, Ciprini S, Giorgi A, De Angelis M, Fioravanti R, Nencioni L, Saladino R. Multicomponent Synthesis of Diaminopurine and Guanine PNA's Analogues Active against Influenza A Virus from Prebiotic Compounds. ACS OMEGA 2022; 7:45253-45264. [PMID: 36530301 PMCID: PMC9753540 DOI: 10.1021/acsomega.2c05754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Peptide nucleic acids (PNAs) play a key role in prebiotic chemistry as a chimera between RNA and proteins. We developed an alternative synthesis of bioactive PNA's diaminopurine and guanine analogues from prebiotic compounds, such as aminomalononitrile (AMN), urea, and guanidine, using a two-step multicomponent microwave-assisted and solvent-free approach in the presence of selected amino acids. The novel derivatives showed selective inhibitory activity against influenza virus A/Puerto Rico/8/34 H1N1 encompassing the range of nanomolar activity. Derivatives decorated with the tyrosine residue showed the highest inhibitory activity against the virus.
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Affiliation(s)
- Bruno Mattia Bizzarri
- Department
of Biological and Ecological Sciences, University
of Tuscia, Viterbo 01100, Italy
| | - Angelica Fanelli
- Department
of Biological and Ecological Sciences, University
of Tuscia, Viterbo 01100, Italy
| | - Stefania Ciprini
- Department
of Biological and Ecological Sciences, University
of Tuscia, Viterbo 01100, Italy
| | - Alessandra Giorgi
- Department
of Biological and Ecological Sciences, University
of Tuscia, Viterbo 01100, Italy
| | - Marta De Angelis
- Department
of Public Health and Infectious Diseases, Laboratory Affiliated to
Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome 00185, Italy
| | - Raoul Fioravanti
- Department
of Public Health and Infectious Diseases, Laboratory Affiliated to
Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome 00185, Italy
| | - Lucia Nencioni
- Department
of Public Health and Infectious Diseases, Laboratory Affiliated to
Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome 00185, Italy
| | - Raffaele Saladino
- Department
of Biological and Ecological Sciences, University
of Tuscia, Viterbo 01100, Italy
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4
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Mitteaux J, Lejault P, Wojciechowski F, Joubert A, Boudon J, Desbois N, Gros CP, Hudson RHE, Boulé JB, Granzhan A, Monchaud D. Identifying G-Quadruplex-DNA-Disrupting Small Molecules. J Am Chem Soc 2021; 143:12567-12577. [PMID: 34346684 DOI: 10.1021/jacs.1c04426] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The quest for small molecules that strongly bind to G-quadruplex-DNA (G4), so-called G4 ligands, has invigorated the G4 research field from its very inception. Massive efforts have been invested to discover or rationally design G4 ligands, evaluate their G4-interacting properties in vitro through a series of now widely accepted and routinely implemented assays, and use them as innovative chemical biology tools to interrogate cellular networks that might involve G4s. In sharp contrast, only uncoordinated efforts aimed at developing small molecules that destabilize G4s have been invested to date, even though it is now recognized that such molecular tools would have tremendous application in neurobiology as many genetic and age-related diseases are caused by an overrepresentation of G4s. Herein, we report on our efforts to develop in vitro assays to reliably identify molecules able to destabilize G4s. This workflow comprises the newly designed G4-unfold assay, adapted from the G4-helicase assay implemented with Pif1, as well as a series of biophysical and biochemical techniques classically used to study G4/ligand interactions (CD, UV-vis, PAGE, and FRET-melting), and a qPCR stop assay, adapted from a Taq-based protocol recently used to identify G4s in the genomic DNA of Schizosaccharomyces pombe. This unique, multipronged approach leads to the characterization of a phenylpyrrolocytosine (PhpC)-based G-clamp analog as a prototype of G4-disrupting small molecule whose properties are validated through many different and complementary in vitro evaluations.
