1
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Das A, Ghosh A, Kundu J, Egli M, Manoharan M, Sinha S. Synthesis and Biophysical Studies of High-Affinity Morpholino Oligomers Containing G-Clamp Analogs. J Org Chem 2023; 88:15168-15175. [PMID: 37843026 DOI: 10.1021/acs.joc.3c01658] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Successful syntheses of chlorophosphoramidate morpholino monomers containing tricyclic cytosine analogs phenoxazine, G-clamp, and G8AE-clamp were accomplished. These modified monomers were incorporated into 12-mer oligonucleotides using trityl-chemistry by an automated synthesizer. The resulting phosphorodiamidate morpholino oligomers, containing a single G-clamp, demonstrated notably higher affinity for complementary RNA and DNA compared to the unmodified oligomers under neutral and acidic conditions. The duplexes of RNA and DNA with G-clamp-modified oligomers adopt a B-type helical conformation, as evidenced by CD-spectra and show excellent base recognition properties. Binding affinities were sequence and position dependent.
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Affiliation(s)
- Arnab Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Jayanta Kundu
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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2
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Mikame Y, Yamayoshi A. Recent Advancements in Development and Therapeutic Applications of Genome-Targeting Triplex-Forming Oligonucleotides and Peptide Nucleic Acids. Pharmaceutics 2023; 15:2515. [PMID: 37896275 PMCID: PMC10609763 DOI: 10.3390/pharmaceutics15102515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/15/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Recent developments in artificial nucleic acid and drug delivery systems present possibilities for the symbiotic engineering of therapeutic oligonucleotides, such as antisense oligonucleotides (ASOs) and small interfering ribonucleic acids (siRNAs). Employing these technologies, triplex-forming oligonucleotides (TFOs) or peptide nucleic acids (PNAs) can be applied to the development of symbiotic genome-targeting tools as well as a new class of oligonucleotide drugs, which offer conceptual advantages over antisense as the antigene target generally comprises two gene copies per cell rather than multiple copies of mRNA that are being continually transcribed. Further, genome editing by TFOs or PNAs induces permanent changes in the pathological genes, thus facilitating the complete cure of diseases. Nuclease-based gene-editing tools, such as zinc fingers, CRISPR-Cas9, and TALENs, are being explored for therapeutic applications, although their potential off-target, cytotoxic, and/or immunogenic effects may hinder their in vivo applications. Therefore, this review is aimed at describing the ongoing progress in TFO and PNA technologies, which can be symbiotic genome-targeting tools that will cause a near-future paradigm shift in drug development.
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Affiliation(s)
- Yu Mikame
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyomachi, Nagasaki 852-8521, Japan
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyomachi, Nagasaki 852-8521, Japan
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3
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Park S, Kim SH, Dezhbord M, Lee EH, Jeon Y, Jung D, Gu SH, Yu C, Lee SH, Kim SC, Kim KH. Cell-permeable peptide nucleic acid antisense oligonucleotide platform targeting human betacoronaviruses. Front Microbiol 2023; 14:1258091. [PMID: 37840724 PMCID: PMC10570754 DOI: 10.3389/fmicb.2023.1258091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction Antisense oligonucleotides (ASOs) with therapeutic potential have recently been reported to target the SARS-CoV-2 genome. Peptide nucleic acids (PNAs)-based ASOs have been regarded as promising drug candidates, but intracellular delivery has been a significant obstacle. Here, we present novel modified PNAs, termed OPNAs, with excellent cell permeability that disrupt the RNA genome of SARS-CoV-2 and HCoV-OC43 by introducing cationic lipid moiety onto the nucleobase of PNA oligomer backbone. Methods HCT-8 cells and Caco-2 cells were treated with 1 μM antisense OPNAs at the time of viral challenge and the Viral RNA levels were measured by RT-qPCR three days post infection. Results NSP 14 targeting OPNA 5 and 11, reduced the viral titer to a half and OPNA 530, 531 and 533 lowered viral gene expression levels to less than 50% of control by targeting the 5' UTR region. Several modifications (oligo size and position, etc.) were introduced to enhance the efficacy of selected OPNAs. Improved OPNAs exhibited a dose-dependent reduction in viral replication and nucleoprotein (NP) protein. When a mixture of oligomers was applied to infected cells, viral titer and NP levels decreased by more than eightfold. Discussion In this study, we have developed a modified PNA ASO platform with exceptional chemical stability, high binding affinity, and cellular permeability. These findings indicate that OPNAs are a promising platform for the development of antivirals to combat future pandemic viral infections that do not require a carrier.
