1
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The role of Nucleic Acid Mimics (NAMs) on FISH-based techniques and applications for microbial detection. Microbiol Res 2022; 262:127086. [PMID: 35700584 DOI: 10.1016/j.micres.2022.127086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 01/07/2023]
Abstract
Fluorescent in situ hybridization (FISH) is a powerful tool that for more than 30 years has allowed to detect and quantify microorganisms as well as to study their spatial distribution in three-dimensional structured environments such as biofilms. Throughout these years, FISH has been improved in order to face some of its earlier limitations and to adapt to new research objectives. One of these improvements is related to the emergence of Nucleic Acid Mimics (NAMs), which are now employed as alternatives to the DNA and RNA probes that have been classically used in FISH. NAMs such as peptide and locked nucleic acids (PNA and LNA) have provided enhanced sensitivity and specificity to the FISH technique, as well as higher flexibility in terms of applications. In this review, we aim to cover the state-of-the-art of the different NAMs and explore their possible applications in FISH, providing a general overview of the technique advancement in the last decades.
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2
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Suparpprom C, Vilaivan T. Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications. RSC Chem Biol 2022; 3:648-697. [PMID: 35755191 PMCID: PMC9175113 DOI: 10.1039/d2cb00017b] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022] Open
Abstract
Peptide nucleic acid or PNA is a synthetic DNA mimic that contains a sequence of nucleobases attached to a peptide-like backbone derived from N-2-aminoethylglycine. The semi-rigid PNA backbone acts as a scaffold that arranges the nucleobases in a proper orientation and spacing so that they can pair with their complementary bases on another DNA, RNA, or even PNA strand perfectly well through the standard Watson-Crick base-pairing. The electrostatically neutral backbone of PNA contributes to its many unique properties that make PNA an outstanding member of the xeno-nucleic acid family. Not only PNA can recognize its complementary nucleic acid strand with high affinity, but it does so with excellent specificity that surpasses the specificity of natural nucleic acids and their analogs. Nevertheless, there is still room for further improvements of the original PNA in terms of stability and specificity of base-pairing, direction of binding, and selectivity for different types of nucleic acids, among others. This review focuses on attempts towards the rational design of new generation PNAs with superior performance by introducing conformational constraints such as a ring or a chiral substituent in the PNA backbone. A large collection of conformationally rigid PNAs developed during the past three decades are analyzed and compared in terms of molecular design and properties in relation to structural data if available. Applications of selected modified PNA in various areas such as targeting of structured nucleic acid targets, supramolecular scaffold, biosensing and bioimaging, and gene regulation will be highlighted to demonstrate how the conformation constraint can improve the performance of the PNA. Challenges and future of the research in the area of constrained PNA will also be discussed.
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Affiliation(s)
- Chaturong Suparpprom
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
| | - Tirayut Vilaivan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
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3
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Giraud T, Hoschtettler P, Pickaert G, Averlant-Petit MC, Stefan L. Emerging low-molecular weight nucleopeptide-based hydrogels: state of the art, applications, challenges and perspectives. NANOSCALE 2022; 14:4908-4921. [PMID: 35319034 DOI: 10.1039/d1nr06131c] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Over the last twenty years, low-molecular weight gelators and, in particular, peptide-based hydrogels, have drawn great attention from scientists thanks to both their inherent advantages in terms of properties and their high modularity (e.g., number and nature of the amino acids). These supramolecular hydrogels originate from specific peptide self-assembly processes that can be driven, modulated and optimized via specific chemical modifications brought to the peptide sequence. Among them, the incorporation of nucleobases, another class of biomolecules well-known for their abilities to self-assemble, has recently appeared as a new promising and burgeoning approach to finely design supramolecular hydrogels. In this minireview, we would like to highlight the interest, high potential, applications and perspectives of these innovative and emerging low-molecular weight nucleopeptide-based hydrogels.