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Affiliation(s)
- Jérémie Mitteaux
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Pauline Lejault
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Filip Wojciechowski
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Alexandra Joubert
- Genome Structure and Instability Laboratory, CNRS UMR 7196, INSERM U1154, National Museum of Natural History, Alliance Sorbonne Université, 75005 Paris, France
| | - Julien Boudon
- Laboratoire Interdisciplinaire Carnot de Bourgogne, ICB CNRS UMR 6303, UBFC, 21078 Dijon, France
| | - Nicolas Desbois
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Claude P Gros
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
| | - Robert H E Hudson
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Jean-Baptiste Boulé
- Genome Structure and Instability Laboratory, CNRS UMR 7196, INSERM U1154, National Museum of Natural History, Alliance Sorbonne Université, 75005 Paris, France
| | - Anton Granzhan
- Institut Curie, CNRS UMR 9187, INSERM U1196, PSL Research University, 91405 Orsay, France.,Université Paris Saclay, CNRS UMR 9187, INSERM U1196, 91405 Orsay, France
| | - David Monchaud
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, UBFC, 21078 Dijon, France
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5
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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: 31] [Impact Index Per Article: 10.3] [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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6
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Gerrits L, Hammink R, Kouwer PHJ. Semiflexible polymer scaffolds: an overview of conjugation strategies. Polym Chem 2021. [DOI: 10.1039/d0py01662d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Semiflexible polymers are excellent scaffolds for the presentation of a wide variety of (bio)molecules. This manuscript reviews advantages and challenges of the most common conjugation strategies for the major classes of semiflexible polymers.
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Affiliation(s)
- Lotte Gerrits
- Institute for Molecules and Materials
- Radboud University
- 6525 AJ Nijmegen
- The Netherlands
| | - Roel Hammink
- Department of Tumor Immunology
- Radboud Institute for Molecular Life Sciences
- Radboud University Medical Center
- 6525 GA Nijmegen
- The Netherlands
| | - Paul H. J. Kouwer
- Institute for Molecules and Materials
- Radboud University
- 6525 AJ Nijmegen
- The Netherlands
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7
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Kotandeniya D, Rogers MS, Fernandez J, Kanugula S, Hudson RHE, Rodriguez F, Lipscomb JD, Tretyakova N. 6-phenylpyrrolocytosine as a fluorescent probe to examine nucleotide flipping catalyzed by a DNA repair protein. Biopolymers 2020; 112:e23405. [PMID: 33098572 DOI: 10.1002/bip.23405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/30/2020] [Accepted: 09/30/2020] [Indexed: 11/05/2022]
Abstract
Cellular exposure to tobacco-specific nitrosamines causes formation of promutagenic O6 -[4-oxo-4-(3-pyridyl)but-1-yl]guanine (O6 -POB-G) and O6 -methylguanine (O6 -Me-G) adducts in DNA. These adducts can be directly repaired by O6 -alkylguanine-DNA alkyltransferase (AGT). Repair begins by flipping the damaged base out of the DNA helix. AGT binding and base-flipping have been previously studied using pyrrolocytosine as a fluorescent probe paired to the O6 -alkylguanine lesion, but low fluorescence yield limited the resolution of steps in the repair process. Here, we utilize the highly fluorescent 6-phenylpyrrolo-2'-deoxycytidine (6-phenylpyrrolo-C) to investigate AGT-DNA interactions. Synthetic oligodeoxynucleotide duplexes containing O6 -POB-G and O6 -Me-G adducts were placed within the CpG sites of codons 158, 245, and 248 of the p53 tumor suppressor gene and base-paired to 6-phenylpyrrolo-C in the opposite strand. Neighboring cytosine was either unmethylated or methylated. Stopped-flow fluorescence measurements were performed by mixing the DNA duplexes with C145A or R128G AGT variants. We observe a rapid, two-step, nearly irreversible binding of AGT to DNA followed by two slower steps, one of which is base-flipping. Placing 5-methylcytosine immediately 5' to the alkylated guanosine causes a reduction in rate constant of nucleotide flipping. O6 -POB-G at codon 158 decreased the base flipping rate constant by 3.5-fold compared with O6 -Me-G at the same position. A similar effect was not observed at other codons.
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Affiliation(s)
- Delshanee Kotandeniya
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Melanie S Rogers
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jenna Fernandez
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sreenivas Kanugula
- Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Robert H E Hudson
- Department of Chemistry, University of Western Ontario, London, Ontario, Canada
| | - Freddys Rodriguez
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Natalia Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
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8
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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.
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9
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Saadati A, Hassanpour S, Guardia MDL, Mosafer J, Hashemzaei M, Mokhtarzadeh A, Baradaran B. Recent advances on application of peptide nucleic acids as a bioreceptor in biosensors development. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.02.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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10
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Abstract
Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.
