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Lai Q, Chen W, Zhang Y, Liu Z. Application strategies of peptide nucleic acids toward electrochemical nucleic acid sensors. Analyst 2021; 146:5822-5835. [PMID: 34581324 DOI: 10.1039/d1an00765c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide nucleic acids (PNAs) have attracted tremendous interest in the fabrication of highly sensitive electrochemical nucleic acid biosensors due to their higher stability and increased sensitivity than common DNA probes. The neutral pseudopeptide backbone of PNAs not only makes the PNA/DNA duplexes more stable but also provides many opportunities to construct ultrasensitive nucleic acid sensors. This review presents the details of various protocols for the construction of PNA-based electrochemical nucleic acid sensors. The crucial factors, origin, and development of PNA, immobilization methods of PNA probes and signal generation mechanisms, are discussed. This review aims to provide a reference for ultrasensitive PNA electrochemical biosensor preparation.
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Affiliation(s)
- Qingteng Lai
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China.
| | - Wei Chen
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China. .,Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha 410008, China
| | - Yanke Zhang
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China.
| | - Zhengchun Liu
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China.
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Dong B, Nie K, Shi H, Yao X, Chao L, Liang B, Liu Z. Synthesis and characterization of (R)-miniPEG-containing chiral γ-peptide nucleic acids using the Fmoc strategy. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.04.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Joshi T, Patra M, Spiccia L, Gasser G. Di-heterometalation of thiol-functionalized peptide nucleic acids. ARTIFICIAL DNA, PNA & XNA 2013; 4:11-8. [PMID: 23422249 PMCID: PMC3654725 DOI: 10.4161/adna.24019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 02/14/2013] [Accepted: 02/15/2013] [Indexed: 12/21/2022]
Abstract
As a proof-of-principle, two hetero-bimetallic PNA oligomers containing a ruthenium(II) polypyridyl and a cyclopentadienyl manganese tricarbonyl complex have been prepared by serial combination of solid-phase peptide coupling and in-solution thiol chemistry. Solid-phase N-terminus attachment of Ru(II)-polypyridyl carboxylic acid derivative, C1, onto the thiol-functionalized PNA backbone (H-a-a-g-t-c-t-g-c-linker-cys-NH 2) has been performed by standard peptide coupling method. As two parallel approaches, the strong affinity of thiols for maleimide and haloacetyl group has been exploited for subsequent post-SPPS addition of cymantrene-based organometallic cores, C2 and C3. Michael-like addition and thioether ligation of thiol functionalized PNA1 (H-gly-a-a-g-t-c-t-g-c-linker-cys-NH 2) and PNA2 (C1-a-a-g-t-c-t-g-c-linker-cys-NH 2) to cymantrene maleimide and chloroacetyl derivatives, C2 and C3, respectively, has been performed. The synthesized ruthenium(II)-cymantrenyl PNA oligomers have been characterized by mass spectrometry (ESI-MS) and IR spectroscopy. The distinct Mn-CO vibrational IR stretches, between 1,924-2,074 cm (-1) , have been used as markers to confirm the presence of cymantrenyl units in the PNA sequences and the purity of the HPLC-purified PNA thioethers assessed using LC-MS.
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Affiliation(s)
- Tanmaya Joshi
- Institute of Inorganic Chemistry; University of Zurich; Zurich, Switzerland
| | - Malay Patra
- Institute of Inorganic Chemistry; University of Zurich; Zurich, Switzerland
| | - Leone Spiccia
- ARC Centre of Excellence for Electromaterials Science and School of Chemistry; Monash University; Clayton, VIC Australia
| | - Gilles Gasser
- Institute of Inorganic Chemistry; University of Zurich; Zurich, Switzerland
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Joshi T, Barbante GJ, Francis PS, Hogan CF, Bond AM, Spiccia L. Electrochemiluminescent peptide nucleic acid-like monomers containing Ru(II)-dipyridoquinoxaline and Ru(II)-dipyridophenazine complexes. Inorg Chem 2011; 50:12172-83. [PMID: 22040143 DOI: 10.1021/ic201911f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A series of Ru(II)-peptide nucleic acid (PNA)-like monomers, [Ru(bpy)(2)(dpq-L-PNA-OH)](2+) (M1), [Ru(phen)(2)(dpq-L-PNA-OH)](2+) (M2), [Ru(bpy)(2)(dppz-L-PNA-OH)](2+) (M3), and [Ru(phen)(2)(dppz-L-PNA-OH)](2+) (M4) (bpy = 2,2'-bipyridine, phen = 1,10-phenanthroline, dpq-L-PNA-OH = 2-(N-(2-(((9H-fluoren-9-yl)methoxy)carbonylamino)ethyl)-6-(dipyrido[3,2-a:2',3'-c]phenazine-11-carboxamido)hexanamido)acetic acid, dppz-L-PNA-OH = 2-(N-(2-(((9H-fluoren-9-yl) methoxy)carbonylamino)ethyl)-6-(dipyrido[3,2-f:2',3'-h]quinoxaline-2-carboxamido)acetic acid) have been synthesized and characterized by IR and (1)H NMR spectroscopy, mass spectrometry, and elemental analysis. As is typical for Ru(II)-tris(diimine) complexes, acetonitrile solutions of these complexes (M1-M4) show MLCT transitions in the 443-455 nm region and emission maxima at 618, 613, 658, and 660 nm, respectively, upon photoexcitation at 450 nm. Changes in the ligand environment