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Affiliation(s)
- Soree Park
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Seong Ho Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Mehrangiz Dezhbord
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Eun-Hwi Lee
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Yeasel Jeon
- OliPass Inc., Yongin, Gyeonggi, Republic of Korea
| | - Daram Jung
- OliPass Inc., Yongin, Gyeonggi, Republic of Korea
| | - Se Hun Gu
- Chem-BioTechnology Center, Advanced Defense Science & Technology Research Institute, Agency for Defense Development, Daejeon, Republic of Korea
| | - Chiho Yu
- Chem-BioTechnology Center, Advanced Defense Science & Technology Research Institute, Agency for Defense Development, Daejeon, Republic of Korea
| | - Seung Ho Lee
- Chem-BioTechnology Center, Advanced Defense Science & Technology Research Institute, Agency for Defense Development, Daejeon, Republic of Korea
| | | | - Kyun-Hwan Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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4
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Yamaji R, Nakagawa O, Kishimoto Y, Fujii A, Matsumura T, Nakayama T, Kamada H, Osawa T, Yamaguchi T, Obika S. Synthesis and physical and biological properties of 1,3-diaza-2-oxophenoxazine-conjugated oligonucleotides. Bioorg Med Chem 2022; 72:116972. [DOI: 10.1016/j.bmc.2022.116972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/26/2022]
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5
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Murase H, Nagatsugi F, Sasaki S. Development of a selective ligand for G-G mismatches of CGG repeat RNA inducing the RNA structural conversion from the G-quadruplex into a hairpin-like structure. Org Biomol Chem 2022; 20:3375-3381. [PMID: 35355034 DOI: 10.1039/d2ob00279e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The trinucleotide CGG repeat is located in the 5'-UTR of FMR1 and its abnormal expansion and formation of a noncanonical RNA structure causes fetal genetic diseases. In this study, a small molecular dimer-type ligand consisting of dual G-clamp units for the recognition of two neighboring guanines was synthesized, and the binding properties for the r(CGG) repeats were investigated. Compound 2 was confirmed to bind to the mismatch guanines in the stem region of the r(CGG) repeat hairpin. In addition, the RNase T1 assay demonstrated that 2 induced the structural conversion of the r(CGG)8 repeat from the G-quadruplex into a hairpin-like structure.
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Affiliation(s)
- Hirotaka Murase
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis ten bosch machi, Sasebo 859-3298, Japan.
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis ten bosch machi, Sasebo 859-3298, Japan.
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6
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Cadoni E, Pennati F, Muangkaew P, Elskens J, Madder A, Manicardi A. Synthesis and structure–activity relationship of peptide nucleic acid probes with improved interstrand-crosslinking abilities: application to biotin-mediated RNA-pulldown. RSC Chem Biol 2022; 3:1129-1143. [PMID: 36128507 PMCID: PMC9428673 DOI: 10.1039/d2cb00095d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
Abstract
After optimization of interstrand crosslink reaction between furan-containing peptide nucleic acids and target oligonucleotides, the reversibility of the formed product is exploited for the pull-down of a sequence of interest from cell lysates.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
| | - Francesca Pennati
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
| | - Penthip Muangkaew
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, 10330 Bangkok, Thailand
| | - Joke Elskens
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-7, 9000 Gent, Belgium
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7
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Brodyagin N, Katkevics M, Kotikam V, Ryan CA, Rozners E. Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications. Beilstein J Org Chem 2021; 17:1641-1688. [PMID: 34367346 PMCID: PMC8313981 DOI: 10.3762/bjoc.17.116] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/28/2021] [Indexed: 12/23/2022] Open
Abstract
Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA's chemistry, optimization of structure and function, applications as probes and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA's binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA therapeutics. While many modifications have improved on PNA's binding affinity and specificity, solubility and other biophysical properties, the original PNA is still most frequently used in diagnostic and other in vitro applications. Development of therapeutics and other in vivo applications of PNA has notably lagged behind and is still limited by insufficient bioavailability and difficulties with tissue specific delivery. Relatively high doses are required to overcome poor cellular uptake and endosomal entrapment, which increases the risk of toxicity. These limitations remain unsolved problems waiting for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Venubabu Kotikam
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Christopher A Ryan
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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8
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Fuchi Y, Murase H, Kai R, Kurata K, Karasawa S, Sasaki S. Artificial Host Molecules to Covalently Capture 8-Nitro-cGMP in Neutral Aqueous Solutions and in Cells. Bioconjug Chem 2021; 32:385-393. [PMID: 33529519 DOI: 10.1021/acs.bioconjchem.1c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New 1,3-diazaphenoxazine derivatives (nitroG-Grasp-Guanidine, NGG) have been developed to covalently capture 8-nitro-cGMP in neutral aqueous solutions, which furnish a thiol reactive group to displace the 8-nitro group and a guanidine unit for interaction with the cyclic phosphate. The thiol group was introduced to the 1,3-diazaphenoxazine skeleton through a 2-aminobenzylthiol group (NGG-H) and its 4-methyl (NGG-pMe) and 6-methyl (NGG-oMe) substituted derivatives. The covalent adducts were formed between the NGG derivatives and 8-nitro-cGMP in neutral aqueous solutions. Among the NGG derivatives, the one with the 6-methyl group (NGG-oMe) exhibited the most efficient capture reaction. Furthermore, NGG-H showed a cell permeability into HEK-293 and RAW 264.7 cells and reduced the intracellular 8-nitro-cGMP level. The NGG derivatives developed in this study would become a valuable tool to study the intracellular role of 8-nitro-cGMP.