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Affiliation(s)
- Tristan Giraud
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
| | | | | | | | - Loic Stefan
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
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4
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Giraud T, Bouguet-Bonnet S, Stébé MJ, Richaudeau L, Pickaert G, Averlant-Petit MC, Stefan L. Co-assembly and multicomponent hydrogel formation upon mixing nucleobase-containing peptides. NANOSCALE 2021; 13:10566-10578. [PMID: 34100504 DOI: 10.1039/d1nr02417e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Peptide-based hydrogels are physical gels formed through specific supramolecular self-assembling processes, leading to ordered nanostructures which constitute the water entrapping scaffold of the soft material. Thanks to the inherent properties of peptides, these hydrogels are highly considered in the biomedical domain and open new horizons in terms of application in advanced therapies and biotechnologies. The use of one, and only one, native peptide to formulate a gel is by far the most reported approach to design such materials, but suffers from several limitations, including in terms of mechanical properties. To improve peptide-based hydrogels interest and give rise to innovative properties, several strategies have been proposed in the recent years, and the development of multicomponent peptide-based hydrogels appears as a promising and relevant strategy. Indeed, mixing two or more compounds to develop new materials is a much-used approach that has proven its effectiveness in a wide variety of domains, including polymers, composites and alloys. While still limited to a handful of examples, we would like to report herein on the formulation and the comprehensive study of multicomponent hybrid DNA-nucleobase/peptide-based hydrogels using a multiscale approach based on a large panel of analytical techniques (i.e., rheometry, proton relaxometry, SAXS, electronic microscopy, infrared, circular dichroism, fluorescence, Thioflavin T assays). Among the six multicomponent systems studied, the results highlight the synergistic role of the presence of the two complementary DNA-nucleobases (i.e., adenine/thymine and guanine/cytosine) on the co-assembling process from structural (e.g., morphology of the nanoobjects) to physicochemical (e.g., kinetics of formation, fluorescence properties) and mechanical (e.g., stiffness, resistance to external stress) properties. All the data confirm the relevance of the multicomponent peptide-based approach in the design of innovative hydrogels and bring another brick in the wall of the understanding of these complex and promising systems.
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Affiliation(s)
- Tristan Giraud
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
| | | | | | | | | | | | - Loic Stefan
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
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5
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Ditmangklo B, Sittiwong W, Boddaert T, Vilaivan T, Aitken DJ. Pyrrolidinyl peptide nucleic acids bearing hydroxy-modified cyclobutane building blocks: Synthesis and binding properties. Biopolymers 2021; 112:e23459. [PMID: 34101824 DOI: 10.1002/bip.23459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 12/19/2022]
Abstract
The conformationally constrained pyrrolidinyl PNA with a dipeptide consisting of an alternating nucleobase-modified D-proline and a cyclic β-amino acid "spacer" exhibited improved nucleic acid binding properties compared to the original PNA. The pyrrolidinyl PNA with the four-membered ring spacer (1S,2S)-2-aminocyclobutanecarboxylic acid (acbcPNA) are among the best performed members of the pyrrolidinyl PNA family. However, these PNA suffer some limitations such as aqueous solubility and non-specific interactions due to their extreme hydrophobicity. In the present work, a hydroxy group is introduced onto the cyclobutane ring spacer of the acbcPNA with the aim of decreasing its hydrophobicity. To this end, a Fmoc/tBu ether-protected 4-hydroxy-2-aminocyclobutanecarboxylic acid building block was synthesized and resolved by chiral HPLC. Each enantiomer was used to synthesize the hydroxy-modified acbcPNA employing Fmoc solid-phase peptide synthesis. DNA/RNA binding studies indicated that the introduction of the hydroxy group to the acbcPNA decreases the binding affinity toward complementary DNA and RNA while maintaining the sequence and directional specificity of unmodified acbcPNA. The hydrophobicity of the hydroxy-modified acbcPNA decreased with the number of hydroxy groups added as indicated by the decrease in the logP values. Only two modifications were sufficient to decrease the logP by an order of magnitude without excessively lowering the binding affinity nor the specificity. This work thus demonstrated that the specific structural modifications for this type of PNA model can be performed in a modular fashion, which paves the way toward the future realization of improving hydrophilicity and nucleic acid binding affinity as well as specificity.