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Affiliation(s)
- Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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11
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Manicardi A, Rozzi A, Korom S, Corradini R. Building on the peptide nucleic acid (PNA) scaffold: a biomolecular engineering approach. Supramol Chem 2017. [DOI: 10.1080/10610278.2017.1371720] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Alex Manicardi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parma, Italy
- Organic and Biomimetic Chemistry Research Group (OBCR), Department of Organic and Macromolecular Chemistry, Faculty of Sciences – Ghent University Campus Sterre, Belgium
| | - Andrea Rozzi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parma, Italy
| | - Saša Korom
- National Institute for Biostructures and Biosystems (INBB), Roma, Italy
| | - Roberto Corradini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parma, Italy
- National Institute for Biostructures and Biosystems (INBB), Roma, Italy
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12
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Gupta A, Mishra A, Puri N. Peptide nucleic acids: Advanced tools for biomedical applications. J Biotechnol 2017; 259:148-159. [PMID: 28764969 PMCID: PMC7114329 DOI: 10.1016/j.jbiotec.2017.07.026] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 05/23/2017] [Accepted: 07/23/2017] [Indexed: 02/01/2023]
Abstract
Peptide Nucleic Acids − DNA/RNA analogues. Different Modifications on PNA backbone and their effects. Neutral backbone − remarkable hybridization properties. PNA based biosensors and their diverse biomedical applications. Potential antigene and antisense agents.
Peptide Nucleic Acids (PNAs) are the DNA/RNA analogues in which sugar-phosphate backbone is replaced by N-2-aminoethylglycine repeating units. PNA contains neutral backbone hence due to the absence of electrostatic repulsion, its hybridization shows remarkable stability towards complementary oligonucleotides. PNAs are highly resistant to cleavage by chemicals and enzymes due to the substrate specific nature of enzymes and therefore not degraded inside the cells. PNAs are emerging as new tools in the market due to their applications in antisense and antigene therapies by inhibiting translation and transcription respectively. Hence, several methods based on PNAs have been developed for designing various anticancer and antigene drugs, detection of mutations or modulation of PCR reactions. The duplex homopurine sequence of DNA may also be recognized by PNA, forming firm PNA/DNA/PNA triplex through strand invasion with a looped-out DNA strand. PNAs have also been found to replace DNA probes in varied investigative purposes. There are several disadvantages regarding cellular uptake of PNA, so modifications in PNA backbone or covalent coupling with cell penetrating peptides is necessary to improve its delivery inside the cells. In this review, hybridization properties along with potential applications of PNA in the field of diagnostics and pharmaceuticals are elaborated.
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Affiliation(s)
- Anjali Gupta
- Department of Chemistry, School of Basic and Applied Sciences, Galgotias University, Greater Noida, U.P., India.
| | - Anuradha Mishra
- School of Vocational Studies & Applied Sciences, Gautam Buddha University, Greater Noida, U.P., India
| | - Nidhi Puri
- Department of Applied Science & Humanities, I.T.S Engineering College, Greater Noida, U.P., India
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13
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Manicardi A, Bertucci A, Rozzi A, Corradini R. A Bifunctional Monomer for On-Resin Synthesis of Polyfunctional PNAs and Tailored Induced-Fit Switching Probes. Org Lett 2016; 18:5452-5455. [PMID: 27768299 DOI: 10.1021/acs.orglett.6b02363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A synthetic strategy for the production of polyfunctional PNAs bearing substituent groups both on the nucleobase and on the backbone C5 carbon of the same monomer is described; this is based on the use of a tris-orthogonally protected monomer and subsequent solid-phase selective functionalization. This strategy can be used for synthesizing PNAs that are not readily accessible by use of preformed modified monomers. As an example, a PNA-based probe that undergoes a switch in its fluorescence emission upon hybridization with a target oligonucleotide, induced by tailor-made movement of two pyrene substituent groups, was synthesized.