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Affiliation(s)
- Yasufumi Fuchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan.,Faculty of Pharmaceutical Sciences, Showa Pharmaceutical University, 3-3165 Higashi-tamagawagakuen, Machida 194-8543, Japan.,Graduate School of Pharmaceutical Sciences, Tokushima Bunri University, 180 Yamashiro-cho, Tokushima 770-8514, Japan
| | - Hirotaka Murase
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch Machi, Sasebo 859-3298, Japan
| | - Ryosuke Kai
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Kakeru Kurata
- Faculty of Pharmaceutical Sciences, Showa Pharmaceutical University, 3-3165 Higashi-tamagawagakuen, Machida 194-8543, Japan
| | - Satoru Karasawa
- Faculty of Pharmaceutical Sciences, Showa Pharmaceutical University, 3-3165 Higashi-tamagawagakuen, Machida 194-8543, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan.,Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch Machi, Sasebo 859-3298, Japan
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9
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Antibacterial Peptide Nucleic Acids-Facts and Perspectives. Molecules 2020; 25:molecules25030559. [PMID: 32012929 PMCID: PMC7038079 DOI: 10.3390/molecules25030559] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance is an escalating, worldwide problem. Due to excessive use of antibiotics, multidrug-resistant bacteria have become a serious threat and a major global healthcare problem of the 21st century. This fact creates an urgent need for new and effective antimicrobials. The common strategies for antibiotic discovery are based on either modifying existing antibiotics or screening compound libraries, but these strategies have not been successful in recent decades. An alternative approach could be to use gene-specific oligonucleotides, such as peptide nucleic acid (PNA) oligomers, that can specifically target any single pathogen. This approach broadens the range of potential targets to any gene with a known sequence in any bacterium, and could significantly reduce the time required to discover new antimicrobials or their redesign, if resistance arises. We review the potential of PNA as an antibacterial molecule. First, we describe the physicochemical properties of PNA and modifications of the PNA backbone and nucleobases. Second, we review the carriers used to transport PNA to bacterial cells. Furthermore, we discuss the PNA targets in antibacterial studies focusing on antisense PNA targeting bacterial mRNA and rRNA.
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10
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Fujii A, Nakagawa O, Kishimoto Y, Nakatsuji Y, Nozaki N, Obika S. Oligonucleotides Containing Phenoxazine Artificial Nucleobases: Triplex-Forming Abilities and Fluorescence Properties. Chembiochem 2019; 21:860-864. [PMID: 31568630 DOI: 10.1002/cbic.201900536] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Indexed: 11/11/2022]
Abstract
1,3-Diaza-2-oxophenoxazine ("phenoxazine"), a tricyclic cytosine analogue, can strongly bind to guanine moieties and improve π-π stacking effects with adjacent bases in a duplex. Phenoxazine has been widely used for improving duplex-forming abilities. In this study, we have investigated whether phenoxazine and its analogue, 1,3,9-triaza-2-oxophenoxazine (9-TAP), could improve triplex-forming abilities. A triplex-forming oligonucleotide (TFO) incorporating a phenoxazine component was found to show considerably decreased binding affinity with homopurine/homopyrimidine double-stranded DNA, so the phenoxazine system was considered not to function as either a protonated cytosine or thymine analogue. Alternatively, a 9-TAP-containing artificial nucleobase developed by us earlier as a new phenoxazine analogue functioned as a thymine analogue with respect to AT base pairs in a parallel triplex DNA motif. The fluorescence of the 9-TAP moiety was maintained even in triplex (9-TAP:AT) formation, so 9-TAP might be useful as an imaging tool for various oligonucleotide nanotechnologies requiring triplex formation.
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Affiliation(s)
- Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yusuke Nakatsuji
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Natsumi Nozaki
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
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11
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Zatsepin TS, Varizhuk AM, Dedkov VG, Shipulin GA, Aralov AV. Oligonucleotide Primers with G 8AE-Clamp Modifications for RT-qPCR Detection of the Low-Copy dsRNA. Methods Mol Biol 2019; 1973:281-297. [PMID: 31016709 DOI: 10.1007/978-1-4939-9216-4_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We developed a new technique suitable for improved detection of low-copy dsRNA using modified oligonucleotides as primers in RT-qPCR. Insertion of G8AE-clamp residues into primers significantly improves thermal stability of duplexes with RNA without decrease of hybridization selectivity. The applicability of modified primers is demonstrated for detection of low-copy Kemerovo virus dsRNA.
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Affiliation(s)
- Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Anna M Varizhuk
- Research and Clinical Center for Physical Chemical Medicine, Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - German A Shipulin
- Central Research Institute of Epidemiology, Moscow, Russia.,Federal State Budgetary Institution "Center for Strategic Planning and Management of Biomedical Health Risks" of the Ministry of Health, Moscow, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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12
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Abstract
Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.
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Affiliation(s)
- Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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13
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Gupta A, Mishra A, Puri N. Peptide nucleic acids: Advanced tools for biomedical applications. J Biotechnol 2017; 259:148-159. [PMID: 28764969 PMCID: PMC7114329 DOI: 10.1016/j.jbiotec.2017.07.026] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 05/23/2017] [Accepted: 07/23/2017] [Indexed: 02/01/2023]
Abstract
Peptide Nucleic Acids − DNA/RNA analogues. Different Modifications on PNA backbone and their effects. Neutral backbone − remarkable hybridization properties. PNA based biosensors and their diverse biomedical applications. Potential antigene and antisense agents.