around the Ru(II) center are reflected in the luminescence and electrochemical response obtained from these monomers. The emission intensity and quantum yield for M1 and M2 were found to be higher than for M3 and M4. Electrochemical studies in acetonitrile show the Ru(II)-PNA monomers to undergo a one-electron redox process associated with Ru(II) to Ru(III) oxidation. A positive shift was observed in the reversible redox potentials for M1-M4 (962, 951, 936, and 938 mV, respectively, vs Fc(0/+) (Fc = ferrocene)) in comparison with [Ru(bpy)(3)](2+) (888 mV vs Fc(0/+)). The ability of the Ru(II)-PNA monomers to generate electrochemiluminescence (ECL) was assessed in acetonitrile solutions containing tripropylamine (TPA) as a coreactant. Intense ECL signals were observed with emission maxima for M1-M4 at 622, 616, 673, and 675 nm, respectively. At an applied potential sufficiently positive to oxidize the ruthenium center, the integrated intensity for ECL from the PNA monomers was found to vary in the order M1 (62%) > M3 (60%) > M4 (46%) > M2 (44%) with respect to [Ru(bpy)(3)](2+) (100%). These findings indicate that such Ru(II)-PNA bioconjugates could be investigated as multimodal labels for biosensing applications.
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Affiliation(s)
- Tanmaya Joshi
- ARC Centre of Excellence for Electromaterials Science and School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
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Concise access to N9-mono-, N2-mono- and N2,N9-di-substituted guanines via efficient Mitsunobu reactions. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.03.118] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Janssen PGA, Meeuwenoord N, van der Marel G, Jabbari-Farouji S, van der Schoot P, Surin M, Tomović Z, Meijer EW, Schenning APHJ. ssPNA templated assembly of oligo(p-phenylenevinylene)s. Chem Commun (Camb) 2009; 46:109-11. [PMID: 20024309 DOI: 10.1039/b913307k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A single-stranded oligothymine peptide nucleic acid (PNA) was used as a template for the assembly of a chiral oligo(p-phenylenevinylene) diaminotriazine derivative (OPV) in methylcyclohexane (MCH) revealing nanostructures in which the size is controlled by the template.
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Affiliation(s)
- Pim G A Janssen
- Laboratory for Macromolecular and Organic Chemistry, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, The Netherlands.
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Poon KWC, Datta A. A rapid synthetic route to conformationally restricted [5,5]-bicyclic nucleoside-amino acid conjugates. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 27:914-30. [PMID: 18696362 DOI: 10.1080/15257770802257820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A concise synthetic route to a novel class of conformationally rigid 3',4'-cis-fused bicyclic nucleoside derivatives has been developed. The synthetic strategy and approach involves initial synthesis of a key [5,5]-bicyclic 6-aminofurofuran-2-one scaffold, employing an L-serine derived aminobutenolide as a strategically functionalized chiral template. Subsequent utilization of the carbonyl functionality of the above bicyclic lactone toward nucleobase incorporation, and linking of the resident amine functionality with appropriately protected amino acids completed the syntheses of the target bicyclic nucleoside-amino acid conjugates. Following the above route, and utilizing a combination of easily available nucleobases (4) and amino acids (4) as the two diversity elements, combinatorial synthesis of a 16-member demonstration library of the title amino acid-linked nucleosides has been accomplished.
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Affiliation(s)
- Kevin W C Poon
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045-7582, USA
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Bromley EHC, Channon K, Moutevelis E, Woolfson DN. Peptide and protein building blocks for synthetic biology: from programming biomolecules to self-organized biomolecular systems. ACS Chem Biol 2008; 3:38-50. [PMID: 18205291 DOI: 10.1021/cb700249v] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There are several approaches to creating synthetic-biological systems. Here, we describe a molecular-design approach. First, we lay out a possible synthetic-biology space, which we define with a plot of complexity of components versus divergence from nature. In this scheme, there are basic units, which range from natural amino acids to totally synthetic small molecules. These are linked together to form programmable tectons, for example, amphipathic alpha-helices. In turn, tectons can interact to give self-assembled units, which can combine and organize further to produce functional assemblies and systems. To illustrate one path through this vast landscape, we focus on protein engineering and design. We describe how, for certain protein-folding motifs, polypeptide chains can be instructed to fold. These folds can be combined to give structured complexes, and function can be incorporated through computational design. Finally, we describe how protein-based systems may be encapsulated to control and investigate their functions.