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Affiliation(s)
- Alex Manicardi
- Department of Chemistry, University of Parma , Parco Area delle Scienze 17/A, Parma 43123, Italy
| | - Alessandro Bertucci
- Department of Chemistry, University of Parma , Parco Area delle Scienze 17/A, Parma 43123, Italy
| | - Andrea Rozzi
- Department of Chemistry, University of Parma , Parco Area delle Scienze 17/A, Parma 43123, Italy
| | - Roberto Corradini
- Department of Chemistry, University of Parma , Parco Area delle Scienze 17/A, Parma 43123, Italy.,I.N.B.B. Consortium , Viale delle Medaglie D'Oro, 305, 00136 Roma, Italy
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14
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Suchý M, Ettles C, Wisner JA, Matarazzo A, Hudson RHE. Unusual C7- versus Normal 5′-O-Dimethoxytritylation of 6-Arylpyrrolocytidine Analogs. J Org Chem 2016; 81:8415-25. [DOI: 10.1021/acs.joc.6b01584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Mojmír Suchý
- Department
of Chemistry and ‡The Centre for Advanced Materials and Biomaterials
Research, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Christie Ettles
- Department
of Chemistry and ‡The Centre for Advanced Materials and Biomaterials
Research, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - James A. Wisner
- Department
of Chemistry and ‡The Centre for Advanced Materials and Biomaterials
Research, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Augusto Matarazzo
- Department
of Chemistry and ‡The Centre for Advanced Materials and Biomaterials
Research, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Robert H. E. Hudson
- Department
of Chemistry and ‡The Centre for Advanced Materials and Biomaterials
Research, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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15
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Elmehriki AAH, Suchý M, Chicas KJ, Wojciechowski F, Hudson RHE. Synthesis and spectral characterization of environmentally responsive fluorescent deoxycytidine analogs. ARTIFICIAL DNA, PNA & XNA 2015; 5:e29174. [PMID: 25483932 DOI: 10.4161/adna.29174] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Herein, we describe the synthesis and spectroscopic properties of five novel pyrrolodeoxycytidine analogs, and the related 5-(1-pyrenylethynyl)-2'-deoxycytidine analog; as well as fluorescence characterization of 5-(p-methoxyphenylethynyl)-2'-deoxyuridine. Within this series of compounds, rigidification of the structure from 6-phenylpyrrolodeoxycytidine to 5,6-benzopyrroldeoxycytidine made remarkable improvement of the fluorescence quantum yield (Φ ~1, EtOH) and substantially increased the Stokes shift. Exchange of the phenyl group of 6-phenylpyrrolodeoxycytidine for other heterocycles (benzofuryl or indolyl) produced an increase in the extinction coefficient at the excitation wavelength while preserving high quantum yields. The steady-state fluorescence response to the environment was determined by sensitivity of Stokes shift to solvent polarity. The effect of solvent polarity on fluorescence emission intensity was concurrently examined and showed that 5,6-benzopyrrolodeoxycytidine is highly sensitive to the presence of water. On the other hand, the previously synthesized 5-(p-methoxyphenylethynyl)-2'-deoxyuridine was found to be sensitive to solvent viscosity indicating molecular rotor behavior.
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Affiliation(s)
- Adam A H Elmehriki
- a Department of Chemistry; The University of Western Ontario; London, ON Canada
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16
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Suchý M, Hudson RHE. Pyrimidine-fused heterocyclic frameworks based on an N4-arylcytosine scaffold: synthesis, characterization, and PNA oligomerization of the fluorescent cytosine analogue 5,6-benzopC. J Org Chem 2014; 79:3336-47. [PMID: 24666330 DOI: 10.1021/jo402873e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A synthesis of an intrinsically fluorescent cytosine analogue 5,6-benzopC has been developed utilizing the reductive Ni-mediated cyclization of an N4-aryl,N4-(Boc)cytosine intermediate as a key step. 5,6-BenzopC was found to possess interesting fluorescence properties (Φ = 0.79, EtOH; Stoke's shift 113 nm). Peptide nucleic acid (PNA) oligomerization of the 5,6-benzopC monomer was carried out, followed by hybridization studies with complementary deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) which showed the modification to be well tolerated in the sequence contexts examined. Initial attempts to synthesize the heterocyclic skeleton present in 5,6-benzopC resulted in the discovery of routes to the pyrimido[1,6-a]benzimidazole, pyrimido[1,6-a]quinazoline, and pyrimido[1,6-a]benzo[b]6-bora-1,3-diazine heterocyclic frameworks.