Peptide Nucleic Acids (PNAs) are the DNA/RNA analogues in which sugar-phosphate backbone is replaced by N-2-aminoethylglycine repeating units. PNA contains neutral backbone hence due to the absence of electrostatic repulsion, its hybridization shows remarkable stability towards complementary oligonucleotides. PNAs are highly resistant to cleavage by chemicals and enzymes due to the substrate specific nature of enzymes and therefore not degraded inside the cells. PNAs are emerging as new tools in the market due to their applications in antisense and antigene therapies by inhibiting translation and transcription respectively. Hence, several methods based on PNAs have been developed for designing various anticancer and antigene drugs, detection of mutations or modulation of PCR reactions. The duplex homopurine sequence of DNA may also be recognized by PNA, forming firm PNA/DNA/PNA triplex through strand invasion with a looped-out DNA strand. PNAs have also been found to replace DNA probes in varied investigative purposes. There are several disadvantages regarding cellular uptake of PNA, so modifications in PNA backbone or covalent coupling with cell penetrating peptides is necessary to improve its delivery inside the cells. In this review, hybridization properties along with potential applications of PNA in the field of diagnostics and pharmaceuticals are elaborated.
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Affiliation(s)
- Anjali Gupta
- Department of Chemistry, School of Basic and Applied Sciences, Galgotias University, Greater Noida, U.P., India.
| | - Anuradha Mishra
- School of Vocational Studies & Applied Sciences, Gautam Buddha University, Greater Noida, U.P., India
| | - Nidhi Puri
- Department of Applied Science & Humanities, I.T.S Engineering College, Greater Noida, U.P., India
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14
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Varizhuk AM, Zatsepin TS, Golovin AV, Belyaev ES, Kostyukevich YI, Dedkov VG, Shipulin GA, Shpakovski GV, Aralov AV. Synthesis of oligonucleotides containing novel G-clamp analogue with C8-tethered group in phenoxazine ring: Implication to qPCR detection of the low-copy Kemerovo virus dsRNA. Bioorg Med Chem 2017; 25:3597-3605. [PMID: 28396019 DOI: 10.1016/j.bmc.2017.03.062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/27/2017] [Accepted: 03/29/2017] [Indexed: 01/20/2023]
Abstract
Nowadays modified oligonucleotides are widely used in diagnostics and as novel therapeutics. Introduction of modified or unnatural residues into oligonucleotides allows fine tuning of their binding properties to complementary nucleic acids and leads to improved stability both in vitro and in vivo. Previously it was demonstrated that insertion of phenoxazine nucleotides with various groups in C9-position into oligonucleotides leads to a significant increase of duplex stability with complementary DNA and RNA. Here the synthesis of a novel G-clamp nucleoside analogue (G8AE-clamp) bearing 2-aminoethyl tether at C8-atom is presented. Introduction of such modified residues into oligonucleotides lead to enhanced specificity of duplex formation towards complementary DNA and RNA targets with increased thermal and 3'-exonuclease stability. According to CD-spectroscopy studies G8AE-clamp does not substantially disrupt helix geometry. Primers containing G8AE-clamp demonstrated superior sensitivity in qPCR detection of dsRNA of Kemerovo virus in comparison to native oligonucleotides.
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Affiliation(s)
- Anna M Varizhuk
- Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Department of Structure-Functional Analysis of Biopolymers, Engelhardt Institute of Molecular Biology, Vavilov Str. 32, Moscow 119991, Russia
| | - Timofei S Zatsepin
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia; Skolkovo Institute of Science and Technology, 3 Nobel Street, Skolkovo, Moscow Region 143026, Russia.
| | - Andrey V Golovin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Evgeny S Belyaev
- Institute for Energy Problems of Chemical Physics of RAS, Leninskij pr. 38/2, Moscow 119334, Russia
| | - Yury I Kostyukevich
- Skolkovo Institute of Science and Technology, 3 Nobel Street, Skolkovo, Moscow Region 143026, Russia
| | - Vladimir G Dedkov
- Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia
| | - German A Shipulin
- Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia
| | - George V Shpakovski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia.
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15
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Yamada K, Masaki Y, Tsunoda H, Ohkubo A, Seio K, Sekine M. A new modified cytosine base capable of base pairing with guanine using four hydrogen bonds. Org Biomol Chem 2014; 12:2255-62. [PMID: 24569493 DOI: 10.1039/c3ob42420k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oligonucleotides, containing 4-N-(1H-pyrrol-2-ylcarbonyl)deoxycytidine (dC(Pyc)) and related derivatives, were synthesized via deprotection using 1.5 M NaOMe/MeOH. Among them, oligodeoxynucleotides containing dC(Pyc) exhibited a higher hybridization affinity for DNA and RNA than the unmodified oligodeoxynucleotides. Comparative analysis between dC(Pyc) and its derivatives by molecular dynamic simulation indicated that the C(Pyc) residue could form four hydrogen bonds with the opposite G nucleobase keeping a more planar structure than the C(Inc) residue where the Pyc group was replaced with a 1H-indol-2-ylcarbonyl group.