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Affiliation(s)
| | - Kevin Channon
- School of Chemistry, University
of Bristol, BS8 1TS, United Kingdom
| | | | - Derek N. Woolfson
- School of Chemistry, University
of Bristol, BS8 1TS, United Kingdom
- Department of Biochemistry, University of Bristol, BS8 1TD, United Kingdom
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Rasmussen LCV, Sperling-Petersen HU, Mortensen KK. Hitting bacteria at the heart of the central dogma: sequence-specific inhibition. Microb Cell Fact 2007; 6:24. [PMID: 17692125 PMCID: PMC1995221 DOI: 10.1186/1475-2859-6-24] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Accepted: 08/10/2007] [Indexed: 12/16/2022] Open
Abstract
An important objective in developing new drugs is the achievement of high specificity to maximize curing effect and minimize side-effects, and high specificity is an integral part of the antisense approach. The antisense techniques have been extensively developed from the application of simple long, regular antisense RNA (asRNA) molecules to highly modified versions conferring resistance to nucleases, stability of hybrid formation and other beneficial characteristics, though still preserving the specificity of the original nucleic acids. These new and improved second- and third-generation antisense molecules have shown promising results. The first antisense drug has been approved and more are in clinical trials. However, these antisense drugs are mainly designed for the treatment of different human cancers and other human diseases. Applying antisense gene silencing and exploiting RNA interference (RNAi) are highly developed approaches in many eukaryotic systems. But in bacteria RNAi is absent, and gene silencing by antisense compounds is not nearly as well developed, despite its great potential and the intriguing possibility of applying antisense molecules in the fight against multiresistant bacteria. Recent breakthrough and current status on the development of antisense gene silencing in bacteria including especially phosphorothioate oligonucleotides (PS-ODNs), peptide nucleic acids (PNAs) and phosphorodiamidate morpholino oligomers (PMOs) will be presented in this review.
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Affiliation(s)
| | - Hans Uffe Sperling-Petersen
- Laboratory of BioDesign, Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
| | - Kim Kusk Mortensen
- Laboratory of BioDesign, Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
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Silvester NC, Bushell GR, Searles DJ, Brown CL. Effect of terminal amino acids on the stability and specificity of PNA-DNA hybridisation. Org Biomol Chem 2007; 5:917-23. [PMID: 17340007 DOI: 10.1039/b615567g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of various charged or hydrophobic amino acids on the hybridisation of fully complementary and mismatch PNA-DNA duplexes was investigated via UV melting curve analysis. The results described here show that the thermal stability and binding specificity of PNA probes can be modified by conjugation to amino acids and these effects should be considered in experimental design when conjugating PNA sequences to solubility enhancing groups or cell transport peptides. Where stabilisation of a duplex is important, without there being a corresponding need for specific binding to fully complementary targets, the conjugation of multiple lysine residues to the C-terminus of PNA may be the best probe design. If, however, the key is to obtain maximum discrimination between fully complementary and mismatch targets, a replacement of glutamic acid for lysine as the routine solubility enhancing group is recommended.
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Affiliation(s)
- Nicole C Silvester
- School of Biomolecular and Physical Science, Griffith University, Nathan, Queensland 4111, Australia
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Lundin KE, Good L, Strömberg R, Gräslund A, Smith CIE. Biological activity and biotechnological aspects of peptide nucleic acid. ADVANCES IN GENETICS 2006; 56:1-51. [PMID: 16735154 DOI: 10.1016/s0065-2660(06)56001-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
During the latest decades a number of different nucleic acid analogs containing natural nucleobases on a modified backbone have been synthesized. An example of this is peptide nucleic acid (PNA), a DNA mimic with a noncyclic peptide-like backbone, which was first synthesized in 1991. Owing to its flexible and neutral backbone PNA displays very good hybridization properties also at low-ion concentrations and has subsequently attracted large interest both in biotechnology and biomedicine. Numerous modifications have been made, which could be of value for particular settings. However, the original PNA does so far perform well in many diverse applications. The high biostability makes it interesting for in vivo use, although the very limited diffusion over lipid membranes requires further modifications in order to make it suitable for treatment in eukaryotic cells. The possibility to use this nucleic acid analog for gene regulation and gene editing is discussed. Peptide nucleic acid is now also used for specific genetic detection in a number of diagnostic techniques, as well as for site-specific labeling and hybridization of functional molecules to both DNA and RNA, areas that are also discussed in this chapter.
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Affiliation(s)
- Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center Karolinska Institutet, Karolinska University Hospital, Huddinge 141 86 Stockholm, Sweden
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Tedeschi T, Sforza S, Corradini R, Marchelli R. Synthesis of new chiral PNAs bearing a dipeptide-mimic monomer with two lysine-derived stereogenic centres. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.09.157] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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