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Cadoni E, Pennati F, Muangkaew P, Elskens J, Madder A, Manicardi A. Synthesis and structure-activity relationship of peptide nucleic acid probes with improved interstrand-crosslinking abilities: application to biotin-mediated RNA-pulldown. RSC Chem Biol 2022; 3:1129-1143. [PMID: 36128507 PMCID: PMC9428673 DOI: 10.1039/d2cb00095d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
Abstract
The development of interstrand-crosslinking (ICL) probes for the covalent targeting of DNA and RNA sequences of interest has been extensively reported in the past decade. However, most of the reactions reported so far induce the formation of a stable adduct that cannot be reverted, thus rendering these chemistries less useful in applications where the reversibility of the reaction is needed for further downstream processing of the targeted and isolated sequences, such as enzymatic amplification steps. In this work, we report on the reversibility of the furan-mediated ICL reaction. ICL formation can be conveniently triggered by either chemical (N-bromo succinimide, NBS) or luminous stimuli (visible light irradiation in presence of a photosensitizer) and quantitative reversion can be achieved by heating the crosslinked sample at 95 °C, while maintaining the structure of the DNA/RNA targets intact. As a proof-of-concept and showing the benefits of the ICL reversibility, we apply furan-mediated ICL to the pulldown of a target RNA strand from cell lysate.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-7 9000 Gent Belgium
| | - Francesca Pennati
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-7 9000 Gent Belgium
| | - Penthip Muangkaew
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-7 9000 Gent Belgium
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Patumwan 10330 Bangkok Thailand
| | - Joke Elskens
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-7 9000 Gent Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-7 9000 Gent Belgium
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-7 9000 Gent Belgium
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2
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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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3
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Söftje M, Acker S, Plarre R, Namyslo JC, Kaufmann DE. Novel nicotinoid structures for covalent modification of wood: an environmentally friendly way for its protection against insects. RSC Adv 2020; 10:15726-15733. [PMID: 35493663 PMCID: PMC9052505 DOI: 10.1039/d0ra02071k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/10/2020] [Indexed: 12/11/2022] Open
Abstract
Timber is constantly exposed to environmental influences under outdoor conditions which limits its lifetime and usability. In order to counteract the damaging processes caused by insects, we have developed a novel and more environmentally friendly method to protect wood materials via covalent modification by organic insecticides. Starting with an important class of synthetic insecticides which are derived from the natural insecticide nicotine, various new carboxylic acid derivatives of imidacloprid were made accessible. These activated neonicotinoids were utilized for the chemical modification of wood hydroxy groups. In contrast to conventional wood preservation methods in which biocides are only physically bound to the surface for a limited time, the covalent fixation of the preservative guarantees a permanent effect against wood pests, demonstrated in standardized biological tests. Additionally, the environmental interaction caused by non-bound neonicotinoids is significantly reduced, since both, a smaller application rate is required and leaching of the active ingredient is prevented. By minimizing the pest infestation, the lifetime of the material increases while preserving the natural appearance of the material.
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Affiliation(s)
- Martin Söftje
- Institute of Organic Chemistry, Clausthal University of Technology Leibnizstraße 6 38678 Clausthal-Zellerfeld Germany
| | - Sophie Acker
- Institute of Organic Chemistry, Clausthal University of Technology Leibnizstraße 6 38678 Clausthal-Zellerfeld Germany
| | - Rudy Plarre
- Bundesanstalt für Materialforschung und -prüfung Unter den Eichen 87 12205 Berlin Germany
| | - Jan C Namyslo
- Institute of Organic Chemistry, Clausthal University of Technology Leibnizstraße 6 38678 Clausthal-Zellerfeld Germany
| | - Dieter E Kaufmann
- Institute of Organic Chemistry, Clausthal University of Technology Leibnizstraße 6 38678 Clausthal-Zellerfeld Germany
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4
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Sabale P, Ambi UB, Srivatsan SG. Clickable PNA Probes for Imaging Human Telomeres and Poly(A) RNAs. ACS OMEGA 2018; 3:15343-15352. [PMID: 30556003 PMCID: PMC6289544 DOI: 10.1021/acsomega.8b02550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 10/31/2018] [Indexed: 05/10/2023]
Abstract
The ability to bind strongly to complementary nucleic acid sequences, invade complex nucleic acid structures, and resist degradation by cellular enzymes has made peptide nucleic acid (PNA) oligomers as very useful hybridization probes in molecular diagnosis. For such applications, the PNA oligomers have to be labeled with appropriate reporters as they lack intrinsic labels that can be used in biophysical assays. Although solid-phase synthesis is commonly used to attach reporters onto PNA, development of milder and modular labeling methods will provide access to PNA oligomers labeled with a wider range of biophysical tags. Here, we describe the establishment of a postsynthetic modification strategy based on bioorthogonal chemical reactions in functionalizing PNA oligomers in solution with a variety of tags. A toolbox composed of alkyne- and azide-modified monomers were site-specifically incorporated into PNA oligomers and postsynthetically click-functionalized with various tags, ranging from sugar, amino acid, biotin, to fluorophores, by using copper(I)-catalyzed azide-alkyne cycloaddition, strain-promoted azide-alkyne cycloaddition, and Staudinger ligation reactions. As a proof of utility of this method, fluorescent PNA hybridization probes were developed and used in imaging human telomeres in chromosomes and poly(A) RNAs in cells. Taken together, this simple approach of generating a wide range of functional PNA oligomers will expand the use of PNA in molecular diagnosis.