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Affiliation(s)
- Ken Yamada
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501 Japan.
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16
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Kim PH, Switzer C. Synthesis and characterization of cationic PNA bearing 5-ω-aminopropyl-uracil. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.08.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Patil VS, Padalkar VS, Phatangare KR, Umape PG, Borase BN, Sekar N. Synthesis, Characterization, and Antibacterial Activity of Novel (1H-Benzo[d]imidazole-2-yl)-6-(diethylamino)-3H-one-xanthene, Phenoxazine, and Oxazine. J Heterocycl Chem 2014. [DOI: 10.1002/jhet.1998] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Vikas S. Patil
- Tinctorial Chemistry Group, Department of Intermediate and Dyestuff Technology; Institute of Chemical Technology (Formerly UDCT); N. P. Marg, Matunga Mumbai 400 019 Maharashtra India
| | - Vikas S. Padalkar
- Tinctorial Chemistry Group, Department of Intermediate and Dyestuff Technology; Institute of Chemical Technology (Formerly UDCT); N. P. Marg, Matunga Mumbai 400 019 Maharashtra India
| | - Kiran R. Phatangare
- Tinctorial Chemistry Group, Department of Intermediate and Dyestuff Technology; Institute of Chemical Technology (Formerly UDCT); N. P. Marg, Matunga Mumbai 400 019 Maharashtra India
| | - Prashant G. Umape
- Tinctorial Chemistry Group, Department of Intermediate and Dyestuff Technology; Institute of Chemical Technology (Formerly UDCT); N. P. Marg, Matunga Mumbai 400 019 Maharashtra India
| | - Bhushan N. Borase
- Tinctorial Chemistry Group, Department of Intermediate and Dyestuff Technology; Institute of Chemical Technology (Formerly UDCT); N. P. Marg, Matunga Mumbai 400 019 Maharashtra India
| | - N. Sekar
- Tinctorial Chemistry Group, Department of Intermediate and Dyestuff Technology; Institute of Chemical Technology (Formerly UDCT); N. P. Marg, Matunga Mumbai 400 019 Maharashtra India
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18
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Manicardi A, Accetta A, Tedeschi T, Sforza S, Marchelli R, Corradini R. PNA bearing 5-azidomethyluracil: a novel approach for solid and solution phase modification. ARTIFICIAL DNA, PNA & XNA 2012; 3:53-62. [PMID: 22772040 PMCID: PMC3429531 DOI: 10.4161/adna.20158] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Fmoc- and Boc-protected modified monomers bearing 5-azidomethyluracil nucleobase were synthesized. Four different solid-phase synthetic strategies were tested in order to evaluate the application of this series of monomers for the solid-phase synthesis of modified PNA. The azide was used as masked amine for the introduction of amide-linked functional groups, allowing the production of a library of compounds starting from a single modified monomer. The azide function was also exploited as reactive group for the modification of PNA in solution via azide-alkyne click cycloaddition.
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Affiliation(s)
- Alex Manicardi
- Dipartimento di Chimica Organica e Industriale, Università di Parma, Parma, Italy.
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19
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Shelke SA, Sigurdsson ST. Noncovalent and Site-Directed Spin Labeling of Nucleic Acids. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002637] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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20
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Shelke SA, Sigurdsson ST. Noncovalent and Site-Directed Spin Labeling of Nucleic Acids. Angew Chem Int Ed Engl 2010; 49:7984-6. [DOI: 10.1002/anie.201002637] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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21
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Wojciechowski F, Hudson RHE. Peptide nucleic acid containing a meta-substituted phenylpyrrolocytosine exhibits a fluorescence response and increased binding affinity toward RNA. Org Lett 2009; 11:4878-81. [PMID: 19788268 DOI: 10.1021/ol9019474] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Peptide nucleic acids (PNA) containing meta-substituted 6-phenylpyrrolocytosine (PhpC), [mono-m-(aminoethoxy)phenyl]pyrrolocytosine (mmePhpC), [mono-m-(aminopropoxy)phenyl]pyrrolocytosine (mmpPhpC), and [mono-m-(guanidinoethoxy)phenyl]pyrrolocytosine (mmguaPhpC), have been synthesized. Meta-substituted PhpCs have been hybridized with overall higher binding affinity toward DNA and RNA than previously synthesized moePhpC or newly synthesized mopPhpC. The guanidinium-containing nucleobase, mmguaPhpC, exhibited the highest increase in binding affinity toward RNA while fluorometrically responding on the state of hybridization.
