1
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Ghosh C, Popella L, Dhamodharan V, Jung J, Dietzsch J, Barquist L, Höbartner C, Vogel J. A comparative analysis of peptide-delivered antisense antibiotics using diverse nucleotide mimics. RNA 2024; 30:624-643. [PMID: 38413166 PMCID: PMC11098465 DOI: 10.1261/rna.079969.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/29/2024]
Abstract
Antisense oligomer (ASO)-based antibiotics that target mRNAs of essential bacterial genes have great potential for counteracting antimicrobial resistance and for precision microbiome editing. To date, the development of such antisense antibiotics has primarily focused on using phosphorodiamidate morpholino (PMO) and peptide nucleic acid (PNA) backbones, largely ignoring the growing number of chemical modalities that have spurred the success of ASO-based human therapy. Here, we directly compare the activities of seven chemically distinct 10mer ASOs, all designed to target the essential gene acpP upon delivery with a KFF-peptide carrier into Salmonella. Our systematic analysis of PNA, PMO, phosphorothioate (PTO)-modified DNA, 2'-methylated RNA (RNA-OMe), 2'-methoxyethylated RNA (RNA-MOE), 2'-fluorinated RNA (RNA-F), and 2'-4'-locked RNA (LNA) is based on a variety of in vitro and in vivo methods to evaluate ASO uptake, target pairing and inhibition of bacterial growth. Our data show that only PNA and PMO are efficiently delivered by the KFF peptide into Salmonella to inhibit bacterial growth. Nevertheless, the strong target binding affinity and in vitro translational repression activity of LNA and RNA-MOE make them promising modalities for antisense antibiotics that will require the identification of an effective carrier.
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Affiliation(s)
- Chandradhish Ghosh
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Linda Popella
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
- Cluster for Nucleic Acid Therapeutics Munich (CNATM), Munich, Germany
| | - V Dhamodharan
- Institute of Organic Chemistry, Center for Nanosystems Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Jakob Jung
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Julia Dietzsch
- Institute of Organic Chemistry, Center for Nanosystems Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080, Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, Center for Nanosystems Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
- Cluster for Nucleic Acid Therapeutics Munich (CNATM), Munich, Germany
- Faculty of Medicine, University of Würzburg, 97080, Würzburg, Germany
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2
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Xu S, Wang G, Feng Y, Zheng J, Huang L, Liu J, Jiang Y, Wang Y, Liu N. PNA-Functionalized, Silica Nanowires-Filled Glass Microtube for Ultrasensitive and Label-Free Detection of miRNA-21. Anal Chem 2024; 96:7470-7478. [PMID: 38696229 DOI: 10.1021/acs.analchem.3c05839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2024]
Abstract
MicroRNAs (miRNAs) are endogenous and noncoding single-stranded RNA molecules with a length of approximately 18-25 nucleotides, which play an undeniable role in early cancer screening. Therefore, it is very important to develop an ultrasensitive and highly specific method for detecting miRNAs. Here, we present a bottom-up assembly approach for modifying glass microtubes with silica nanowires (SiNWs) and develop a label-free sensing platform for miRNA-21 detection. The three-dimensional (3D) networks formed by SiNWs make them abundant and highly accessible sites for binding with peptide nucleic acid (PNA). As a receptor, PNA has no phosphate groups and exhibits an overall electrically neutral state, resulting in a relatively small repulsion between PNA and RNA, which can improve the hybridization efficiency. The SiNWs-filled glass microtube (SiNWs@GMT) sensor enables ultrasensitive, label-free detection of miRNA-21 with a detection limit as low as 1 aM at a detection range of 1 aM-100 nM. Noteworthy, the sensor can still detect miRNA-21 in the range of 102-108 fM in complex solutions containing 1000-fold homologous interference of miRNAs. The high anti-interference performance of the sensor enables it to specifically recognize target miRNA-21 in the presence of other miRNAs and distinguish 1-, 3-mismatch nucleotide sequences. Significantly, the sensor platform is able to detect miRNA-21 in the lysate of breast cancer cell lines (e.g., MCF-7 cells and MDA-MB-231 cells), indicating that it has good potential in the screening of early breast cancers.
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Affiliation(s)
- Shiwei Xu
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Guofeng Wang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Yueyue Feng
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Juanjuan Zheng
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Liying Huang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Jiahao Liu
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Yisha Jiang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Yajun Wang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Nannan Liu
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
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3
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Svenningsen SW, Luige O, Abdulkarim Z, Strömberg R, Williams NH. Zinc N, N-bis(2-picolyl)amine Chelates Show Substitution-Dependent Cleavage of Phosphodiesters in Models as Well as of PNAzyme-RNA Bulges. Molecules 2024; 29:2123. [PMID: 38731616 PMCID: PMC11085541 DOI: 10.3390/molecules29092123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/20/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
PNAzymes are a group of artificial enzymes which show promising results in selective and efficient cleavage of RNA targets. In the present study, we introduce a series of metal chelating groups based on N,N-bis(2-picolyl) groups (parent, 6-methyl and 6-amino substituted) as the active sites of novel PNAzymes. An improved synthetic route for the 6-amino analogues is described. The catalytic activity of the chelating groups for cleaving phosphodiesters were assessed with the model substrate 2-hydroxypropyl p-nitrophenyl phosphate (HPNPP), confirming that the zinc complexes have the reactivity order of parent < 2-methyl < 2-amino. The three ligands were conjugated to a PNA oligomer to form three PNAzymes which showed the same order of reactivity and some sensitivity to the size of the RNA bulge designed into the catalyst-substrate complex. This work demonstrates that the kinetic activity observed for the model substrate HPNPP could be translated onto the PNAzymes, but that more reactive Zn complexes are required for such PNAzymes to be viable therapeutic agents.
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Affiliation(s)
- Søren W. Svenningsen
- Department of Chemistry, University of Sheffield, Richard Roberts Building, Sheffield S3 7HF, UK; (S.W.S.); (Z.A.)
| | - Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, Halsovagen 9, 14157 Huddinge, Sweden;
| | - Zeyed Abdulkarim
- Department of Chemistry, University of Sheffield, Richard Roberts Building, Sheffield S3 7HF, UK; (S.W.S.); (Z.A.)
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, Halsovagen 9, 14157 Huddinge, Sweden;
- Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Nobels alle 8 B, 14152 Huddinge, Sweden
| | - Nicholas H. Williams
- Department of Chemistry, University of Sheffield, Richard Roberts Building, Sheffield S3 7HF, UK; (S.W.S.); (Z.A.)
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4
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Sarkar S. Recent advancements in bionanomaterial applications of peptide nucleic acid assemblies. Biopolymers 2024; 115:e23567. [PMID: 37792292 DOI: 10.1002/bip.23567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/02/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023]
Abstract
Peptide nucleic acid (PNA) is a unique combination of peptides and nucleic acids. PNA can exhibit hydrogen bonding interactions with complementary nucleobases like DNA/RNA. Also, its polyamide backbone allows easy incorporation of biomolecules like peptides and proteins to build hybrid molecular constructs. Because of chimeric structural properties, PNA has lots of potential to build diverse nanostructures. However, progress in the PNA material field is still immature compared with its massive applications in antisense oligonucleotide research. Examples of well-defined molecular assemblies have been reported with PNA amphiphiles, self-assembling guanine-PNA monomers/dimers, and PNA-decorated nucleic acids/ polymers/ peptides. All these works indicate the great potential of PNA to be used as bionanomaterials. The review summarizes the recent reports on PNA-based nanostructures and their versatile applications. Additionally, this review shares a perspective to promote a better understanding of controlling molecular assembly by the systematic structural modifications of PNA monomers.
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Affiliation(s)
- Srijani Sarkar
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
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5
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El-Fateh M, Chatterjee A, Zhao X. A systematic review of peptide nucleic acids (PNAs) with antibacterial activities: Efficacy, potential and challenges. Int J Antimicrob Agents 2024; 63:107083. [PMID: 38185398 DOI: 10.1016/j.ijantimicag.2024.107083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/11/2023] [Accepted: 12/30/2023] [Indexed: 01/09/2024]
Abstract
Peptide nucleic acids (PNAs) are synthetic molecules that are like DNA/RNA, but with different building blocks. PNAs target and bind to mRNAs and disrupt the function of a targeted gene, hence they have been studied as potential antibacterials. The aim of this systematic review was to provide an in-depth analysis of the current status of PNAs as antibacterial agents, define the characteristics of the effective PNA constructs, and address the gap in advancing PNAs to become clinically competent agents. Following the PRISMA model, four electronic databases were searched: Web of Science, PubMed, SciFinder and Scopus. A total of 627 articles published between 1994 and 2023 were found. After screening and a rigorous selection process using explicit inclusion and exclusion criteria, 65 scientific articles were selected, containing 656 minimum inhibitory concentration (MIC) data. The antibacterial activity of PNAs was assessed against 20 bacterial species. The most studied Gram-negative and Gram-positive bacteria were Escherichia coli (n=266) and Staphylococcus aureus (n=53), respectively. In addition, the effect of PNA design, including construct length, binding location, and carrier agents, on antibacterial activity was shown. Finally, antibacterial test models to assess the inhibitory effects of PNAs were examined, emphasising gaps and prospects. This systematic review provides a comprehensive assessment of the potential of PNAs as antibacterial agents and offers valuable insights for researchers and clinicians seeking novel therapeutic strategies in the context of increasing rates of antibiotic-resistant bacteria.
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Affiliation(s)
- Mohamed El-Fateh
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada, H9X3V9; Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, 35516, El-Dakhelia, Egypt; Antimicrobial Regeneration Consortium Labs, Louisville, CO, 80027, USA
| | - Anushree Chatterjee
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Antimicrobial Regeneration Consortium Labs, Louisville, CO, 80027, USA
| | - Xin Zhao
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada, H9X3V9; Antimicrobial Regeneration Consortium Labs, Louisville, CO, 80027, USA.
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6
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Katkevics M, MacKay JA, Rozners E. Triplex-forming peptide nucleic acids as emerging ligands to modulate structure and function of complex RNAs. Chem Commun (Camb) 2024; 60:1999-2008. [PMID: 38259187 PMCID: PMC10922694 DOI: 10.1039/d3cc05409h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Over the last three decades, our view of RNA has changed from a simple intermediate supporting protein synthesis to a major regulator of biological processes. In the expanding area of RNA research, peptide nucleic acid (PNA) is emerging as a promising ligand for triple-helical recognition of complex RNAs. As discussed in this feature article, the key advantages of PNAs are high sequence specificity and affinity for RNA (>10 fold higher than for DNA) that are difficult to achieve with small molecule ligands. Emerging studies demonstrate that triple-helical binding of PNAs can modulate biological function and control dynamic conformational equilibria of complex folded RNAs. These results suggest that PNA has a unique potential as a research tool and therapeutic compound targeting RNA. The remaining problems hampering advances in these directions are limitations of sequences that can be recognized by Hoogsteen triplexes (typically purine rich tracts), poor cellular uptake and bioavailability of PNA, and potential off-target effects in biological systems. Recent exciting studies are discussed that illustrate how synthetic nucleic acid chemistry provides innovative solutions for these problems.