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5
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Gahtory D, Murtola M, Smulders MMJ, Wennekes T, Zuilhof H, Strömberg R, Albada B. Facile functionalization of peptide nucleic acids (PNAs) for antisense and single nucleotide polymorphism detection. Org Biomol Chem 2018; 15:6710-6714. [PMID: 28766647 DOI: 10.1039/c7ob01592e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this report, we show how a convenient on-resin copper-click functionalization of azido-functionalized peptide nucleic acids (PNAs) allows various PNA-based detection strategies. Firstly, a thiazole orange (TO) clicked PNA probe facilitates a binary readout when combined with F/Q labeled DNA, giving increased sensitivity for antisense detection. Secondly, our TO-PNA conjugate also allows single nucleotide polymorphism detection. Since antisense detection is also possible in the absence of the TO label, our sensing platform based on azido-d-ornithine containing PNA even allows for additional and more advanced functionalization and sensing strategies.
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Affiliation(s)
- Digvijay Gahtory
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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6
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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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7
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Elskens J, Manicardi A, Costi V, Madder A, Corradini R. Synthesis and Improved Cross-Linking Properties of C5-Modified Furan Bearing PNAs. Molecules 2017; 22:molecules22112010. [PMID: 29156637 PMCID: PMC6150320 DOI: 10.3390/molecules22112010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 11/07/2017] [Accepted: 11/09/2017] [Indexed: 12/21/2022] Open
Abstract
Over the past decades, peptide nucleic acid/DNA (PNA:DNA) duplex stability has been improved via backbone modification, often achieved via introducing an amino acid side chain at the α- or γ-position in the PNA sequence. It was previously shown that interstrand cross-linking can further enhance the binding event. In this work, we combined both strategies to fine-tune PNA crosslinking towards single stranded DNA sequences using a furan oxidation-based crosslinking method; for this purpose, γ-l-lysine and γ-l-arginine furan-PNA monomers were synthesized and incorporated in PNA sequences via solid phase synthesis. It was shown that the l-lysine γ-modification had a beneficial effect on crosslink efficiency due to pre-organization of the PNA helix and a favorable electrostatic interaction between the positively-charged lysine and the negatively-charged DNA backbone. Moreover, the crosslink yield could be optimized by carefully choosing the type of furan PNA monomer. This work is the first to describe a selective and biocompatible furan crosslinking strategy for crosslinking of γ-modified PNA sequences towards single-stranded DNA.
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Affiliation(s)
- Joke Elskens
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium.
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium.
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Valentina Costi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium.
| | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
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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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9
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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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10
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Manicardi A, Gyssels E, Corradini R, Madder A. Furan-PNA: a mildly inducible irreversible interstrand crosslinking system targeting single and double stranded DNA. Chem Commun (Camb) 2016; 52:6930-3. [PMID: 27147261 DOI: 10.1039/c6cc02062c] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We here report on the design and synthesis of tailor-made furan-modified peptide nucleic acid (PNA) probes for covalent targeting of single stranded DNA through a crosslinking strategy. After introducing furan-containing building blocks into a PNA sequence, hybridization and furan-oxidation based crosslinking to DNA is investigated. The structure of the crosslinked products is characterized and preliminary investigations concerning the application of these systems to double stranded DNA are shown.
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Affiliation(s)
- A Manicardi
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, Parma 43124, Italy.