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Affiliation(s)
- Mojmír Suchý
- Department of Chemistry, The University of Western Ontario , London, ON N6A 5B7, Canada
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17
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Ming X, Matter B, Song M, Veliath E, Shanley R, Jones R, Tretyakova N. Mapping structurally defined guanine oxidation products along DNA duplexes: influence of local sequence context and endogenous cytosine methylation. J Am Chem Soc 2014; 136:4223-35. [PMID: 24571128 PMCID: PMC3985951 DOI: 10.1021/ja411636j] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Indexed: 02/07/2023]
Abstract
DNA oxidation by reactive oxygen species is nonrandom, potentially leading to accumulation of nucleobase damage and mutations at specific sites within the genome. We now present the first quantitative data for sequence-dependent formation of structurally defined oxidative nucleobase adducts along p53 gene-derived DNA duplexes using a novel isotope labeling-based approach. Our results reveal that local nucleobase sequence context differentially alters the yields of 2,2,4-triamino-2H-oxal-5-one (Z) and 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG) in double stranded DNA. While both lesions are overproduced within endogenously methylated (Me)CG dinucleotides and at 5' Gs in runs of several guanines, the formation of Z (but not OG) is strongly preferred at solvent-exposed guanine nucleobases at duplex ends. Targeted oxidation of (Me)CG sequences may be caused by a lowered ionization potential of guanine bases paired with (Me)C and the preferential intercalation of riboflavin photosensitizer adjacent to (Me)C:G base pairs. Importantly, some of the most frequently oxidized positions coincide with the known p53 lung cancer mutational "hotspots" at codons 245 (GGC), 248 (CGG), and 158 (CGC) respectively, supporting a possible role of oxidative degradation of DNA in the initiation of lung cancer.
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Affiliation(s)
- Xun Ming
- Department of Medicinal Chemistry and the Masonic Cancer Center and Biostatistics and
Bioinformatics Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brock Matter
- Department of Medicinal Chemistry and the Masonic Cancer Center and Biostatistics and
Bioinformatics Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Matthew Song
- Department of Medicinal Chemistry and the Masonic Cancer Center and Biostatistics and
Bioinformatics Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Elizabeth Veliath
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Ryan Shanley
- Department of Medicinal Chemistry and the Masonic Cancer Center and Biostatistics and
Bioinformatics Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Roger Jones
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Natalia Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center and Biostatistics and
Bioinformatics Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Dodonova J, Tumkevicius S. Access to 6-arylpyrrolo[2,3-d]pyrimidines via a palladium-catalyzed direct C–H arylation reaction. RSC Adv 2014. [DOI: 10.1039/c4ra07088g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A route to 6-arylpyrrolo[2,3-d]pyrimidines via a direct palladium-catalyzed C–H arylation reaction.
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Affiliation(s)
- Jelena Dodonova
- Vilnius University
- Department of Organic Chemistry
- LT-03225 Vilnius, Lithuania
| | - Sigitas Tumkevicius
- Vilnius University
- Department of Organic Chemistry
- LT-03225 Vilnius, Lithuania
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19
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Ming X, Seela F. A Nucleobase-Discriminating Pyrrolo-dC Click Adduct Designed for DNA Fluorescence Mismatch Sensing. Chemistry 2012; 18:9590-600. [DOI: 10.1002/chem.201103385] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 04/17/2012] [Indexed: 11/10/2022]
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20
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Manderville RA, Omumi A, Rankin née Schlitt KM, Wilson KA, Millen AL, Wetmore SD. Fluorescent C-linked C8-aryl-guanine probe for distinguishing syn from anti structures in duplex DNA. Chem Res Toxicol 2012; 25:1271-82. [PMID: 22667322 DOI: 10.1021/tx300152q] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The synthesis and optical properties of the carbon (C)-linked C(8)-(2"-benzo[b]thienyl)-2'-deoxyguanosine ((Bth)dG), which acts as a fluorescent reporter of syn versus anti glycosidic conformations in duplex DNA, are described. In the syn-conformation, the probe stabilizes a G:G mismatch, emits at ∼385 nm (excitation ∼285 nm), and shows an induced circular dichroism (ICD) signal at ∼320 nm. Molecular dynamics (MD) simulations predict a wedge (W)-conformation for the mismatched duplex with the C(8)-benzo[b]thienyl moiety residing in the minor groove. In contrast, the probe destabilizes the duplex when base paired with its normal pyrimidine partner C. With flanking purine bases, a major groove B-type duplex is favored with (Bth)dG present in the anti-conformation emitting at ∼413 nm (excitation ∼326 nm) and no ICD signal. However, with flanking pyrimidine bases, (Bth)dG adopts the syn-conformation when base paired with C, and MD simulations predict a base-displaced stacked (S)-conformation, with the opposing C flipped out of the helix. The different duplex (B-, S-, and W-) conformers formed upon incorporation of (Bth)dG are known to play a critical role in the biological activity of N-linked C8-dG adducts formed by arylamine carcinogens. Bulky environment-sensitive fluorescent C(8)-dG adducts that mimic the duplex structures formed by carcinogens may be useful in luminescence-based DNA polymerase assays.