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Affiliation(s)
- Boonsong Ditmangklo
- Department of Chemistry, Faculty of Science, Organic Synthesis Research Unit, Chulalongkorn University, Bangkok, Thailand
| | - Wantanee Sittiwong
- Department of Chemistry, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Pathum Thani, Thailand
| | | | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Organic Synthesis Research Unit, Chulalongkorn University, Bangkok, Thailand
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6
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Saikia N, Taha M, Pandey R. Molecular insights on the dynamic stability of peptide nucleic acid functionalized carbon and boron nitride nanotubes. Phys Chem Chem Phys 2021; 23:219-228. [PMID: 33325925 DOI: 10.1039/d0cp05759b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The strategic approaches to the design of self-assembled hybrids of biomolecular systems at the nanoscale such as deoxyribonucleic acid (DNA) with single-wall carbon nanotubes (CNTs) and their structural analog, boron nitride nanotubes (BNNTs), rely on understanding how biomolecules recognize and mediate intermolecular interactions with the nanomaterial's surface. In this paper, we consider peptide nucleic acid (PNA), which is a synthetic analog of DNA, and investigate its interaction with a zigzag CNT and BNNT of similar diameter. The results based on the molecular dynamics method find that PNA provides definitive contrasts in the adsorption on the tubular surface in aqueous solution: it prefers to wrap along the circumferential direction on a (11,0) CNT, whereas it binds along the axial direction adopting an extended configuration on a (11,0) BNNT. Moreover, gas-phase Monte Carlo simulations show a dependence of the nanotube diameter on the calculated adsorption energy, with BNNTs exhibiting higher adsorption energy compared to CNTs, and the largest-diameter (25,0) tubular configuration facilitates encapsulation of PNA rather than PNA being adsorbed on its sidewall. The results are expected to be of relevance in the design of novel PNA-based archetypal hybrid materials for nanoscale applications in health-related areas including biosensing.
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Affiliation(s)
- Nabanita Saikia
- Department of Physics, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA.
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7
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Giraud T, Bouguet-Bonnet S, Marchal P, Pickaert G, Averlant-Petit MC, Stefan L. Improving and fine-tuning the properties of peptide-based hydrogels via incorporation of peptide nucleic acids. NANOSCALE 2020; 12:19905-19917. [PMID: 32985645 DOI: 10.1039/d0nr03483e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Peptide self-assemblies have attracted intense research interest over the last few decades thanks to their implications in key biological processes (e.g., amyloid formation) and their use in biotechnological and (bio)material fields. In particular, peptide-based hydrogels have been highly considered as high potential supramolecular materials in the biomedical domain and open new horizons in terms of applications. To further understand their self-assembly mechanisms and to optimize their properties, several strategies have been proposed with the modification of the constituting amino acid chains via, per se, the introduction of d-amino acids, halogenated amino acids, pseudopeptide bonds, or other chemical moieties. In this context, we report herein on the incorporation of DNA-nucleobases into their peptide nucleic acid (PNA) forms to develop a new series of hybrid nucleopeptides. Thus, depending on the nature of the nucleobase (i.e., thymine, cytosine, adenine or guanine), the physicochemical and mechanical properties of the resulting hydrogels can be significantly improved and fine-tuned with, for instance, drastic enhancements of both the gel stiffness (up to 70-fold) and the gel resistance to external stress (up to 40-fold), and the generation of both thermo-reversible and uncommon red-edge excitation shift (REES) properties. To decipher the actual role of each PNA moiety in the self-assembly processes, the induced modifications from the molecular to the macroscopic scales are studied thanks to the multiscale approach based on a large panel of analytical techniques (i.e., rheology, NMR relaxometry, TEM, thioflavin T assays, FTIR, CD, fluorescence, NMR chemical shift index). Thus, such a strategy provides new opportunities to adapt and fit hydrogel properties to the intended ones and pushes back the limits of supramolecular materials.