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Affiliation(s)
- Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - James A MacKay
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, NY 13902, USA.
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7
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Sivakrishna
Rao G, Saleh AH, Melliti F, Muntjeeb S, Mahfouz M. Harnessing Peptide Nucleic Acids and the Eukaryotic Resolvase MOC1 for Programmable, Precise Generation of Double-Strand DNA Breaks. Anal Chem 2024; 96:2599-2609. [PMID: 38300270 PMCID: PMC10867802 DOI: 10.1021/acs.analchem.3c05133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/02/2024]
Abstract
Programmable site-specific nucleases (SSNs) hold extraordinary promise to unlock myriad gene editing applications in medicine and agriculture. However, developing small and specific SSNs is needed to overcome the delivery and specificity translational challenges of current genome engineering technologies. Structure-guided nucleases have been harnessed to generate double-strand DNA breaks but with limited success and translational potential. Here, we harnessed the power of peptide nucleic acids (PNAs) for site-specific DNA invasion and the generation of localized DNA structures that are recognized and cleaved by the eukaryotic resolvase AtMOC1 from Arabidopsis thaliana. We named this technology PNA-assisted Resolvase-mediated (PNR) editing. We tested the PNR editing concept in vitro and demonstrated its precise target specificity, examined the nucleotide requirement around the PNA invasion for the AtMOC1-mediated cleavage, mapped the AtMOC1-mediated cleavage sites, tested the role of different types and lengths of PNA molecules invasion into dsDNA for the AtMOC1-mediated cleavage, optimized the in vitro PNA invasion and AtMOC1 cleavage conditions such as temperature, buffer conditions, and cleavage time points, and demonstrated the multiplex cleavage for precise fragment release. We discuss the best design parameters for efficient, site-specific in vitro cleavage using PNR editors.
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Affiliation(s)
- Gundra Sivakrishna
Rao
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Ahmed H. Saleh
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Firdaws Melliti
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Syed Muntjeeb
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Magdy Mahfouz
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi
Arabia
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8
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Sakar S, Anderson CF, Schneider JP. The Design of a Participatory Peptide Nucleic Acid Duplex Crosslinker to Enhance the Stiffness of Self-Assembled Peptide Gels. Angew Chem Int Ed Engl 2024; 63:e202313507. [PMID: 38057633 PMCID: PMC10872331 DOI: 10.1002/anie.202313507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/08/2023]
Abstract
Herein, peptide nucleic acids (PNAs) are employed in the design of a participatory duplex PNA-peptide crosslinking agent. Biophysical and mechanical studies show that crosslinkers present during peptide assembly leading to hydrogelation participate in the formation of fibrils while simultaneously installing crosslinks into the higher-order network that constitutes the peptide gel. The addition of 2 mol % crosslinker into the assembling system results in a ~100 % increase in mechanical stiffness without affecting the rate of peptide assembly or the local morphology of fibrils within the gel network. Stiffness enhancement is realized by only affecting change in the elastic component of the viscoelastic gel. A synthesis of the PNA-peptide duplex crosslinkers is provided that allows facile variation in peptide composition and addresses the notorious hydrophobic content of PNAs. This crosslinking system represents a new tool for modulating the mechanical properties of peptide-based hydrogels.
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Affiliation(s)
- Srijani Sakar
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, 376 Boyles Street, Frederick, MD 21702, USA
| | - Caleb F Anderson
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, 376 Boyles Street, Frederick, MD 21702, USA
| | - Joel P Schneider
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, 376 Boyles Street, Frederick, MD 21702, USA
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9
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Waliczek M, Gancarz W, Pochwała P, Pehlivan Ö, Stefanowicz P. Visible Light-Induced Templated Metathesis of Peptide-Nucleic Acid Conjugates with a Diselenide Bridge. Biomolecules 2023; 13:1676. [PMID: 38002358 PMCID: PMC10669671 DOI: 10.3390/biom13111676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
The use of template molecules as chemical scaffolds that significantly influence the course of the reaction has recently been intensively studied. Peptide nucleic acids (PNA) are molecules that mimic natural nucleic acids. They are a promising matrix in such reactions because they possess high affinity and specificity in their interactions. The manner of PNA interaction is predictable based on sequence complementarity. Recently, we report the visible light-induced metathesis reaction in peptides containing a diselenide bond. Herein, we present an efficient and straightforward method of the visible light-driven diselenide-based metathesis of peptide-nucleic acid conjugates. Compared to a similar photochemical transformation in peptides, a significant increase in the metathesis efficiency was obtained due to the template effect.
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Affiliation(s)
- Mateusz Waliczek
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland
| | | | | | | | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland
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10
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Talbott JM, Tessier BR, Harding EE, Walby GD, Hess KJ, Baskevics V, Katkevics M, Rozners E, MacKay JA. Improved Triplex-Forming Isoorotamide PNA Nucleobases for A-U Recognition of RNA Duplexes. Chemistry 2023; 29:e202302390. [PMID: 37647091 DOI: 10.1002/chem.202302390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Four new isoorotamide (Io)-containing PNA nucleobases have been designed for A-U recognition of double helical RNA. New PNA monomers were prepared efficiently and incorporated into PNA nonamers for binding A-U in a PNA:RNA2 triplex. Isothermal titration calorimetry and UV thermal melting experiments revealed slightly improved binding affinity for singly modified PNA compared to known A-binding nucleobases. Molecular dynamics simulations provided further insights into binding of Io bases in the triple helix. Together, the data revealed interesting insights into binding modes including the notion that three Hoogsteen hydrogen bonds are unnecessary for strong selective binding of an extended nucleobase. Cationic monomer Io8 additionally gave the highest affinity observed for an A-binding nucleobase to date. These results will help inform future nucleobase design toward the goal of recognizing any sequence of double helical RNA.
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Affiliation(s)
- John M Talbott
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | - Brandon R Tessier
- Department of Chemistry, Binghamton University, Binghamton, NY 13902, USA
| | - Emily E Harding
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | - Grant D Walby
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | - Kyle J Hess
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | | | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, NY 13902, USA
| | - James A MacKay
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
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11
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Nandhini KP, Noki S, Brasil E, Albericio F, de la Torre BG. A safety-catch protecting group strategy compatible with Boc-chemistry for the synthesis of peptide nucleic acids (PNAs). Org Biomol Chem 2023; 21:8125-8135. [PMID: 37772422 DOI: 10.1039/d3ob01348k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Peptide Nucleic Acids (PNAs) are an intriguing class of synthetic biomolecules with great potential in medicine. Although PNAs could be considered analogs of oligonucleotides, their synthesis is more like that of peptides. In both cases, a Solid-Phase Synthesis (SPS) approach is used. Herein, the advantage using Boc as a temporal protecting group has been demonstrated to be more favored than Fmoc. In this context, a new PNA SPS strategy has been developed based on a safety-catch protecting group scheme for the exocyclic nitrogen of the side-chain bases and the linker. Sulfinyl (sulfoxide)-containing moieties are fully stable to the trifluoroacetic acid (TFA) used to remove the Boc group, but they can be reduced to the corresponding sulfide derivatives, which are labile in the presence of TFA. The efficiency of this novel synthetic strategy has been demonstrated in the synthesis of the PNA pentamer H-PNA(TATCT)-βAla-OH.
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Affiliation(s)
- K P Nandhini
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa.
| | - Sikabwe Noki
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa.
| | - Edikarlos Brasil
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa.
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa.
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, and Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, 08028 Barcelona, Spain
| | - Beatriz G de la Torre
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
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12
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Tsylents U, Siekierska I, Trylska J. Peptide nucleic acid conjugates and their antimicrobial applications-a mini-review. Eur Biophys J 2023; 52:533-544. [PMID: 37610696 PMCID: PMC10618302 DOI: 10.1007/s00249-023-01673-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 08/24/2023]
Abstract
Peptide nucleic acid (PNA) is a nucleic acid mimic with high specificity and binding affinity to natural DNA or RNA, as well as resistance to enzymatic degradation. PNA sequences can be designed to selectively silence gene expression, which makes PNA a promising tool for antimicrobial applications. However, the poor membrane permeability of PNA remains the main limiting factor for its applications in cells. To overcome this obstacle, PNA conjugates with different molecules have been developed. This mini-review focuses on covalently linked conjugates of PNA with cell-penetrating peptides, aminosugars, aminoglycoside antibiotics, and non-peptidic molecules that were tested, primarily as PNA carriers, in antibacterial and antiviral applications. The chemistries of the conjugation and the applied linkers are also discussed.
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Affiliation(s)
- Uladzislava Tsylents
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Izabela Siekierska
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland.
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13
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Mosseri A, Sancho-Albero M, Mercurio FA, Leone M, De Cola L, Romanelli A. Tryptophan-PNA gc Conjugates Self-Assemble to Form Fibers. Bioconjug Chem 2023; 34:1429-1438. [PMID: 37486977 PMCID: PMC10436247 DOI: 10.1021/acs.bioconjchem.3c00200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/07/2023] [Indexed: 07/26/2023]
Abstract
Peptide nucleic acids and their conjugates to peptides can self-assemble and generate complex architectures. In this work, we explored the self-assembly of PNA dimers conjugated to the dipeptide WW. Our studies suggest that the indole ring of tryptophan promotes aggregation of the conjugates. The onset of fluorescence is observed upon self-assembly. The structure of self-assembled WWgc is concentration-dependent, being spherical at low concentrations and fibrous at high concentrations. As suggested by molecular modeling studies, fibers are stabilized by stacking interactions between tryptophans and Watson-Crick hydrogen bonds between nucleobases.