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Affiliation(s)
- Filip Wojciechowski
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
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22
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Sen A, Nielsen PE. Hydrogen bonding versus stacking stabilization by modified nucleobases incorporated in PNA.DNA duplexes. Biophys Chem 2008; 141:29-33. [PMID: 19162391 DOI: 10.1016/j.bpc.2008.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 12/17/2008] [Accepted: 12/17/2008] [Indexed: 11/17/2022]
Abstract
The effects of incorporation of the modified nucleobases, 2,6-diaminopurine (D) (substituting for adenine) and 7-chloro-1,8-naphthyridin-2-(1H)-one (bicyclic thymine, bT) (substituting for thymine), that stabilize PNA.DNA duplex formation by increasing hydrogen bonding and/or base pair stacking interactions have been studied by thermal denaturation in terms of thermodynamics. Although the stabilizing effect of the bT base (in contrast to that of D base) is abolished upon addition of dimethyl formamide, thereby indicating that the stabilization is predominantly due to hydrophobic stacking forces, duplex stabilization was found to be enthalpic for both nucleobases. Increased stabilization (although not fully linearly) was observed with increasing numbers of modified bases, and single base sequence discrimination was only slightly compromised, but showed significant dependence on the sequence context.
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Affiliation(s)
- Anjana Sen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Denmark
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23
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Chenna V, Rapireddy S, Sahu B, Ausin C, Pedroso E, Ly DH. A simple cytosine to G-clamp nucleobase substitution enables chiral gamma-PNAs to invade mixed-sequence double-helical B-form DNA. Chembiochem 2008; 9:2388-91. [PMID: 18816545 DOI: 10.1002/cbic.200800441] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Venugopal Chenna
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
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24
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Wojciechowski F, Hudson RHE. Fluorescence and hybridization properties of peptide nucleic acid containing a substituted phenylpyrrolocytosine designed to engage Guanine with an additional H-bond. J Am Chem Soc 2008; 130:12574-5. [PMID: 18761442 DOI: 10.1021/ja804233g] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new pyrrolocytosine derivative has been designed to selectively interact with guanine and has been evaluated in peptide nucleic acid where it imparts increased selective binding affinity for complementary oligonucleotides. The modified nucleobase also possesses an exceptionally high fluorescence quantum yield that is responsive to hybridization.
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Affiliation(s)
- Filip Wojciechowski
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, N6A 5B7
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25
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Sandin P, Börjesson K, Li H, Mårtensson J, Brown T, Wilhelmsson LM, Albinsson B. Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue. Nucleic Acids Res 2007; 36:157-67. [PMID: 18003656 PMCID: PMC2248743 DOI: 10.1093/nar/gkm1006] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
This article presents the first evidence that the DNA base analogue 1,3-diaza-2-oxophenoxazine, tC(O), is highly fluorescent, both as free nucleoside and incorporated in an arbitrary DNA structure. tC(O) is thoroughly characterized with respect to its photophysical properties and structural performance in single- and double-stranded oligonucleotides. The lowest energy absorption band at 360 nm (epsilon = 9000 M(-1) cm(-1)) is dominated by a single in-plane polarized electronic transition and the fluorescence, centred at 465 nm, has a quantum yield of 0.3. When incorporated into double-stranded DNA, tC(O) shows only minor variations in fluorescence intensity and lifetime with neighbouring bases, and the average quantum yield is 0.22. These features make tC(O), on average, the brightest DNA-incorporated base analogue so far reported. Furthermore, it base pairs exclusively with guanine and causes minimal perturbations to the native structure of DNA. These properties make tC(O) a promising base analogue that is perfectly suited for e.g. photophysical studies of DNA interacting with macromolecules (proteins) or for determining size and shape of DNA tertiary structures using techniques such as fluorescence anisotropy and fluorescence resonance energy transfer (FRET).
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Affiliation(s)
- Peter Sandin
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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26
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Ortega JA, Blas JR, Orozco M, Grandas A, Pedroso E, Robles J. Binding affinities of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are unusually sequence-dependent. Org Lett 2007; 9:4503-6. [PMID: 17915883 DOI: 10.1021/ol701826x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Melting temperatures of DNA duplexes containing the phenoxazine (P) and G-clamp (X) cytosine analogues exhibited a strong and unusual dependence on the nucleoside flanking the modified nucleobase, and the same trend was observed in PNA-DNA duplexes incorporating X in the PNA chain. Molecular dynamics simulations of the DNA duplexes show that generalized stacking (including secondary interactions of the ammonium group of X) and hydrogen bonding are good descriptors of the different duplex stabilities.
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Affiliation(s)
- José-Antonio Ortega
- Departament de Química Orgànica, Universitat de Barcelona, Martí i Franquès 1-11, E-08028 Barcelona, Spain
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27
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Pensato S, Saviano M, Romanelli A. New peptide nucleic acid analogues: synthesis and applications. Expert Opin Biol Ther 2007; 7:1219-32. [PMID: 17696820 DOI: 10.1517/14712598.7.8.1219] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Peptide nucleic acids are oligonucleotide mimics characterised by high chemical and enzymatic stability, high specificity and affinity toward complementary DNA/RNA. The lack of charge and polar groups in the backbone decrease their solubility in aqueous environment and their ability to cross cell membranes, reducing their performance in in vivo applications. To improve solubility, increase affinity and specificity of binding and to control recognition between nucleic acids, several analogues bearing modifications on the nucleobase, nucleobase-backbone linker and on the backbone were synthesised. This paper describes the synthesis and applications of Peptide nucleic acid analogues and discusses the potential of analogues for which no application is reported.