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Affiliation(s)
- Tristan Giraud
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
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8
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Singh KRB, Sridevi P, Singh RP. Potential applications of peptide nucleic acid in biomedical domain. ENGINEERING REPORTS : OPEN ACCESS 2020; 2:e12238. [PMID: 32838227 PMCID: PMC7404446 DOI: 10.1002/eng2.12238] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 05/03/2023]
Abstract
Peptide Nucleic Acid (PNA) are DNA/RNA synthetic analogs with 2-([2-aminoethyl] amino) acetic acid backbone. They partake unique antisense and antigene properties, just due to its inhibitory effect on transcription and translation; they also undergo complementary binding to RNA/DNA with high affinity and specificity. Hence, to date, many methods utilizing PNA for diagnosis and treatment of various diseases namely cancer, AIDS, human papillomavirus, and so on, have been designed and developed. They are being used widely in polymerase chain reaction modulation/mutation, fluorescent in-situ hybridization, and in microarray as a probe; they are also utilized in many in-vitro and in-vivo assays and for developing micro and nano-sized biosensor/chip/array technologies. Earlier reviews, focused only on PNA properties, structure, and modifications related to diagnostics and therapeutics; our review emphasizes on PNA properties and synthesis along with its potential applications in diagnosis and therapeutics. Furthermore, prospects in biomedical applications of PNAs are being discussed in depth.
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Affiliation(s)
- Kshitij RB Singh
- Department of Biotechnology, Faculty of ScienceIndira Gandhi National Tribal UniversityAmarkantakMadhya Pradesh484887India
| | - Parikipandla Sridevi
- Department of Biotechnology, Faculty of ScienceIndira Gandhi National Tribal UniversityAmarkantakMadhya Pradesh484887India
| | - Ravindra Pratap Singh
- Department of Biotechnology, Faculty of ScienceIndira Gandhi National Tribal UniversityAmarkantakMadhya Pradesh484887India
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9
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Basavalingappa V, Bera S, Xue B, Azuri I, Tang Y, Tao K, Shimon LJW, Sawaya MR, Kolusheva S, Eisenberg DS, Kronik L, Cao Y, Wei G, Gazit E. Mechanically rigid supramolecular assemblies formed from an Fmoc-guanine conjugated peptide nucleic acid. Nat Commun 2019; 10:5256. [PMID: 31748568 PMCID: PMC6868146 DOI: 10.1038/s41467-019-13250-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 10/23/2019] [Indexed: 01/25/2023] Open
Abstract
The variety and complexity of DNA-based structures make them attractive candidates for nanotechnology, yet insufficient stability and mechanical rigidity, compared to polyamide-based molecules, limit their application. Here, we combine the advantages of polyamide materials and the structural patterns inspired by nucleic-acids to generate a mechanically rigid fluorenylmethyloxycarbonyl (Fmoc)-guanine peptide nucleic acid (PNA) conjugate with diverse morphology and photoluminescent properties. The assembly possesses a unique atomic structure, with each guanine head of one molecule hydrogen bonded to the Fmoc carbonyl tail of another molecule, generating a non-planar cyclic quartet arrangement. This structure exhibits an average stiffness of 69.6 ± 6.8 N m-1 and Young's modulus of 17.8 ± 2.5 GPa, higher than any previously reported nucleic acid derived structure. This data suggests that the unique cation-free "basket" formed by the Fmoc-G-PNA conjugate can serve as an attractive component for the design of new materials based on PNA self-assembly for nanotechnology applications.
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Affiliation(s)
- Vasantha Basavalingappa
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Santu Bera
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Bin Xue
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, 210093, Nanjing, People's Republic of China
| | - Ido Azuri
- Department of Materials and Interfaces, Weizmann Institute of Science, 76100, Rehovoth, Israel
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, 200433, Shanghai, People's Republic of China
| | - Kai Tao
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Linda J W Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, 76100, Rehovoth, Israel
| | - Michael R Sawaya
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sofiya Kolusheva
- Ilse Katz Institute for Nanotechnology, Ben Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - David S Eisenberg
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Leeor Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science, 76100, Rehovoth, Israel
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, 210093, Nanjing, People's Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, 200433, Shanghai, People's Republic of China
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel.