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Affiliation(s)
- Andrea Mosseri
- Dipartimento
di Scienze Farmaceutiche, Università
Degli Studi di Milano, via Venezian 21, 20133 Milano, Italy
| | - María Sancho-Albero
- Department
of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milano, Italy
| | - Flavia Anna Mercurio
- Istituto
di Biostrutture e Bioimmagini—CNR, via Pietro Castellino 111, 80131 Naples, Italy
| | - Marilisa Leone
- Istituto
di Biostrutture e Bioimmagini—CNR, via Pietro Castellino 111, 80131 Naples, Italy
| | - Luisa De Cola
- Dipartimento
di Scienze Farmaceutiche, Università
Degli Studi di Milano, via Venezian 21, 20133 Milano, Italy
- Department
of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milano, Italy
| | - Alessandra Romanelli
- Dipartimento
di Scienze Farmaceutiche, Università
Degli Studi di Milano, via Venezian 21, 20133 Milano, Italy
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14
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Riela S, Borrego-Sánchez A, Cauteruccio S, de Melo Barbosa R, Massaro M, Sainz-Díaz CI, Sánchez-Espejo R, Viseras-Iborra C, Licandro E. Exploiting the interaction between halloysite and charged PNAs for their controlled release. J Mater Chem B 2023; 11:6685-6696. [PMID: 37377023 DOI: 10.1039/d3tb00637a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The design and development of nanomaterials that could be used in nanomedicine are of fundamental importance to obtain smart nanosystems for the treatment of several diseases. Halloysite, because of its interesting features, represents a suitable nanomaterial for the delivery of different biologically active species. Among them, peptide nucleic acids (PNAs) have attracted considerable attention in recent decades for their potential applications in both molecular antisense diagnosis and as therapeutic agents, although up to now, the actual clinical applications have been very limited. Herein we report a systematic study on the supramolecular interaction of three differently charged PNAs with halloysite. Understanding the interaction mode of charged molecules with the clay surfaces represents a key factor for the future design and development of halloysite based materials which could be used for the delivery and subsequent intracellular release of PNA molecules. Thus, three different PNA tetramers, chosen as models, were synthesized and loaded onto the clay. The obtained nanomaterials were characterized using spectroscopic studies and thermogravimetric analysis, and their morphologies were studied using high angle annular dark field transmission electron microscopy (HAADF/STEM) coupled with Energy Dispersive X-ray spectroscopy (EDX). The aqueous mobility of the three different nanomaterials was investigated by dynamic light scattering (DLS) and ζ-potential measurements. The release of PNA tetramers from the nanomaterials was investigated at two different pH values, mimicking physiological conditions. Finally, to better understand the stability of the synthesized PNAs and their interactions with HNTs, molecular modelling calculations were also performed. The obtained results showed that PNA tetramers interact in different ways with HNT surfaces according to their charge which influences their kinetic release in media mimicking physiological conditions.
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Affiliation(s)
- Serena Riela
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo Viale delle Scienze, Ed. 17 90128 Palermo, Italy.
| | - Ana Borrego-Sánchez
- Instituto de Ciencia Molecular, Universitat de València, Carrer del Catedrátic José Beltrán Martinez 2, 46980 Paterna, Spain
| | - Silvia Cauteruccio
- Department of Chemistry, University of Milan, via Golgi 19 20133 Milan, Italy.
| | - Raquel de Melo Barbosa
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 s/n, Granada, Spain
| | - Marina Massaro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo Viale delle Scienze, Ed. 17 90128 Palermo, Italy.
| | - C Ignacio Sainz-Díaz
- Andalusian Institute of Earth Sciences, CSIC-UGR, Avenida de las Palmeras 4, 18100, Armilla, Granada, Spain
| | - Rita Sánchez-Espejo
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 s/n, Granada, Spain
| | - César Viseras-Iborra
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, 18071 s/n, Granada, Spain
- Andalusian Institute of Earth Sciences, CSIC-UGR, Avenida de las Palmeras 4, 18100, Armilla, Granada, Spain
| | - Emanuela Licandro
- Department of Chemistry, University of Milan, via Golgi 19 20133 Milan, Italy.
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15
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Ryan C, Rahman MM, Kumar V, Rozners E. Triplex-Forming Peptide Nucleic Acid Controls Dynamic Conformations of RNA Bulges. J Am Chem Soc 2023; 145:10497-10504. [PMID: 37155726 PMCID: PMC10198159 DOI: 10.1021/jacs.2c12488] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Indexed: 05/10/2023]
Abstract
RNA folding is driven by the formation of double-helical segments interspaced by loops of unpaired nucleotides. Among the latter, bulges formed by one or several unpaired nucleotides are one of the most common structural motifs that play an important role in stabilizing RNA-RNA, RNA-protein, and RNA-small molecule interactions. Single-nucleotide bulges can fold in alternative structures where the unpaired nucleobase is either looped-out (flexible) in a solvent or stacked-in (intercalated) between the base pairs. In the present study, we discovered that triplex-forming peptide nucleic acids (PNAs) had unusually high affinity for single-purine-nucleotide bulges in double-helical RNA. Depending on the PNA's sequence, the triplex formation shifted the equilibrium between looped-out and stacked-in conformations. The ability to control the dynamic equilibria of RNA's structure will be an important tool for studying structure-function relationships in RNA biology and may have potential in novel therapeutic approaches targeting disease-related RNAs.
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Affiliation(s)
- Christopher
A. Ryan
- Department of Chemistry, The State
University of New York, Binghamton University, Binghamton, New York 13902, United States
| | - Md Motiar Rahman
- Department of Chemistry, The State
University of New York, Binghamton University, Binghamton, New York 13902, United States
| | - Vipin Kumar
- Department of Chemistry, The State
University of New York, Binghamton University, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, The State
University of New York, Binghamton University, Binghamton, New York 13902, United States
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16
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Jung J, Popella L, Do PT, Pfau P, Vogel J, Barquist L. Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server. RNA 2023; 29:570-583. [PMID: 36750372 PMCID: PMC10158992 DOI: 10.1261/rna.079263.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 01/10/2023] [Indexed: 05/06/2023]
Abstract
Antisense oligomers (ASOs), such as peptide nucleic acids (PNAs), designed to inhibit the translation of essential bacterial genes, have emerged as attractive sequence- and species-specific programmable RNA antibiotics. Yet, potential drawbacks include unwanted side effects caused by their binding to transcripts other than the intended target. To facilitate the design of PNAs with minimal off-target effects, we developed MASON (make antisense oligomers now), a web server for the design of PNAs that target bacterial mRNAs. MASON generates PNA sequences complementary to the translational start site of a bacterial gene of interest and reports critical sequence attributes and potential off-target sites. We based MASON's off-target predictions on experiments in which we treated Salmonella enterica serovar Typhimurium with a series of 10-mer PNAs derived from a PNA targeting the essential gene acpP but carrying two serial mismatches. Growth inhibition and RNA-sequencing (RNA-seq) data revealed that PNAs with terminal mismatches are still able to target acpP, suggesting wider off-target effects than anticipated. Comparison of these results to an RNA-seq data set from uropathogenic Escherichia coli (UPEC) treated with eleven different PNAs confirmed that our findings are not unique to Salmonella We believe that MASON's off-target assessment will improve the design of specific PNAs and other ASOs.
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Affiliation(s)
- Jakob Jung
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Linda Popella
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Phuong Thao Do
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Patrick Pfau
- Faculty of Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080 Würzburg, Germany
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17
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Kumar V, Wahane A, Gupta A, Manautou JE, Bahal R. Multivalent Lactobionic Acid and N-Acetylgalactosamine-Conjugated Peptide Nucleic Acids for Efficient In Vivo Targeting of Hepatocytes. Adv Healthc Mater 2023; 12:e2202859. [PMID: 36636995 PMCID: PMC10175146 DOI: 10.1002/adhm.202202859] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/27/2022] [Indexed: 01/14/2023]
Abstract
Peptide nucleic acids (PNAs) are used/applied in various studies to target genomic DNA and RNA to modulate gene expression. Non-specific targeting and rapid elimination always remain a challenge for PNA-based applications. Here, the synthesis, characterization, in vitro and in vivo study of di lactobionic acid (diLBA) and tris N-acetyl galactosamine (tGalNAc) conjugated PNAs for liver-targeted delivery are reported. For proof of concept, diLBA, and tGalNAc conjugated PNAs (anti-miR-122 PNAs) were synthesized to target microRNA-122 (miR-122) which is over-expressed in the hepatic tissue. Different lengths of anti-miR-122 PNAs conjugated with diLBA and tGalNAc are tested. Cell culture and in vivo analyses to determine biodistribution, efficacy, and toxicity profile are performed. This work indicates that diLBA conjugates show significant retention in hepatocytes in addition to tGalNAc conjugates after in vivo delivery. Full-length PNA conjugates show significant downregulation of miR-122 levels and subsequent de-repression of its downstream targets with no evidence of toxicity. The results provide a robust framework for ligand-conjugated delivery systems for PNAs that can be explored for broader biomedical applications.
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Affiliation(s)
- Vikas Kumar
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
| | - Aniket Wahane
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
| | - Anisha Gupta
- School of Pharmacy, University of Saint Joseph, West Hartford, CT, 06117, USA
| | - José E Manautou
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
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18
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Pradeep SP, Malik S, Slack FJ, Bahal R. Unlocking the potential of chemically modified peptide nucleic acids for RNA-based therapeutics. RNA 2023; 29:434-445. [PMID: 36653113 PMCID: PMC10019372 DOI: 10.1261/rna.079498.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/12/2023] [Indexed: 05/27/2023]
Abstract
RNA therapeutics have emerged as next-generation therapy for the treatment of many diseases. Unlike small molecules, RNA targeted drugs are not limited by the availability of binding pockets on the protein, but rather utilize Watson-Crick (WC) base-pairing rules to recognize the target RNA and modulate gene expression. Antisense oligonucleotides (ASOs) present a powerful therapeutic approach to treat disorders triggered by genetic alterations. ASOs recognize the cognate site on the target RNA to alter gene expression. Nine single-stranded ASOs have been approved for clinical use and several candidates are in late-stage clinical trials for both rare and common diseases. Several chemical modifications, including phosphorothioates, locked nucleic acid, phosphorodiamidate, morpholino, and peptide nucleic acids (PNAs), have been investigated for efficient RNA targeting. PNAs are synthetic DNA mimics where the deoxyribose phosphate backbone is replaced by N-(2-aminoethyl)-glycine units. The neutral pseudopeptide backbone of PNAs contributes to enhanced binding affinity and high biological stability. PNAs hybridize with the complementary site in the target RNA and act by a steric hindrance--based mechanism. In the last three decades, various PNA designs, chemical modifications, and delivery strategies have been explored to demonstrate their potential as an effective and safe RNA-targeting platform. This review covers the advances in PNA-mediated targeting of coding and noncoding RNAs for a myriad of therapeutic applications.
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Affiliation(s)
- Sai Pallavi Pradeep
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Shipra Malik
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Frank J Slack
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
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19
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Kato TA. Nontraditional Method for Telomere Staining by PNA Probes. Methods Mol Biol 2023; 2519:111-116. [PMID: 36066716 DOI: 10.1007/978-1-0716-2433-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The standard FISH uses DNA probes to hybridize to the designated complementary strands. This is DNA-DNA interaction, and it usually takes much longer time to obtain detectable signals compared to other reactions such as immunochemical reactions and simple chemical reactions. Certain proteins bind to specific DNA sequences and regulate the biological function of DNA. These DNA-binding proteins have specific domains to interact with single- or double-stranded DNA. Some of telomere proteins apparently bind to telomere sequence and form nucleoprotein complex to protect chromosome ends. Using telomere PNA probes, probes can be accumulated at the telomere sites in a non-hybridization manner. This chapter introduces nontraditional PNA telomere staining protocol without DNA-DNA hybridization to visualize telomere locations on metaphase chromosomes.