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Fabbri E, Brognara E, Borgatti M, Lampronti I, Finotti A, Bianchi N, Sforza S, Tedeschi T, Manicardi A, Marchelli R, Corradini R, Gambari R. miRNA therapeutics: delivery and biological activity of peptide nucleic acids targeting miRNAs. Epigenomics 2012; 3:733-45. [PMID: 22126292 DOI: 10.2217/epi.11.90] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Peptide nucleic acids (PNAs) are DNA/RNA mimics extensively used for pharmacological regulation of gene expression in a variety of cellular and molecular systems, and they have been described as excellent candidates for antisense and antigene therapies. At present, very few data are available on the use of PNAs as molecules targeting miRNAs. miRNAs are a family of small nc RNAs that regulate gene expression by sequence-selective targeting of mRNAs, leading to a translational repression or mRNA degradation to the control of highly regulated biological functions, such as differentiation, cell cycle and apoptosis. The aim of this article is to present the state-of-the-art concerning the possible use of PNAs to target miRNAs and modify their biological metabolism within the cells. The results present in the literature allow to propose PNA-based molecules as very promising reagents to modulate the biological activity of miRNAs. In consideration of the involvement of miRNAs in human pathologies, PNA-mediated targeting of miRNAs has been proposed as a potential novel therapeutic approach.
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Affiliation(s)
- Enrica Fabbri
- Department of Biochemistry & Molecular Biology, University of Ferrara, Ferrara, Italy
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22
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Joshi T, Barbante GJ, Francis PS, Hogan CF, Bond AM, Gasser G, Spiccia L. Electrochemiluminescent monomers for solid support syntheses of Ru(II)-PNA bioconjugates: multimodal biosensing tools with enhanced duplex stability. Inorg Chem 2012; 51:3302-15. [PMID: 22339152 DOI: 10.1021/ic202761w] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The feasibility of devising a solid support mediated approach to multimodal Ru(II)-peptide nucleic acid (PNA) oligomers is explored. Three Ru(II)-PNA-like monomers, [Ru(bpy)(2)(Cpp-L-PNA-OH)](2+) (M1), [Ru(phen)(2)(Cpp-L-PNA-OH)](2+) (M2), and [Ru(dppz)(2)(Cpp-L-PNA-OH)](2+) (M3) (bpy = 2,2'-bipyridine, phen = 1,10-phenanthroline, dppz = dipyrido[3,2-a:2',3'-c]phenazine, Cpp-L-PNA-OH = [2-(N-9-fluorenylmethoxycarbonyl)aminoethyl]-N-[6-(2-(pyridin-2yl)pyrimidine-4-carboxamido)hexanoyl]-glycine), have been synthesized as building blocks for Ru(II)-PNA oligomers and characterized by IR and (1)H NMR spectroscopy, mass spectrometry, electrochemistry and elemental analysis. As a proof of principle, M1 was incorporated on the solid phase within the PNA sequences H-g-c-a-a-t-a-a-a-a-Lys-NH(2) (PNA1) and H-P-K-K-K-R-K-V-g-c-a-a-t-a-a-a-a-lys-NH(2) (PNA4) to give PNA2 (H-g-c-a-a-t-a-a-a-a-M1-lys-NH(2)) and PNA3 (H-P-K-K-K-R-K-V-g-c-a-a-t-a-a-a-a-M1-lys-NH(2)), respectively. The two Ru(II)-PNA oligomers, PNA2 and PNA3, displayed a metal to ligand charge transfer (MLCT) transition band centered around 445 nm and an emission maximum at about 680 nm following 450 nm excitation in aqueous solutions (10 mM PBS, pH 7.4). The absorption and emission response of the duplexes formed with the cDNA strand (DNA: 5'-T-T-T-T-T-T-T-A-T-T-G-C-T-T-T-3') showed no major variations, suggesting that the electronic properties of the Ru(II) complexes are largely unaffected by hybridization. The thermal stability of the PNA·DNA duplexes, as evaluated from UV melting experiments, is enhanced compared to the corresponding nonmetalated duplexes. The melting temperature (T(m)) was almost 8 °C higher for PNA2·DNA duplex, and 4 °C for PNA3·DNA duplex, with the stabilization attributed to the electrostatic interaction between the cationic residues (Ru(II) unit and positively charged lysine/arginine) and the polyanionic DNA backbone. In presence of tripropylamine (TPA) as co-reactant, PNA2, PNA3, PNA2·DNA and PNA3·DNA displayed strong electrochemiluminescence (ECL) signals even at submicromolar concentrations. Importantly, the combination of spectrochemical, thermal and ECL properties possessed by the Ru(II)-PNA sequences offer an elegant approach for the design of highly sensitive multimodal biosensing tools.