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10
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Carloni LE, Mohnani S, Bonifazi D. Synthesis of 3,5-Disubstituted Isoxazoles through a 1,3-Dipolar Cycloaddition Reaction between Alkynes and Nitrile Oxides Generated from O
-Silylated Hydroxamic Acids. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Laure-Elie Carloni
- Department of Chemistry and Namur Research College (NARC); University of Namur; Rue de Bruxelles 61 5000 Namur Belgium
| | - Stefan Mohnani
- Department of Chemistry and Namur Research College (NARC); University of Namur; Rue de Bruxelles 61 5000 Namur Belgium
| | - Davide Bonifazi
- School of Chemistry, Park Place, Main Building, CF10 3AT; Cardiff University; Cardiff Wales UK
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11
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Berger O, Gazit E. Molecular self-assembly using peptide nucleic acids. Biopolymers 2017; 108. [PMID: 27486924 DOI: 10.1002/bip.22930] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/15/2016] [Accepted: 07/25/2016] [Indexed: 12/17/2022]
Abstract
Peptide nucleic acids (PNAs) are extensively studied for the control of genetic expression since their design in the 1990s. However, the application of PNAs in nanotechnology is much more recent. PNAs share the specific base-pair recognition characteristic of DNA together with material-like properties of polyamides, both proteins and synthetic polymers, such as Kevlar and Nylon. The first application of PNA was in the form of PNA-amphiphiles, resulting in the formation of either lipid integrated structures, hydrogels or fibrillary assemblies. Heteroduplex DNA-PNA assemblies allow the formation of hybrid structures with higher stability as compared with pure DNA. A systematic screen for minimal PNA building blocks resulted in the identification of guanine-containing di-PNA assemblies and protected guanine-PNA monomer spheres showing unique optical properties. Finally, the co-assembly of PNA with thymine-like three-faced cyanuric acid allowed the assembly of poly-adenine PNA into fibers. In summary, we believe that PNAs represent a new and important family of building blocks which converges the advantages of both DNA- and peptide-nanotechnologies.
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Affiliation(s)
- Or Berger
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel.,Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, 69978, Israel
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12
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Surin M. From nucleobase to DNA templates for precision supramolecular assemblies and synthetic polymers. Polym Chem 2016. [DOI: 10.1039/c6py00480f] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In this minireview, we report on the recent advances of utilization of nucleobases and DNA as templates to achieve well-defined supramolecular polymers, synthetic polymers, and sequence-controlled polymers.
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Affiliation(s)
- Mathieu Surin
- Laboratory for Chemistry of Novel Materials
- Center for Innovation and Research in Materials and Polymers
- University of Mons – UMONS
- B-7000 Mons
- Belgium
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13
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Berger O, Adler-Abramovich L, Levy-Sakin M, Grunwald A, Liebes-Peer Y, Bachar M, Buzhansky L, Mossou E, Forsyth VT, Schwartz T, Ebenstein Y, Frolow F, Shimon LJW, Patolsky F, Gazit E. Light-emitting self-assembled peptide nucleic acids exhibit both stacking interactions and Watson-Crick base pairing. NATURE NANOTECHNOLOGY 2015; 10:353-360. [PMID: 25775151 DOI: 10.1038/nnano.2015.27] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 02/02/2015] [Indexed: 06/04/2023]
Abstract
The two main branches of bionanotechnology involve the self-assembly of either peptides or DNA. Peptide scaffolds offer chemical versatility, architectural flexibility and structural complexity, but they lack the precise base pairing and molecular recognition available with nucleic acid assemblies. Here, inspired by the ability of aromatic dipeptides to form ordered nanostructures with unique physical properties, we explore the assembly of peptide nucleic acids (PNAs), which are short DNA mimics that have an amide backbone. All 16 combinations of the very short di-PNA building blocks were synthesized and assayed for their ability to self-associate. Only three guanine-containing di-PNAs-CG, GC and GG-could form ordered assemblies, as observed by electron microscopy, and these di-PNAs efficiently assembled into discrete architectures within a few minutes. The X-ray crystal structure of the GC di-PNA showed the occurrence of both stacking interactions and Watson-Crick base pairing. The assemblies were also found to exhibit optical properties including voltage-dependent electroluminescence and wide-range excitation-dependent fluorescence in the visible region.