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Affiliation(s)
- Takamitsu A Kato
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.
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20
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Yokoi Y, Kawabuchi Y, Zulmajdi AA, Tanaka R, Shibata T, Muraoka T, Mori T. Cell-Penetrating Peptide-Peptide Nucleic Acid Conjugates as a Tool for Protein Functional Elucidation in the Native Bacterium. Molecules 2022; 27:molecules27248944. [PMID: 36558072 PMCID: PMC9788395 DOI: 10.3390/molecules27248944] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Approximately 30% or more of the total proteins annotated from sequenced bacteria genomes are annotated as hypothetical or uncharacterized proteins. However, elucidation on the function of these proteins is hindered by the lack of simple and rapid screening methods, particularly with novel or hard-to-transform bacteria. In this report, we employed cell-penetrating peptide (CPP) -peptide nucleotide acid (PNA) conjugates to elucidate the function of such uncharacterized proteins in vivo within the native bacterium. Paenibacillus, a hard-to-transform bacterial genus, was used as a model. Two hypothetical genes showing amino acid sequence similarity to ι-carrageenases, termed cgiA and cgiB, were identified from the draft genome of Paenibacillus sp. strain YYML68, and CPP-PNA probes targeting the mRNA of the acyl carrier protein gene, acpP, and the two ι-carrageenase candidate genes were synthesized. Upon direct incubation of CPP-PNA targeting the mRNA of the acpP gene, we successfully observed growth inhibition of strain YYML68 in a concentration-dependent manner. Similarly, both the function of the candidate ι-carrageenases were also inhibited using our CPP-PNA probes allowing for the confirmation and characterization of these hypothetical proteins. In summary, we believe that CPP-PNA conjugates can serve as a simple and efficient alternative approach to characterize proteins in the native bacterium.
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Affiliation(s)
- Yasuhito Yokoi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi 184-8588, Tokyo, Japan
| | - Yugo Kawabuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi 184-8588, Tokyo, Japan
| | - Abdullah Adham Zulmajdi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi 184-8588, Tokyo, Japan
| | - Reiji Tanaka
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurima-machiya-cho, Tsu-shi 514-8507, Mie, Japan
| | - Toshiyuki Shibata
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurima-machiya-cho, Tsu-shi 514-8507, Mie, Japan
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi 184-8588, Tokyo, Japan
| | - Tetsushi Mori
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi 184-8588, Tokyo, Japan
- Correspondence:
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21
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Emehiser RG, Dhuri K, Shepard C, Karmakar S, Bahal R, Hrdlicka PJ. Serine-γPNA, Invader probes, and chimeras thereof: three probe chemistries that enable sequence-unrestricted recognition of double-stranded DNA. Org Biomol Chem 2022; 20:8714-8724. [PMID: 36285843 PMCID: PMC9707317 DOI: 10.1039/d2ob01567f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2023]
Abstract
Three probe chemistries are evaluated with respect to thermal denaturation temperatures, UV-Vis and fluorescence characteristics, recognition of complementary and mismatched DNA hairpin targets, and recognition of chromosomal DNA targets in the context of non-denaturing fluorescence in situ hybridization (nd-FISH) experiments: (i) serine-γPNAs (SγPNAs), i.e., single-stranded peptide nucleic acid (PNA) probes that are modified at the γ-position with (R)-hydroxymethyl moieties, (ii) Invader probes, i.e., DNA duplexes modified with +1 interstrand zippers of 2'-O-(pyren-1-yl)methyl-RNA monomers, a molecular arrangement that results in a violation of the neighbor exclusion principle, and (iii) double-stranded chimeric SγPNAs:Invader probes, i.e., duplexes between complementary SγPNA and Invader strands, which are destabilized due to the poor compatibility between intercalators and PNA:DNA duplexes. Invader probes resulted in efficient, highly specific, albeit comparatively slow recognition of the model DNA hairpin targets. Recognition was equally efficient and faster with the single-stranded SγPNA probes but far less specific, whilst the double-stranded chimeric SγPNAs:Invader probes displayed recognition characteristics that were intermediate of the parent probes. All three probe chemistries demonstrated the capacity to target chromosomal DNA in nd-FISH experiments, with Invader probes resulting in the most favorable and consistent characteristics (signals in >90% of interphase nuclei against a low background and no signal in negative control experiments). These probe chemistries constitute valuable additions to the molecular toolbox needed for DNA-targeting applications.
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Affiliation(s)
| | - Karishma Dhuri
- Pharmaceutical Sciences, University of Connecticut, Storrs, CT-06269, USA
| | - Caroline Shepard
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA.
| | - Saswata Karmakar
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA.
| | - Raman Bahal
- Pharmaceutical Sciences, University of Connecticut, Storrs, CT-06269, USA
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22
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Castañeda-Ramírez GS, López-Guillén G, Aguilar-Marcelino L, Siu-Rivas A, Cruz-López L. Insecticidal effect of metabolites identified in edible mushrooms against Rhyssomatus nigerrimus Fahraeus. BRAZ J BIOL 2022; 84:e264786. [PMID: 36287529 DOI: 10.1590/1519-6984.264786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023] Open
Abstract
Excessive use of insecticides has led to resistance of some pathogenic organisms (nematodes, bacteria and fungi), environmental contamination, and the presence of hazardous residues. Therefore, the aim of the present study was to evaluate synthetic metabolites derived from previous studies with edible mushrooms against the soybean weevil Rhyssomatus nigerrimus Fahraeus (Curculonidae) because of the relevance of pest control in an economically important crop. Furthermore, this is one of the first studies where edible fungal molecules are evaluated for the control of these insects. Initially, two in vitro tests (toxic effect and immersion) were evaluated against R. nigerrimus. In these tests, sensitivity and viability were determined in the 2% Tween control in water. For these two tests, the synthetic metabolites pentadecanoic acid (PNA), palmitic acid (PMA), stearic acid (STA), linoleic acid (LNA), β-sitosterol (βT) were evaluated individually as well as in combinations, "the fraction of standards (E1)". Based on the results obtained, the dip test was selected to evaluate the mixtures of two standards (1. PMA + βT, 2. PMA + PNA, 3. PMA + LNA, 4. PMA + STA, 5. STA + βT, 6. STA + PNA, 7. STA + LNA, 8. PNA + βT, 9. PNA + LNA, 10. LNA + βT), three (1. PNA + βT + LNA, 2. PNA + βT + STA, 3. STA + LNA + PNA and 4. STA + LNA + βT) and four (PNA, βT, LNA and STA). The results showed that the mixture of three standards caused a higher percentage of mortality relative to the control group: l. PNA + βT + LNA and 2. PNA + βT + STA with 54.44 and 48% mortality of R. nigerrimus insects exposed for 15 days. These results show the importance of evaluating mixtures of molecules against R. nigerrimus.
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Affiliation(s)
- G S Castañeda-Ramírez
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias - INIFAP, Campo Experimental Rosario Izapa, Tuxtla Chico, Chiapas, México
| | - G López-Guillén
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias - INIFAP, Campo Experimental Rosario Izapa, Tuxtla Chico, Chiapas, México
| | - L Aguilar-Marcelino
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, INIFAP, Jiutepec, Morelos, México
| | - A Siu-Rivas
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias - INIFAP, Campo Experimental Rosario Izapa, Tuxtla Chico, Chiapas, México
| | - L Cruz-López
- El Colegio de la Frontera Sur, Tapachula, Chiapas, México
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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.)
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24
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Abstract
Peptide nucleic acids (PNAs) are charge-neutral polyamide oligomers having extremely favorable thermal stability and high affinity to cell membranes when coupled with cationic cell-penetrating peptides (CPPs), as well as the encouraging antisense and antigene activity in cell-free systems. The study of the mechanical properties of short PNA molecules is rare both in experiments and theoretical calculations. Here, we studied the microscopic structures and elastic properties; namely, persistence length, stretch modulus, twist-stretch coupling, and structural crookedness of double-stranded PNA (dsPNA) and their hybrid derivatives using all-atom MD simulation and compared them with those of double-stranded DNA (dsDNA) and double-stranded RNA (dsRNA). The stretch modulus of the dsPNA is found to be ∼160 pN, an order of magnitude lower than that of dsDNA and smaller than dsRNA, respectively. Similarly, the persistence length of dsPNA is found to be ∼35 nm, significantly smaller than those of dsDNA and dsRNA. The PNA-DNA and PNA-RNA hybrid duplexes have elastic properties lying between that of dsPNA and dsDNA/dsRNA. We argue that the neutral backbones of the PNA make it less stiff than dsDNA and dsRNA molecules. Measurement of structural crookedness and principal component analysis additionally support the bending flexibility of dsPNA. Detailed analysis of the helical-rise coupled to helical-twist indicates that the PNA-DNA hybrid over-winds like dsDNA, while PNA-PNA and PNA-RNA unwind like dsRNA upon stretching. Because of the highly flexible nature of PNA, it can bind other biomolecules by adopting a wide range of conformations and is believed to be crucial for future nanobiotechnology research studies.
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Affiliation(s)
- Khadka B Chhetri
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
- Department of Physics, Prithvinarayan Campus, Tribhuvan University, Nepal
| | - Akshara Sharma
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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25
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Munyaradzi O, Rundell S, Bong D. Impact of bPNA Backbone Structural Constraints and Composition on Triplex Hybridization with DNA. Chembiochem 2022; 23:e202100707. [PMID: 35167719 PMCID: PMC9136932 DOI: 10.1002/cbic.202100707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/18/2022] [Indexed: 11/07/2022]
Abstract
We report herein a study on the impact of bifacial peptide nucleic acid (bPNA) amino acid composition and backbone modification on DNA binding. A series of bPNA backbone variants with identical net charge were synthesized to display either 4 or 6 melamine (M) bases. These bases form thymine-melamine-thymine (TMT) base-triples, resulting in triplex hybrid stem structures with T-rich DNAs. Analyses of 6 M bPNA-DNA hybrids suggested that hybrid stability was linked to amino acid secondary structure propensities, prompting a more detailed study in shorter 4 M bPNAs. We synthesized 4 M bPNAs predisposed to adopt helical secondary structure via helix-turn nucleation in 7-residue bPNAs using double-click covalent stapling. Generally, hybrid stability improved upon stapling, but amino acid composition had a more significant effect. We also pursued an alternative strategy for bPNA structural preorganization by incorporation of residues with strong backbone amide conformational preferences such as 4R- and 4S-fluoroprolines. Notably, these derivatives exhibited an additional improvement in hybrid stability beyond both unsubstituted proline bPNA analogues and the helically patterned bPNAs. Overall, these findings demonstrate the tunability of bPNA-DNA hybrid stability through bPNA backbone structural propensities and amino acid composition.