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11
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Wang X, Hudson RHE. PNA Molecular Beacons Assembled by Post-Synthetic Click Chemistry Functionalization. Chembiochem 2015; 16:2156-61. [PMID: 26227668 DOI: 10.1002/cbic.201500248] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Indexed: 12/12/2022]
Abstract
To avoid the tedious synthesis of functionalized peptide nucleic acid (PNA) monomers for probe development, we proposed a simple approach to modify PNA oligomers by post-synthetic on-resin click chemistry. PNA molecular beacons (MBs) were prepared by incorporation of azide-containing monomers into the oligomer by automatic solid-phase peptide synthesis and subsequent derivatization with pyrene moieties by copper-catalyzed azide-alkyne cycloaddition. Two pyrene-based quencher-free PNA molecular beacons, a stemless MB and one possessing a stem-loop structure, targeting a portion of the cystic fibrosis gene, were successfully synthesized by using this method. Fluorescence studies showed that the stem-loop MB exhibited better discrimination of changes in excimer/monomer ratios as compared to the stemless MB construct.
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Affiliation(s)
- Xiaoxiao Wang
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON, N6A 2K5, Canada
| | - Robert H E Hudson
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON, N6A 2K5, Canada.
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12
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Manicardi A, Guidi L, Ghidini A, Corradini R. Pyrene-modified PNAs: Stacking interactions and selective excimer emission in PNA2DNA triplexes. Beilstein J Org Chem 2014; 10:1495-503. [PMID: 25161706 PMCID: PMC4142857 DOI: 10.3762/bjoc.10.154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/03/2014] [Indexed: 12/17/2022] Open
Abstract
Pyrene derivatives can be incorporated into nucleic acid analogs in order to obtain switchable probes or supramolecular architectures. In this paper, peptide nucleic acids (PNAs) containing 1 to 3 1-pyreneacetic acid units (PNA1–6) with a sequence with prevalence of pyrimidine bases, complementary to cystic fibrosis W1282X point mutation were synthesized. These compounds showed sequence-selective switch-on of pyrene excimer emission in the presence of target DNA, due to PNA2DNA triplex formation, with stability depending on the number and positioning of the pyrene units along the chain. An increase in triplex stability and a very high mismatch-selectivity, derived from combined stacking and base-pairing interactions, were found for PNA2, bearing two distant pyrene units.
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Affiliation(s)
- Alex Manicardi
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410
| | - Lucia Guidi
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410
| | - Alice Ghidini
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410 ; Present Address: Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Hälsovägen 7, 14183, Huddinge, Sweden
| | - Roberto Corradini
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410
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Jain DR, Ganesh KN. Clickable Cγ-azido(methylene/butylene) peptide nucleic acids and their clicked fluorescent derivatives: synthesis, DNA hybridization properties, and cell penetration studies. J Org Chem 2014; 79:6708-14. [PMID: 24941399 DOI: 10.1021/jo500834u] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Synthesis, characterization, and DNA complementation studies of clickable C(γ)-substituted methylene (azm)/butylene (azb) azido PNAs show that these analogues enhance the stability of the derived PNA:DNA duplexes. The fluorescent PNA oligomers synthesized by their click reaction with propyne carboxyfluorescein are seen to accumulate around the nuclear membrane in 3T3 cells.
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Affiliation(s)
- Deepak R Jain
- Chemical Biology Unit, Indian Institute of Science Education and Research , Dr Homi Bhabha Road, Pune 411008, India
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14
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St. Amant AH, Engbers C, Hudson RH. A solid-phase CuAAC strategy for the synthesis of PNA containing nucleobase surrogates. ARTIFICIAL DNA, PNA & XNA 2013; 4:4-10. [PMID: 23422048 PMCID: PMC3654728 DOI: 10.4161/adna.23982] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/11/2013] [Accepted: 02/12/2013] [Indexed: 11/19/2022]
Abstract
The synthesis of an azide containing PNA monomer is described. The monomer was incorporated into two PNA sequences for the purpose of synthesizing an intercalating fluorophore-labeled PNA and a metal binding hairpin using a solid phase copper catalyzed azide-alkyne Huisgen cycloaddition (CuAAC). Click chemistry was performed using 2-ethynylfluorene or 1-ethynylpyrene to add a fluorophore to the PNA, which were tested for their ability to recognize an abasic site on a DNA target. A PNA hairpin possessing azide monomers at each termini was synthesized and reacted with 2-ethynylpyridine to form a hairpin that is stabilized by Ni²⁺.
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Affiliation(s)
- André H. St. Amant
- Department of Chemistry; The University of Western Ontario; London, ON Canada
| | - Christopher Engbers
- Department of Chemistry; The University of Western Ontario; London, ON Canada
| | - Robert H.E. Hudson
- Department of Chemistry; The University of Western Ontario; London, ON Canada
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