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Affiliation(s)
- Or Berger
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Lihi Adler-Abramovich
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Michal Levy-Sakin
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Assaf Grunwald
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Yael Liebes-Peer
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Mor Bachar
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Ludmila Buzhansky
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Estelle Mossou
- 1] Partnership for Structural Biology, Institut Laue Langevin, 71 Avenue des Martyrs, Grenoble Cedex 9 38042, France [2] Faculty of Natural Sciences, Keele University, Staffordshire ST5 5BG, UK
| | - V Trevor Forsyth
- 1] Partnership for Structural Biology, Institut Laue Langevin, 71 Avenue des Martyrs, Grenoble Cedex 9 38042, France [2] Faculty of Natural Sciences, Keele University, Staffordshire ST5 5BG, UK
| | - Tal Schwartz
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Yuval Ebenstein
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Felix Frolow
- 1] Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel [2] Daniella Rich Institute for Structural Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Linda J W Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Fernando Patolsky
- 1] School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Israel [2] Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Ehud Gazit
- 1] Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel [2] Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Ramat Aviv 69978, Israel
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14
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He X, Wu DF, Ji J, Ling WP, Chen XL, Chen YX. Ultrasound microbubble-carried PNA targeting to c-myc mRNA inhibits the proliferation of rabbit iliac arterious smooth muscle cells and intimal hyperplasia. Drug Deliv 2015; 23:2482-2487. [PMID: 25726989 DOI: 10.3109/10717544.2015.1014947] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE To elucidate the transfected effect of albumin ultrasound microbubbles carrying peptide nucleic acids (PNAs) against c-myc gene to the vascular walls and their effect on the intimal proliferation induced by vascular denudation. METHODS A rabbit iliac artery intimal proliferation model was constructed and PNA against c-myc mRNA was designed and synthesized and was added to albumin solution before ultrasound microbubbles were prepared and encapsulated in matrix of albumin. The ultrasound microbubbles carrying PNA were transfected to intima under ultrasound exposure. The transfected effect was identified by a histochemical method and the expression of c-myc was detected by in situ hybridization. The proliferation of intimal smooth muscle cells was estimated by the expression of proliferative cell nuclear antigen (PCNA) of them. The intimal area and thickness were judged morphologically for intimal hyperplasia. RESULTS The ultrasound microbubbles with PNA were successfully prepared and c-myc PNA was transfected to vascular intimal cells. The expression of c-myc and PCNA by intimal vascular smooth muscle cells (vSMCs) was inhibited significantly and the intimal thickness and area were reduced remarkably. CONCLUSION Transfection of c-myc PNA could inhibit proliferartion of vSMCs and intima in the rabbit iliac artery intimal proliferation model and the targeted transfection of albumin ultrasound microbubbles carrying PNA offers a feasible way to facilitate its access to specific cells in vivo and produce bioavailability.
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Affiliation(s)
- Xia He
- a The Department of Pathology , Shenzhen Sun Yet-Sen Cardiovascular Hospital , Shenzhen , PR China and
| | - Da-Fang Wu
- b Department of Endocrinology , 451 Hospital of PLA , Xi'an, Shanxi , PR China
| | - Jun Ji
- a The Department of Pathology , Shenzhen Sun Yet-Sen Cardiovascular Hospital , Shenzhen , PR China and
| | - Wen-Ping Ling
- a The Department of Pathology , Shenzhen Sun Yet-Sen Cardiovascular Hospital , Shenzhen , PR China and
| | - Xiao-Ling Chen
- a The Department of Pathology , Shenzhen Sun Yet-Sen Cardiovascular Hospital , Shenzhen , PR China and
| | - Yue-Xuan Chen
- a The Department of Pathology , Shenzhen Sun Yet-Sen Cardiovascular Hospital , Shenzhen , PR China and
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Manicardi A, Corradini R. Effect of chirality in gamma-PNA: PNA interaction, another piece in the picture. ARTIFICIAL DNA, PNA & XNA 2014; 5:e1131801. [PMID: 26744081 PMCID: PMC5329894 DOI: 10.1080/1949095x.2015.1131801] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 12/09/2015] [Accepted: 12/10/2015] [Indexed: 12/23/2022]
Abstract
Modification of the PNA backbone can be used to broaden their utility by introducing new functional groups. In particular, gamma-modified PNA have been found to be quite effective in a number of applications, and exhibit particularly high DNA binding affinity. The introduction of one side chain imply that the achiral backbone of PNA becomes chiral, and binding properties depend on the stereochemistry. A new paper on gamma-modified PNA by Ly and co-workers complete the existing knowledge by displaying that in binding to complementary PNA stereochemical orthogonality can be demonstrated. This opens the way to the exploitation of stereochemical features in diagnostic assays and in nanofabrication.
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Affiliation(s)
- Alex Manicardi
- Dipartimento di Chimica; University of Parma; Parma, Italy
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