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Affiliation(s)
- Oliver Munyaradzi
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio, 43210, USA
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio, 43210, USA
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio, 43210, USA
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26
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Cesaro E, Falanga AP, Catapano R, Greco F, Romano S, Borbone N, Pastore A, Marzano M, Chiurazzi F, D’Errico S, Piccialli G, Oliviero G, Costanzo P, Grosso M. Exploring a peptide nucleic acid-based antisense approach for CD5 targeting in chronic lymphocytic leukemia. PLoS One 2022; 17:e0266090. [PMID: 35358273 PMCID: PMC8970396 DOI: 10.1371/journal.pone.0266090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
We herein report an innovative antisense approach based on Peptide Nucleic Acids (PNAs) to down-modulate CD5 expression levels in chronic lymphocytic leukemia (CLL). Using bioinformatics tools, we selected a 12-mer tract of the CD5 mRNA as the molecular target and synthesized the complementary and control PNA strands bearing a serine phosphate dipeptide tail to enhance their water solubility and bioavailability. The specific recognition of the 12-mer DNA strand, corresponding to the target mRNA sequence by the complementary PNA strand, was confirmed by non-denaturing polyacrylamide gel electrophoresis, thermal difference spectroscopy, circular dichroism (CD), and CD melting studies. Cytofluorimetric assays and real-time PCR analysis demonstrated the downregulation of CD5 expression due to incubation with the anti-CD5 PNA at RNA and protein levels in Jurkat cell line and peripheral blood mononuclear cells from B-CLL patients. Interestingly, we also observed that transfection with the anti-CD5 PNA increases apoptotic response induced by fludarabine in B-CLL cells. The herein reported results suggest that PNAs could represent a potential candidate for the development of antisense therapeutic agents in CLL.
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MESH Headings
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukocytes, Mononuclear
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/pharmacology
- Peptide Nucleic Acids/chemistry
- RNA, Messenger/genetics
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Affiliation(s)
- Elena Cesaro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
| | | | - Rosa Catapano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
| | - Francesca Greco
- Department of Pharmacy, University of Naples Federico II, Napoli, Italy
| | - Simona Romano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Napoli, Italy
- ISBE-IT, University of Naples Federico II, Napoli, Italy
| | - Arianna Pastore
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
| | - Maria Marzano
- Department of Pharmacy, University of Naples Federico II, Napoli, Italy
| | - Federico Chiurazzi
- Department of Clinical and Experimental Medicine, Division of Hematology, University of Naples Federico II, Napoli, Italy
| | - Stefano D’Errico
- Department of Pharmacy, University of Naples Federico II, Napoli, Italy
| | - Gennaro Piccialli
- Department of Pharmacy, University of Naples Federico II, Napoli, Italy
- ISBE-IT, University of Naples Federico II, Napoli, Italy
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
- ISBE-IT, University of Naples Federico II, Napoli, Italy
- * E-mail:
| | - Paola Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
| | - Michela Grosso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
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27
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Tarvirdipour S, Skowicki M, Schoenenberger CA, Palivan CG. Peptide-Assisted Nucleic Acid Delivery Systems on the Rise. Int J Mol Sci 2021; 22:9092. [PMID: 34445799 PMCID: PMC8396486 DOI: 10.3390/ijms22169092] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 12/12/2022] Open
Abstract
Concerns associated with nanocarriers' therapeutic efficacy and side effects have led to the development of strategies to advance them into targeted and responsive delivery systems. Owing to their bioactivity and biocompatibility, peptides play a key role in these strategies and, thus, have been extensively studied in nanomedicine. Peptide-based nanocarriers, in particular, have burgeoned with advances in purely peptidic structures and in combinations of peptides, both native and modified, with polymers, lipids, and inorganic nanoparticles. In this review, we summarize advances on peptides promoting gene delivery systems. The efficacy of nucleic acid therapies largely depends on cell internalization and the delivery to subcellular organelles. Hence, the review focuses on nanocarriers where peptides are pivotal in ferrying nucleic acids to their site of action, with a special emphasis on peptides that assist anionic, water-soluble nucleic acids in crossing the membrane barriers they encounter on their way to efficient function. In a second part, we address how peptides advance nanoassembly delivery tools, such that they navigate delivery barriers and release their nucleic acid cargo at specific sites in a controlled fashion.
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Affiliation(s)
- Shabnam Tarvirdipour
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland; (S.T.); (M.S.)
- Department of Biosystem Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Michal Skowicki
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland; (S.T.); (M.S.)
- NCCR-Molecular Systems Engineering, BPR1095, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Cora-Ann Schoenenberger
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland; (S.T.); (M.S.)
- NCCR-Molecular Systems Engineering, BPR1095, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Cornelia G. Palivan
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland; (S.T.); (M.S.)
- NCCR-Molecular Systems Engineering, BPR1095, Mattenstrasse 24a, 4058 Basel, Switzerland
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28
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Scognamiglio PL, Platella C, Napolitano E, Musumeci D, Roviello GN. From Prebiotic Chemistry to Supramolecular Biomedical Materials: Exploring the Properties of Self-Assembling Nucleobase-Containing Peptides. Molecules 2021; 26:3558. [PMID: 34200901 PMCID: PMC8230524 DOI: 10.3390/molecules26123558] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022] Open
Abstract
Peptides and their synthetic analogs are a class of molecules with enormous relevance as therapeutics for their ability to interact with biomacromolecules like nucleic acids and proteins, potentially interfering with biological pathways often involved in the onset and progression of pathologies of high social impact. Nucleobase-bearing peptides (nucleopeptides) and pseudopeptides (PNAs) offer further interesting possibilities related to their nucleobase-decorated nature for diagnostic and therapeutic applications, thanks to their reported ability to target complementary DNA and RNA strands. In addition, these chimeric compounds are endowed with intriguing self-assembling properties, which are at the heart of their investigation as self-replicating materials in prebiotic chemistry, as well as their application as constituents of innovative drug delivery systems and, more generally, as novel nanomaterials to be employed in biomedicine. Herein we describe the properties of nucleopeptides, PNAs and related supramolecular systems, and summarize some of the most relevant applications of these systems.
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Affiliation(s)
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
- Istituto di Biostrutture e Bioimmagini IBB-CNR, via Tommaso De Amicis 95, I-80145 Naples, Italy
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29
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Schwach J, Kolobynina K, Brandstetter K, Gerlach M, Ochtrop P, Helma J, Hackenberger CPR, Harz H, Cardoso MC, Leonhardt H, Stengl A. Site-Specific Antibody Fragment Conjugates for Reversible Staining in Fluorescence Microscopy. Chembiochem 2021; 22:1205-1209. [PMID: 33207032 PMCID: PMC8048457 DOI: 10.1002/cbic.202000727] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/17/2020] [Indexed: 12/16/2022]
Abstract
Antibody conjugates have taken a great leap forward as tools in basic and applied molecular life sciences that was enabled by the development of chemoselective reactions for the site-specific modification of proteins. Antibody-oligonucleotide conjugates combine the antibody's target specificity with the reversible, sequence-encoded binding properties of oligonucleotides like DNAs or peptide nucleic acids (PNAs), allowing sequential imaging of large numbers of targets in a single specimen. In this report, we use the Tub-tag® technology in combination with Cu-catalyzed azide-alkyne cycloaddition for the site-specific conjugation of single DNA and PNA strands to an eGFP-binding nanobody. We show binding of the conjugate to recombinant eGFP and subsequent sequence-specific annealing of fluorescently labelled imager strands. Furthermore, we reversibly stain eGFP-tagged proteins in human cells, thus demonstrating the suitability of our conjugation strategy to generate antibody-oligonucleotides for reversible immunofluorescence imaging.
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Affiliation(s)
- Jonathan Schwach
- Ludwig-Maximilians-Universität MünchenDepartment of Biology II, Human Biology and BioImaging82152Planegg-MartinsriedGermany
| | - Ksenia Kolobynina
- Technical University of DarmstadtDepartment of Biology, Cell Biology and EpigeneticsSchnittspahnstr. 1064287DarmstadtGermany
| | - Katharina Brandstetter
- Ludwig-Maximilians-Universität MünchenDepartment of Biology II, Human Biology and BioImaging82152Planegg-MartinsriedGermany
| | - Marcus Gerlach
- Tubulis GmbH, BioSysMButenandtstrasse 181377MunichGermany
| | - Philipp Ochtrop
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Department Chemical BiologyRobert-Rössle-Strasse 1013125BerlinGermany
| | - Jonas Helma
- Tubulis GmbH, BioSysMButenandtstrasse 181377MunichGermany
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Department Chemical BiologyRobert-Rössle-Strasse 1013125BerlinGermany
- Humboldt Universität zu BerlinDepartment of ChemistryBrook-Taylor-Strasse 212489BerlinGermany
| | - Hartmann Harz
- Ludwig-Maximilians-Universität MünchenDepartment of Biology II, Human Biology and BioImaging82152Planegg-MartinsriedGermany
| | - M. Cristina Cardoso
- Technical University of DarmstadtDepartment of Biology, Cell Biology and EpigeneticsSchnittspahnstr. 1064287DarmstadtGermany
| | - Heinrich Leonhardt
- Ludwig-Maximilians-Universität MünchenDepartment of Biology II, Human Biology and BioImaging82152Planegg-MartinsriedGermany
| | - Andreas Stengl
- Ludwig-Maximilians-Universität MünchenDepartment of Biology II, Human Biology and BioImaging82152Planegg-MartinsriedGermany
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30
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Barkowsky G, Kreikemeyer B, Patenge N. Validation of Suitable Carrier Molecules and Target Genes for Antisense Therapy Using Peptide-Coupled Peptide Nucleic Acids (PNAs) in Streptococci. Methods Mol Biol 2021; 2136:339-345. [PMID: 32430835 DOI: 10.1007/978-1-0716-0467-0_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Antisense peptide nucleic acids (PNAs) targeting genes involved in metabolism or virulence are a possible means to treat infections or to investigate pathogenic bacteria. Potential targets include essential genes, virulence factor genes, or antibiotic resistance genes. For efficient cellular uptake, PNAs can be coupled to cell-penetrating peptides (CPPs). CPPs are peptides that serve as molecular transporters and are characterized by a comparably low cytotoxicity. So far, there is only limited information about CPPs that mediate PNA uptake by Gram-positive bacteria. Here, we describe two methods to identify suitable CPP-antisense PNA conjugates, novel carrier molecules, and efficient target genes for streptococcal species and to evaluate their antimicrobial efficiency.
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Affiliation(s)
- Gina Barkowsky
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Nadja Patenge
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany.
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31
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Topham CM, Smith JC. Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases. J Comput Aided Mol Des 2021; 35:355-369. [PMID: 33624202 DOI: 10.1007/s10822-021-00375-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. In geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T-A and U-A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.
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Affiliation(s)
- Christopher M Topham
- Molecular Forces Consulting, 24 Avenue Jacques Besse, 81500, Lavaur, France.
- Computational Molecular Biophysics, IWR Der Universität Heidelberg, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany.