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Affiliation(s)
- Tanmaya Joshi
- ARC Centre of Excellence for Electromaterials Science and School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
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Ming X, Ding P, Leonard P, Budow S, Seela F. Parallel-stranded DNA: Enhancing duplex stability by the ‘G-clamp’ and a pyrrolo-dC derivative. Org Biomol Chem 2012; 10:1861-9. [DOI: 10.1039/c2ob06606h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Koripelly G, Meguellati K, Ladame S. Dual sensing of hairpin and quadruplex DNA structures using multicolored peptide nucleic acid fluorescent probes. Bioconjug Chem 2010; 21:2103-9. [PMID: 20923172 DOI: 10.1021/bc100335f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Synthesis of water-soluble 5-mer peptide nucleic acids (PNAs) functionalized at their 5'- and 3'-ends with two original precursors of pentamethine cyanine dye synthesis is reported. The successful use of these PNA probes for sensing DNA hairpin structures in vitro was also demonstrated where specific hairpin formation was associated with the appearance of a characteristic fluorescence signal at 660 nm. A comparative study between three different strategies where PNAs were targeting either the stem or the loop of the hairpin was carried out. Best sensitivity was obtained using PNA sequences complementary to the loop sequence and directing both functional moieties toward the base of loop. Unprecedented proof-of-concept for the simultaneous sensing of hairpin and quadruplex DNAs with a nonoverlapping two-color system (C3 and C5) is also demonstrated.
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Affiliation(s)
- Girish Koripelly
- Institut de Science et d'Ingénierie Supramoléculaires, CNRS UMR, Université de Strasbourg, France
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25
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Santana AG, Francisco CG, Suárez E, González CC. Synthesis of Guanidines From Azides: A General and Straightforward Methodology In Carbohydrate Chemistry. J Org Chem 2010; 75:5371-4. [DOI: 10.1021/jo100876r] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrés G. Santana
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez, 3, 38206 La Laguna Tenerife, Spain
| | - Cosme G. Francisco
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez, 3, 38206 La Laguna Tenerife, Spain
| | - Ernesto Suárez
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez, 3, 38206 La Laguna Tenerife, Spain
| | - Concepción C. González
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez, 3, 38206 La Laguna Tenerife, Spain
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Abstract
The use of fluorescent nucleic acid base analogues is becoming increasingly important in the fields of biology, biochemistry and biophysical chemistry as well as in the field of DNA nanotechnology. The advantage of being able to incorporate a fluorescent probe molecule close to the site of examination in the nucleic acid-containing system of interest with merely a minimal perturbation to the natural structure makes fluorescent base analogues highly attractive. In recent years, there has been a growing interest in developing novel candidates in this group of fluorophores for utilization in various investigations. This review describes the different classes of fluorophores that can be used for studying nucleic acid-containing systems, with an emphasis on choosing the right kind of probe for the system under investigation. It describes the characteristics of the large group of base analogues that has an emission that is sensitive to the surrounding microenvironment and gives examples of investigations in which this group of molecules has been used so far. Furthermore, the characterization and use of fluorescent base analogues that are virtually insensitive to changes in their microenvironment are described in detail. This group of base analogues can be used in several fluorescence investigations of nucleic acids, especially in fluorescence anisotropy and fluorescence resonance energy transfer (FRET) measurements. Finally, the development and characterization of the first nucleic base analogue FRET pair, tC(O)-tC(nitro), and its possible future uses are discussed.
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