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Affiliation(s)
- Soccorsa Pensato
- Università degli Studi di Napoli Federico II, Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Napoli, Italy
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28
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Debaene F, Da Silva JA, Pianowski Z, Duran FJ, Winssinger N. Expanding the scope of PNA-encoded libraries: divergent synthesis of libraries targeting cysteine, serine and metallo-proteases as well as tyrosine phosphatases. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.03.033] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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29
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Structure-Based Design and Synthesis of the First Weak Non-Phosphate Inhibitors for IspF, an Enzyme in the Non-Mevalonate Pathway of Isoprenoid Biosynthesis. Helv Chim Acta 2007. [DOI: 10.1002/hlca.200790105] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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30
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Hudson RHE, Wojciechowski F. The detrimental effect of orotic acid substitution in the peptide nucleic acid strand on the stability of PNA2:NA triple helices. CAN J CHEM 2005. [DOI: 10.1139/v05-180] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have investigated the incorporation of C6 derivatives of uracil into polypyrimidine peptide nucleic acid oligomers. Starting with uracil-6-carboxylic acid (orotic acid), a peptide nucleic acid monomer compatible with Fmoc-based synthesis was prepared. This monomer then served as a convertible nucleobase whereupon treatment of the resin-bound methyl orotate containing hexamers with hydroxide or amines cleanly converted the ester to an orotic acid or orotamide-containing peptide nucleic acid. Peptide nucleic acid hexamers containing the C6-modified nucleobase hybridized to both poly(riboadenylic acid) and poly(deoxyriboadenylic acid) via triplex formation. Complexes formed with poly(riboadenylic acid) were more stable than those formed with poly(dexoyriboadenylic acid), as measured by temperature-dependent UV spectroscopy. However, both of these complexes were destabilized relative to the complexes formed by an unmodified peptide nucleic acid oligomers. Internal or doubly substituted hexamers are destabilized more strongly than a terminally substituted one, and the type of substitution (carboxamide, ester, carboxylic acid) affects the overall triplex stability. These results clearly show that incorporation of a C6-substituted uracil into polypyrimidine PNA is detrimental to triplex formation. We have also extended this chemistry to incorporate uracil-5-methylcarboxylate into a peptide nucleic acid hexamer. After on-resin conversion of the C5 ester to the 3-(N,N-dimethylamino)propylamide, significant stabilization of the triplex formed with poly(riboadenylic acid) was observed, which illustrates the compatibility of C5 substitution with peptide nucleic acid directed triple helix formation. Key words: peptide nucleic acid, triple helix, orotic acid, orotamide, PNA.
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31
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Sandin P, Wilhelmsson LM, Lincoln P, Powers VEC, Brown T, Albinsson B. Fluorescent properties of DNA base analogue tC upon incorporation into DNA--negligible influence of neighbouring bases on fluorescence quantum yield. Nucleic Acids Res 2005; 33:5019-25. [PMID: 16147985 PMCID: PMC1201328 DOI: 10.1093/nar/gki790] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The quantum yield of the fluorescent tricyclic cytosine analogue, 1,3-diaza-2-oxophenothiazine, tC, is high and virtually unaffected by incorporation into both single- and double-stranded DNA irrespective of neighbouring bases (0.17-0.24 and 0.16-0.21, respectively) and the corresponding fluorescence decay curves are all mono-exponential, properties that are unmatched by any base analogue so far. The fluorescence lifetimes increase when going from tC free in solution (3.2 ns) to single- and double-stranded DNA (on average 5.7 and 6.3 ns, respectively). The mono-exponential decays further support previous NMR results where it was found that tC has a well-defined position and geometry within the DNA helix. Furthermore, we find that the oxidation potential of tC is 0.4 V lower than for deoxyguanosine, the natural base with the lowest oxidation potential. This suggests that tC may be of interest in charge transfer studies in DNA as an electron hole acceptor. We also present a novel synthetic route to the phosphoramidite form of tC. The results presented here together with previous work show that tC is a very good C-analogue that induces minimal perturbation to the native structure of DNA. This makes tC unique as a fluorescent base analogue and is thus highly interesting in a range of applications for studying e.g. structure, dynamics and kinetics in nucleic acid systems.