- Center for Molecular Biophysics, University of Tennessee / Oak Ridge National Laboratory, P.O.Box 2008, Oak Ridge, TN, 37831-6309, USA.
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA.
| | - Jeremy C Smith
- Computational Molecular Biophysics, IWR Der Universität Heidelberg, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany
- Center for Molecular Biophysics, University of Tennessee / Oak Ridge National Laboratory, P.O.Box 2008, Oak Ridge, TN, 37831-6309, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA
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32
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Zheng H, Botos I, Clausse V, Nikolayevskiy H, Rastede E, Fouz M, Mazur S, Appella D. Conformational constraints of cyclopentane peptide nucleic acids facilitate tunable binding to DNA. Nucleic Acids Res 2021; 49:713-725. [PMID: 33406227 PMCID: PMC7826248 DOI: 10.1093/nar/gkaa1249] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 12/03/2020] [Accepted: 12/15/2020] [Indexed: 12/28/2022] Open
Abstract
We report a series of synthetic, nucleic acid mimics with highly customizable thermodynamic binding to DNA. Incorporation of helix-promoting cyclopentanes into peptide nucleic acids (PNAs) increases the melting temperatures (Tm) of PNA+DNA duplexes by approximately +5°C per cyclopentane. Sequential addition of cyclopentanes allows the Tm of PNA + DNA duplexes to be systematically fine-tuned from +5 to +50°C compared with the unmodified PNA. Containing only nine nucleobases and an equal number of cyclopentanes, cpPNA-9 binds to complementary DNA with a Tm around 90°C. Additional experiments reveal that the cpPNA-9 sequence specifically binds to DNA duplexes containing its complementary sequence and functions as a PCR clamp. An X-ray crystal structure of the cpPNA-9-DNA duplex revealed that cyclopentanes likely induce a right-handed helix in the PNA with conformations that promote DNA binding.
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Affiliation(s)
- Hongchao Zheng
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Room 404, Bethesda, MD 20892, USA
| | - Istvan Botos
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Victor Clausse
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Room 404, Bethesda, MD 20892, USA
| | - Herman Nikolayevskiy
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Room 404, Bethesda, MD 20892, USA
| | - Elizabeth E Rastede
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Room 404, Bethesda, MD 20892, USA
| | - Munira F Fouz
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Room 404, Bethesda, MD 20892, USA
| | - Sharlyn J Mazur
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Room 404, Bethesda, MD 20892, USA
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33
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Abstract
Cyclopentane modified FIT-PNA (cpFIT-PNA) probes are reported as highly emissive RNA sensors with the highest reported brightness for FIT-PNAs. Compared to FIT-PNAs, cpFIT-PNAs have improved mismatch discrimination for several pyrimidine-pyrimidine single nucleotide variants (SNVs).
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Affiliation(s)
- Odelia Tepper
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 91120, Israel.
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34
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Higashi SL, Rozi N, Hanifah SA, Ikeda M. Supramolecular Architectures of Nucleic Acid/Peptide Hybrids. Int J Mol Sci 2020; 21:E9458. [PMID: 33322664 PMCID: PMC7763079 DOI: 10.3390/ijms21249458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022] Open
Abstract
Supramolecular architectures that are built artificially from biomolecules, such as nucleic acids or peptides, with structural hierarchical orders ranging from the molecular to nano-scales have attracted increased attention in molecular science research fields. The engineering of nanostructures with such biomolecule-based supramolecular architectures could offer an opportunity for the development of biocompatible supramolecular (nano)materials. In this review, we highlighted a variety of supramolecular architectures that were assembled from both nucleic acids and peptides through the non-covalent interactions between them or the covalently conjugated molecular hybrids between them.
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Affiliation(s)
- Sayuri L. Higashi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan;
| | - Normazida Rozi
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.R.); (S.A.H.)
| | - Sharina Abu Hanifah
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.R.); (S.A.H.)
| | - Masato Ikeda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan;
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Institute for Glyco-Core Research (iGCORE), Gifu University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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35
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Abstract
Peptide nucleic acid (PNA) forms a triple helix with double-stranded RNA (dsRNA) stabilized by a hydrogen-bonding zipper formed by PNA's backbone amides (N-H) interacting with RNA phosphate oxygens. This hydrogen-bonding pattern is enabled by the matching ∼5.7 Å spacing (typical for A-form dsRNA) between PNA's backbone amides and RNA phosphate oxygens. We hypothesized that extending the PNA's backbone by one -CH2 - group might bring the distance between PNA amide groups closer to 7 Å, which is favourable for hydrogen bonding to the B-form dsDNA phosphate oxygens. Extension of the PNA backbone was expected to selectively stabilize PNA-DNA triplexes compared to PNA-RNA. To test this hypothesis, we synthesized triplex-forming PNAs that had the pseudopeptide backbones extended by an additional -CH2 - group in three different positions. Isothermal titration calorimetry measurements of the binding affinity of these extended PNA analogues for the matched dsDNA and dsRNA showed that, contrary to our structural reasoning, extending the PNA backbone at any position had a strong negative effect on triplex stability. Our results suggest that PNAs might have an inherent preference for A-form-like conformations when binding double-stranded nucleic acids. It appears that the original six-atom-long PNA backbone is an almost perfect fit for binding to A-form nucleic acids.
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Affiliation(s)
- Vipin Kumar
- Department of Chemistry, Binghamton University Binghamton, New York, 13902, USA
| | - Nikita Brodyagin
- Department of Chemistry, Binghamton University Binghamton, New York, 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University Binghamton, New York, 13902, USA
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36
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Boback K, Bacchi K, O’Neill S, Brown S, Dorsainvil J, Smith-Carpenter JE. Impact of C-Terminal Chemistry on Self-Assembled Morphology of Guanosine Containing Nucleopeptides. Molecules 2020; 25:E5493. [PMID: 33255230 PMCID: PMC7727710 DOI: 10.3390/molecules25235493] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/16/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023] Open
Abstract
Herein, we report the design and characterization of guanosine-containing self-assembling nucleopeptides that form nanosheets and nanofibers. Through spectroscopy and microscopy analysis, we propose that the peptide component of the nucleopeptide drives the assembly into β-sheet structures with hydrogen-bonded guanosine forming additional secondary structures cooperatively within the peptide framework. Interestingly, the distinct supramolecular morphologies are driven not by metal cation responsiveness common to guanine-based materials, but by the C-terminal peptide chemistry. This work highlights the structural diversity of self-assembling nucleopeptides and will help advance the development of applications for these supramolecular guanosine-containing nucleopeptides.
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Affiliation(s)
| | | | | | | | | | - Jillian E. Smith-Carpenter
- Department of Chemistry and Biochemistry, Fairfield University, 1073 N. Benson Rd, Fairfield, CT 06824, USA; (K.B.); (K.B.); (S.O.); (S.B.); (J.D.)
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37
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Patel R, Sarma S, Shukla A, Parmar P, Goswami D, Saraf M. Walking through the wonder years of artificial DNA: peptide nucleic acid. Mol Biol Rep 2020; 47:8113-8131. [PMID: 32990905 DOI: 10.1007/s11033-020-05819-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 09/04/2020] [Indexed: 11/26/2022]
Abstract
Peptide Nucleic Acid (PNA) serves as an artificial functional analog of DNA. Being immune to enzymatic degradation and possessing strong affinity towards DNA and RNA, it is an ideal candidate for many medical and biotechnological applications that are of antisense and antigene in nature. PNAs are anticipated to have its application in DNA and RNA detection as well as quantification, to serve as antibacterial and antiviral agents, and silencing gene for developing anticancer strategies. Although, their restricted entry in both eukaryotic and prokaryotic cells limit their applications. In addition, aggregation of PNA in storage containers reduces the quality and quantity of functional PNA that makes it inadequate for their mass production and storage. To overcome these limitations, researchers have modified PNA either by the addition of diverse functional groups at various loci on its backbone, or by synthesizing chimeras with other moieties associated with various delivery agents that aids their entry into the cell. Here, this review article summarizes few of the structural modifications that are performed with PNA, methods used to improve their cellular uptake and shedding light on the applications of PNA in various prospects in biological sciences.
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Affiliation(s)
- Rohit Patel
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Sameera Sarma
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Arpit Shukla
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Paritosh Parmar
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Dweipayan Goswami
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Meenu Saraf
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India.
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38
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Abstract
Light-activated ("caged") oligonucleotides provide a strategy for modulating the activity of antisense oligos, siRNA, miRNA, aptamers, DNAzymes, and mRNA-capturing probes with high spatiotemporal resolution. However, the near-UV and visible wavelengths that promote these bond-breaking reactions poorly penetrate living tissue, which limits some biological applications. To address this issue, we describe the first example of a protease-activated oligonucleotide probe, capable of reporting on caspase-3 during cellular apoptosis. The 2'-F RNA-peptide substrate-peptide nucleic acid (PNA) hairpin structure was generated in 30% yield in a single bioconjugation step.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - James H Eberwine
- Department of Pharmacology, University of Pennsylvania, 38 John Morgan Building, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104-6084, United States
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
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39
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Höger GA, Wiegand M, Worbs B, Diederichsen U. Membrane-Associated Nucleobase-Functionalized β-Peptides (β-PNAs) Affecting Membrane Support and Lipid Composition. Chembiochem 2020; 21:2599-2603. [PMID: 32346953 PMCID: PMC7540700 DOI: 10.1002/cbic.202000172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/26/2020] [Indexed: 11/18/2022]
Abstract
Protein-membrane interactions are essential to maintain membrane integrity and control membrane morphology and composition. Cytoskeletal proteins in particular are known to interact to a high degree with lipid bilayers and to line the cytoplasmic side of the plasma membrane with an extensive network structure. In order to gain a better mechanistical understanding of the protein-membrane interplay and possible membrane signaling, we started to develop a model system based on β-peptide nucleic acids (β-PNAs). These β-peptides are known to form stable hydrogen-bonded aggregates due to their helical secondary structure, which serve to pre-organize the attached nucleobases. After optimization of the β-PNA solid-phase peptide synthesis and validation of helix formation, the ability of the novel β-PNAs to dimerize and interact with lipid bilayers was investigated by both fluorescence and circular dichroism spectroscopy. It was shown that duplex formation occurs rapidly and with high specificity and could also be detected on the surfaces of the lipid bilayers. Hereby, the potential of a β-PNA-based peptide system to mimic membrane-associated protein networks could be demonstrated.
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Affiliation(s)
- Geralin A. Höger
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität GöttingenTammannstraße 237077GöttingenGermany
| | - Markus Wiegand
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität GöttingenTammannstraße 237077GöttingenGermany
| | - Brigitte Worbs
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität GöttingenTammannstraße 237077GöttingenGermany
| | - Ulf Diederichsen
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität GöttingenTammannstraße 237077GöttingenGermany
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40
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Farrera-Soler L, Daguer JP, Barluenga S, Vadas O, Cohen P, Pagano S, Yerly S, Kaiser L, Vuilleumier N, Winssinger N. Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma. PLoS One 2020; 15:e0238089. [PMID: 32903266 PMCID: PMC7480855 DOI: 10.1371/journal.pone.0238089] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/10/2020] [Indexed: 01/09/2023] Open
Abstract
A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) is the source of a current pandemic (COVID-19) with devastating consequences in public health and economic stability. Using a peptide array to map the antibody response of plasma from healing patients (12) and heathy patients (6), we identified three immunodominant linear epitopes, two of which correspond to key proteolytic sites on the spike protein (S1/S2 and S2') known to be critical for cellular entry. We show biochemical evidence that plasma positive for the epitope adjacent to the S1/S2 cleavage site inhibits furin-mediated proteolysis of spike.
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Affiliation(s)
- Lluc Farrera-Soler
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Jean-Pierre Daguer
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Oscar Vadas
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Patrick Cohen
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Sabrina Pagano
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Sabine Yerly
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Laurent Kaiser
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
- Division of Infectious Diseases¸ Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Nicolas Vuilleumier
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
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41
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Kelly IB, Fletcher RB, McBride JR, Weiss SM, Duvall CL. Tuning Composition of Polymer and Porous Silicon Composite Nanoparticles for Early Endosome Escape of Anti-microRNA Peptide Nucleic Acids. ACS Appl Mater Interfaces 2020; 12:39602-39611. [PMID: 32805967 PMCID: PMC8356247 DOI: 10.1021/acsami.0c05827] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Porous silicon nanoparticles (PSNPs) offer tunable pore structure and easily modified surface chemistry, enabling high loading capacity for drugs with diverse chemicophysical properties. While PSNPs are also cytocompatible and degradable, PSNP integration into composite structures can be a useful approach to enhance carrier colloidal stability, drug-cargo loading stability, and endosome escape. Here, we explored PSNP polymer composites formed by coating of oxidized PSNPs with a series of poly[ethylene glycol-block-(dimethylaminoethyl methacrylate-co-butyl methacrylate)] (PEG-DB) diblock copolymers with varied molar ratios of dimethylaminoethyl methacrylate (D) and butyl methacrylate (B) in the random copolymer block. We screened and developed PSNP composites specifically toward intracellular delivery of microRNA inhibitory peptide nucleic acids (PNA). While a copolymer with 50 mol % B (50B) is optimal for early endosome escape in free polymer form, its pH switch was suppressed when it was formed into 50B polymer-coated PSNP composites (50BCs). We demonstrate that a lower mol % B (30BC) is the ideal PEG-DB composition for PSNP/PEG-DB nanocomposites based on having both the highest endosome disruption potential and miR-122 inhibitory activity. At a 1 mM PNA dose, 30BCs facilitated more potent inhibition of miR-122 in comparison to 40BC (p = 0.0095), 50BC (p < 0.0001), or an anti-miR-122 oligonucleotide delivered with the commercial transfection reagent Fugene 6. Using a live cell galectin 8-based endosome disruption reporter, 30BCs had greater endosomal escape than 40BCs and 50BCs within 2 h after treatment, suggesting that rapid endosome escape correlates with higher intracellular bioactivity. This study provides new insight on the polymer structure-dependent effects on stability, endosome escape, and cargo intracellular bioavailability for endosomolytic polymer-coated PSNPs.
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Affiliation(s)
- Isom B Kelly
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - R Brock Fletcher
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - James R McBride
- Vanderbilt Institute of Nanoscale Science and Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Sharon M Weiss
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Craig L Duvall
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
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42
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Altrichter Y, Seitz O. Simultaneous Targeting of Two Master Regulators of Apoptosis with Dual-Action PNA- and DNA-Peptide Conjugates. Bioconjug Chem 2020; 31:1928-1937. [PMID: 32567853 PMCID: PMC7583637 DOI: 10.1021/acs.bioconjchem.0c00284] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/21/2020] [Indexed: 01/31/2023]
Abstract
Conjugation of peptides with oligonucleotides offers opportunities for combining the strengths of both biopolymer classes. Herein, we show that the combination of a peptide-based module with an antisense oligonucleotide module provides for enhancements of potency and a widened scope of cell delivery options. The peptide unit comprises a Smac mimetic compound (SMCs) which antagonizes the action of inhibitor of apoptosis proteins (IAPs) frequently overexpressed in cancer cells. To counteract SMC resistance, the antisense module downregulates the cellular FLICE-like protein (c-FLIP), a master regulator of the extrinsic apoptosis pathway. We compared c-FLIP antisense units based on oligophosphorothioate (PSO) and peptide nucleic acid (PNA) architectures. Owing to the ease of synthesis, PNA conjugates combined with a cell penetrating peptide (CPP) offer a seemingly ideal solution for cell delivery of dual activity agents. However, our investigations revealed that such congeners have to be handled with care to avoid off-target effects. By contrast, PSO conjugates provided a more robust and specific activity for inducing death of SMC-resistant A549 cells due to a simultaneous activation of caspases and c-FLIP knockdown. We show that lipofection is a convenient approach for delivery of peptide-PSO conjugates into cells. The results highlight that the combination of the peptide and the DNA world confers properties inaccessible by the unconjugated components.
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Affiliation(s)
- Yannic Altrichter
- Department of Chemistry, Humboldt-Universität
zu Berlin, 12489 Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität
zu Berlin, 12489 Berlin, Germany
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43
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Movilli J, Kolkman RW, Rozzi A, Corradini R, Segerink LI, Huskens J. Increasing the Sensitivity of Electrochemical DNA Detection by a Micropillar-Structured Biosensing Surface. Langmuir 2020; 36:4272-4279. [PMID: 32239946 PMCID: PMC7191753 DOI: 10.1021/acs.langmuir.0c00144] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/06/2020] [Indexed: 06/01/2023]
Abstract
The available active surface area and the density of probes immobilized on this surface are responsible for achieving high specificity and sensitivity in electrochemical biosensors that detect biologically relevant molecules, including DNA. Here, we report the design of gold-coated, silicon micropillar-structured electrodes functionalized with modified poly-l-lysine (PLL) as an adhesion layer to concomitantly assess the increase in sensitivity with the increase of the electrochemical area and control over the probe density. By systematically reducing the center-to-center distance between the pillars (pitch), denser micropillar arrays were formed at the electrode, resulting in a larger sensing area. Azido-modified peptide nucleic acid (PNA) probes were click-reacted onto the electrode interface, exploiting PLL with appended oligo(ethylene glycol) (OEG) and dibenzocyclooctyne (DBCO) moieties (PLL-OEG-DBCO) for antifouling and probe binding properties, respectively. The selective electrochemical sandwich assay formation, composed of consecutive hybridization steps of the target complementary DNA (cDNA) and reporter DNA modified with the electroactive ferrocene functionality (rDNA-Fc), was monitored by quartz crystal microbalance. The DNA detection performance of micropillared electrodes with different pitches was evaluated by quantifying the cyclic voltammetric response of the surface-confined rDNA-Fc. By decrease of the pitch of the pillar array, the area of the electrode was enhanced by up to a factor 10.6. A comparison of the electrochemical data with the geometrical area of the pillared electrodes confirmed the validity of the increased sensitivity of the DNA detection by the design of the micropillar array.
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Affiliation(s)
- Jacopo Movilli
- Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Ruben W Kolkman
- Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Technical Medical Centre, Max Planck Institute for Complex Fluid Dynamics, University of Twente, 7522 NB Enschede, The Netherlands
| | - Andrea Rozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Loes I Segerink
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Technical Medical Centre, Max Planck Institute for Complex Fluid Dynamics, University of Twente, 7522 NB Enschede, The Netherlands
| | - Jurriaan Huskens
- Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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44
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López-Andarias J, Saarbach J, Moreau D, Cheng Y, Derivery E, Laurent Q, González-Gaitán M, Winssinger N, Sakai N, Matile S. Cell-Penetrating Streptavidin: A General Tool for Bifunctional Delivery with Spatiotemporal Control, Mediated by Transport Systems Such as Adaptive Benzopolysulfane Networks. J Am Chem Soc 2020; 142:4784-4792. [PMID: 32109058 PMCID: PMC7307903 DOI: 10.1021/jacs.9b13621] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Indexed: 12/17/2022]
Abstract
In this report, cell-penetrating streptavidin (CPS) is introduced to exploit the full power of streptavidin-biotin biotechnology in cellular uptake. For this purpose, transporters, here cyclic oligochalcogenides (COCs), are covalently attached to lysines of wild-type streptavidin. This leaves all four biotin binding sites free for at least bifunctional delivery. To maximize the standards of the quantitative evaluation of cytosolic delivery, the recent chloroalkane penetration assay (CAPA) is coupled with automated high content (HC) imaging, a technique that combines the advantages of fluorescence microscopy and flow cytometry. According to the resulting HC-CAPA, cytosolic delivery of CPS equipped with four benzopolysulfanes was the best among all tested CPSs, also better than the much smaller TAT peptide, the original cell-penetrating peptide from HIV. HaloTag-GFP fusion proteins expressed on mitochondria were successfully targeted using CPS carrying two different biotinylated ligands, HaloTag substrates or anti-GFP nanobodies, interfaced with peptide nucleic acids, flipper force probes, or fluorescent substrates. The delivered substrates could be released from CPS into the cytosol through desthiobiotin-biotin exchange. These results validate CPS as a general tool which enables unrestricted use of streptavidin-biotin biotechnology in cellular uptake.
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Affiliation(s)
- Javier López-Andarias
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Jacques Saarbach
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Dimitri Moreau
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Yangyang Cheng
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Emmanuel Derivery
- MRC
Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Quentin Laurent
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Marcos González-Gaitán
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Nicolas Winssinger
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Naomi Sakai
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
| | - Stefan Matile
- School
of Chemistry and Biochemistry and National Centre of Competence in
Research (NCCR) Chemical Biology, University
of Geneva, Geneva 1211, Switzerland
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45
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Zhao Y, Sarkar A, Wang X. Peptide nucleic acid based tension sensor for cellular force imaging with strong DNase resistance. Biosens Bioelectron 2020; 150:111959. [PMID: 31929090 PMCID: PMC6961813 DOI: 10.1016/j.bios.2019.111959] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/06/2019] [Accepted: 12/08/2019] [Indexed: 11/17/2022]
Abstract
DNA is a versatile biomaterial with well-defined mechanical and biochemical properties. It has been broadly adopted to synthesize tension sensors that calibrate and visualize cellular forces at the cell-matrix interface. Here we showed that DNA-based tension sensors are vulnerable to deoxyribonucleases (DNases) which cells may express on cell membrane or secret to the culture environment. These DNases can damage the sensors, lower signal-to-noise ratio or even produce false signal in cellular force imaging. To address this issue, we tested peptide nucleic acid (PNA), chemically modified RNA and their hybrids with DNA as alternative biomaterials for constructing tension sensors. Four duplexes: double-stranded DNA (dsDNA), PNA/DNA, dsRNA (modified RNA) and PNA/RNA, were tested and evaluated in terms of DNase resistance, cellular force imaging ability and material robustness. The results showed that all PNA/DNA, dsRNA and PNA/RNA exhibited strong resistance to both soluble DNase I and membrane-bound DNase on cells. However, PNA/RNA-based tension sensor had low signal-to-noise ratio in cellular force imaging, and dsRNA-based tension sensor exhibited strong non-specific signal unrelated to cellular forces. Only PNA/DNA-based tension sensor reported cellular forces with highest signal-to-noise ratio and specificity. Collectively, we confirmed that PNA/DNA hybrid is an accessible material for the synthesis of DNase-resistant tension sensor that retains the force-reporting capability and remains stable in DNase-expressing cells. This new class of tension sensors will broaden the application of tension sensors in the study of cell mechanobiology.
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Affiliation(s)
- Yuanchang Zhao
- Department of Physics and Astronomy, Iowa State University, Ames, IA, 50011, USA
| | - Anwesha Sarkar
- Department of Physics and Astronomy, Iowa State University, Ames, IA, 50011, USA
| | - Xuefeng Wang
- Department of Physics and Astronomy, Iowa State University, Ames, IA, 50011, USA; Molecular, Cellular, and Developmental Biology interdepartmental program, Iowa State University, Ames, IA, 50011, USA.
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46
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Takase S, Miyagawa K, Ikeda H. Label-Free Detection of Zeptomol miRNA via Peptide Nucleic Acid Hybridization Using Novel Cyclic Voltammetry Method. Sensors (Basel) 2020; 20:s20030836. [PMID: 32033197 PMCID: PMC7038687 DOI: 10.3390/s20030836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 11/26/2022]
Abstract
To harness the applicability of microribonucleic acid (miRNA) as a cancer biomarker, the detection sensitivity of serum miRNA needs to be improved. This study evaluated the detection sensitivity of miRNA hybridization using cyclic voltammograms (CVs) and microelectrode array chips modified with peptide nucleic acid (PNA) probes and 6-hydroxy-1-hexanethiol. We investigated the PNA probe modification pattern on array chips using fluorescently labeled cDNA. The pattern was not uniformly spread over the working electrode (WE) and had a one-dimensional swirl-like pattern. Accordingly, we established a new ion-channel sensor model wherein the WE is negatively biased through the conductive π–π stacks of the PNA/DNA duplexes. This paper discusses the mechanism underlying the voltage shift in the CV curves based on the electric double-layer capacitance. Additionally, the novel hybridization evaluation parameter ΔE is introduced. Compared to conventional evaluation using oxidation current changes, ΔE was more sensitive. Using ΔE and a new hybridization system for ultrasmall amounts of aqueous solutions (as low as 35 pL), 140 zeptomol label-free miRNA were detected without polymerase chain reaction (PCR) amplification at an adequate sensitivity. Herein, the differences in the target molar amount and molar concentration are elucidated from the viewpoint of hybridization sensitivity.
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Affiliation(s)
- Shintaro Takase
- New Business Management Division, Management Planning H.Q., YOKOWO CO. LTD., 5-11, Takinogawa 7-Chome, Kita-ku, Tokyo 114-8515, Japan;
- Correspondence: ; Tel.: +81-90-8313-9108; Fax: +81-3-3962-6001
| | - Kouta Miyagawa
- New Business Management Division, Management Planning H.Q., YOKOWO CO. LTD., 5-11, Takinogawa 7-Chome, Kita-ku, Tokyo 114-8515, Japan;
| | - Hisafumi Ikeda
- Department of Environmental Science and Education, Faculty of Home Economics, Tokyo Kasei University, 1-18-1 Kaga, Itabashi City, Tokyo 173-8602, Japan;
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47
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Zheng X, Liu Q, Li M, Feng W, Yang H, Kong J. Dual atom transfer radical polymerization for ultrasensitive electrochemical DNA detection. Bioelectrochemistry 2020; 133:107462. [PMID: 32058273 DOI: 10.1016/j.bioelechem.2020.107462] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 12/13/2022]
Abstract
Atom transfer radical polymerization as a form of controlled/living radical polymerization is particularly attractive. In this work, dual atom transfer radical polymerization (ATRP) is reported for ultrasensitive DNA detection. Firstly, a peptide nucleic acid (PNA) modified with a thiol group was self-assembled on an electrode surface to capture target DNA (TDNA). The initiator of the first ATRP (ATRP-1), α-bromoisobutyric acid (BIBA), was linked to forming PNA/DNA heteroduplexes via coordination of Zr4+. The polymer chain formed by the monomer of ATRP-1 (2-(2-bromoisobutyryloxy) ethyl methacrylate, BIEM) was also one of initiators of the second ATRP (eATRP-2). The other initiator of eATRP-2 was additional BIBA. ATRP-1 involves activator regeneration by electron transfer (ARGET) ATRP, regulated via excess reducing agent. eATRP-2 is electrochemically mediated ATRP which can control the polymerization via an appropriate applied potential. Compared with one ATRP, more monomers of eATRP-2 modified with ferrocene are attached to electrode surface. Under optimal conditions, this dual ATRP strategy provides a low limit of detection (25 aM, ~150 molecules) with satisfactory selectivity and stability. Importantly, this strategy presents a useful prospect for the field of biomolecule detection.
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Affiliation(s)
- Xiaoke Zheng
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou 450046, PR China
| | - Qianrui Liu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Manman Li
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou 450046, PR China
| | - Weisheng Feng
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou 450046, PR China.
| | - Huaixia Yang
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou 450046, PR China
| | - Jinming Kong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China.
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48
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Oyaghire SN, Quijano E, Piotrowski-Daspit AS, Saltzman WM, Glazer PM. Poly(Lactic-co-Glycolic Acid) Nanoparticle Delivery of Peptide Nucleic Acids In Vivo. Methods Mol Biol 2020; 2105:261-281. [PMID: 32088877 PMCID: PMC7199467 DOI: 10.1007/978-1-0716-0243-0_17] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Many important biological applications of peptide nucleic acids (PNAs) target nucleic acid binding in eukaryotic cells, which requires PNA translocation across at least one membrane barrier. The delivery challenge is further exacerbated for applications in whole organisms, where clearance mechanisms rapidly deplete and/or deactivate exogenous agents. We have demonstrated that nanoparticles (NPs) composed of biodegradable polymers can encapsulate and release PNAs (alone or with co-reagents) in amounts sufficient to mediate desired effects in vitro and in vivo without deleterious reactions in the recipient cell or organism. For example, poly(lactic-co-glycolic acid) (PLGA) NPs can encapsulate and deliver PNAs and accompanying reagents to mediate gene editing outcomes in cells and animals, or PNAs alone to target oncogenic drivers in cells and correct cancer phenotypes in animal models. In this chapter, we provide a primer on PNA-induced gene editing and microRNA targeting-the two PNA-based biotechnological applications where NPs have enhanced and/or enabled in vivo demonstrations-as well as an introduction to the PLGA material and detailed protocols for formulation and robust characterization of PNA/DNA-laden PLGA NPs.
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Affiliation(s)
- Stanley N. Oyaghire
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - Elias Quijano
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | | | - W. Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Chemical & Environmental Engineering, Yale University, New Haven, CT, USA
- Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Peter M. Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
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Abstract
Antisense PNA-peptide conjugates targeting essential bacterial genes have shown interesting potential for discovery of novel precision antibiotics. In this context, the minimal inhibitory concentration (MIC) assay is used to assess and compare the antimicrobial activity of natural as well as synthetic antimicrobial compounds. Here, we describe the determination of the minimal inhibitory concentration of peptide-PNA conjugates against Escherichia coli. This method can be expanded to include minimal bactericidal concentration (MBC) determination and kill-curve kinetics.
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Affiliation(s)
- Lise Goltermann
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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50
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Liu B, Sun H, Li L, Zhang J, Kong J, Zhang X. A dual signal amplification strategy combining thermally initiated SI-RAFT polymerization and DNA-templated silver nanoparticles for electrochemical determination of DNA. Mikrochim Acta 2019; 187:35. [PMID: 31820104 DOI: 10.1007/s00604-019-3912-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/11/2019] [Indexed: 10/25/2022]
Abstract
A highly sensitive method is described for determination of DNA. It is based on dual signal amplification, viz. (a)DNA-templated metal deposition, and (b) thermally initiated surface-initiated reversible addition-fragmentation chain transfer (SI-RAFT) polymerization. A peptide nucleic acid (PNA) with a terminal thiol group was grasped onto a gold electrode by self-assembly. The modified electrode serves as a probe to selectively capture target DNA (tDNA). In the next step, Zr(IV) ions are bound to the phosphate groups of the tDNA. A chain-transfer agent (CTA) for thermally initiated SI-RAFT polymerization, 4-cyano-4-(phenylcarbonothioylthio)pentanoic acid (CPAD), was immobilized on tDNA by conjugation of the carboxy group to Zr(IV) ions. Subsequently, numerous monomers of glycosyloxyethyl methacrylate (GEMA) were connected to the CPAD by thermally initiated SI-RAFT polymerization with azobisisobutyronitrile (AIBN) serving as the free-radical thermal initiator. Afterwards, hydroxyl groups of the GEMA were oxidized to aldehyde groups reacting with sodium periodate, and silver nanoparticles were further introduced on the surface of electrode via "silver mirror reaction". This results in a large electrochemical signal amplification. Under optimized conditions, the electrochemical signal (best measured at a working potential of 0 V vs. SCE (KCl; 3 M)) increases linearly with the logarithm of tDNA concentration in the 10 to 106 aM concentration range. The detection limit is as low as 5.6 aM (~34 molecules in a 10 μL sample). This is lower by factors between 2 and 1800 times than detection limits of most other ultra-sensitive electrochemical DNA assays. Graphical abstractSchematic representation of a dual signal amplification strategy combining thermally initiated surface-initiated reversible addition-fragmentation chain transfer polymerization (SI-RAFT) and DNA-templated silver nanoparticles for electrochemical determination of DNA.
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Affiliation(s)
- Bang Liu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu, 210094, People's Republic of China
- Laboratory of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, No.100, Shizi Street, Hongshan Road, Qixia District, Nanjing, 210028, Jiangsu Province, People's Republic of China
| | - Haobo Sun
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu, 210094, People's Republic of China
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, China
| | - Jian Zhang
- Laboratory of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, No.100, Shizi Street, Hongshan Road, Qixia District, Nanjing, 210028, Jiangsu Province, People's Republic of China.
| | - Jinming Kong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu, 210094, People's Republic of China.
| | - Xueji Zhang
- School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, Guangdong, 518060, People's Republic of China
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