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Affiliation(s)
| | - L. Marcus Wilhelmsson
- To whom the correspondence should be addressed. Tel: +46 31 7723051; Fax: +46 31 7723858;
| | | | - Vicki E. C. Powers
- School of Chemistry, University of SouthamptonHighfield, Southampton SO17 1BJ, UK
| | - Tom Brown
- School of Chemistry, University of SouthamptonHighfield, Southampton SO17 1BJ, UK
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32
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Jarikote DV, Köhler O, Socher E, Seitz O. Divergent and Linear Solid-Phase Synthesis of PNA Containing Thiazole Orange as Artificial Base. European J Org Chem 2005. [DOI: 10.1002/ejoc.200500201] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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33
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Köhler O, Jarikote DV, Seitz O. Forced intercalation probes (FIT Probes): thiazole orange as a fluorescent base in peptide nucleic acids for homogeneous single-nucleotide-polymorphism detection. Chembiochem 2005; 6:69-77. [PMID: 15584015 DOI: 10.1002/cbic.200400260] [Citation(s) in RCA: 193] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Fluorescent base analogues in DNA are versatile probes of nucleic acid-nucleic acid and nucleic acid-protein interactions. New peptide nucleic acid (PNA) based probes are described in which the intercalator dye thiazole orange (TO) serves as a base surrogate. The investigation of six TO derivatives revealed that the linker length and the conjugation site decided whether a base surrogate conveys sequence-selective DNA binding and whether fluorescence is increased or decreased upon single-mismatched hybridization. One TO derivative conferred universal PNA-DNA base pairing while maintaining duplex stability and hybridization selectivity. TO fluorescence increased up to 26-fold upon hybridization. In contrast to most other probes, in which fluorescence is invariant once hybridization had occurred, the emission of TO-containing PNA probes is attenuated when forced to intercalate next to a mismatched base pair. The specificity of DNA detection is therefore not limited by the selectivity of probe-target binding and a DNA target can be distinguished from its single-base mutant under nonstringent hybridization conditions. This property should be of advantage for real-time quantitative PCR and nucleic acid detection within living cells.
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Affiliation(s)
- Olaf Köhler
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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34
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Hollenstein M, Leumann CJ. Fluorinated olefinic peptide nucleic acid: synthesis and pairing properties with complementary DNA. J Org Chem 2005; 70:3205-17. [PMID: 15822983 DOI: 10.1021/jo047753e] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fluorinated olefinic peptide nucleic acid (F-OPA) system was designed as a peptide nucleic acid (PNA) analogue in which the base carrying amide moiety was replaced by an isostructural and isoelectrostatic fluorinated C-C double bond, locking the nucleobases in one of the two possible rotameric forms. By comparison of the base-pairing properties of this analogue with its nonfluorinated analogue OPA and PNA, we aimed at a closer understanding of the role of this amide function in complementary DNA recognition. Here we present the synthesis of the F-OPA monomer building blocks containing the nucleobases A, T, and G according to the MMTr/Acyl protecting group scheme. Key steps are a selective desymmetrization of the double bond in the monomer precursor via lactonization as well as a highly regioselective Mitsunobu reaction for the introduction of the bases. PNA decamers containing single F-OPA mutations and fully modified F-OPA decamers and pentadecamers containing the bases A and T were synthesized by solid-phase peptide chemistry, and their hybridization properties with complementary parallel and antiparallel DNA were assessed by UV melting curves and CD spectroscopic methods. The stability of the duplexes formed by the decamers containing single (Z)-F-OPA modifications with parallel and antiparallel DNA was found to be strongly dependent on their position in the sequence with T(m) values ranging from +2.4 to -8.1 degrees C/modification as compared to PNA. Fully modified F-OPA decamers and pentadecamers were found to form parallel duplexes with complementary DNA with reduced stability compared to PNA or OPA. An asymmetric F-OPA pentadecamer was found to form a stable self-complex (T(m) approximately 65 degrees C) of unknown structure. The generally reduced affinity to DNA may therefore be due to an increased propensity for self-aggregation.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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35
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Abstract
Peptide nucleic acids (PNA) are deoxyribonucleic acid (DNA) mimics with a pseudopeptide backbone. PNA is an extremely good structural mimic of DNA (or of ribonucleic acid [RNA]), and PNA oligomers are able to form very stable duplex structures with Watson-Crick complementary DNA and RNA (or PNA) oligomers, and they can also bind to targets in duplex DNA by helix invasion. Therefore, these molecules are of interest in many areas of chemistry, biology, and medicine, including drug discovery, genetic diagnostics, molecular recognition, and the origin of life. Recent progress in studies of PNA properties and applications is reviewed.
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Affiliation(s)
- Peter E Nielsen
- Center for Biomolecular Recognition, IMBG, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, Copenhagen DK-2200N, Denmark.
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36
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Chien CH, Leung MK, Su JK, Li GH, Liu YH, Wang Y. Substituent Effects on Pyrid-2-yl Ureas toward Intramolecular Hydrogen Bonding and Cytosine Complexation. J Org Chem 2004; 69:1866-71. [PMID: 15058931 DOI: 10.1021/jo0355808] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Equilibria between two conformational isomers of pyrid-2-yl ureas, the (E,Z) and (Z,Z) forms, have been studied in DMF-d(7) at -70 degrees C. Most of them show a small preference for the (E,Z) form with an equilibrium constant K(i) around 1-2. However, the K(i) value for 1-methyl-2-(3-(pyrid-2-yl)ureido)pyridinium iodide (12) was found to be 14.2 +/- 1.2. That is 1 order of magnitude larger than those of the others, which indicates that the positively charged 1-methylpyridinium-2-yl substituent would facilitate the (E,Z) form formation. Pyrid-2-yl ureas bind cytosine in DMF-d(7) with binding constants K(B) ranging from 30 to 1700 M(-1). Electron withdrawing substituents, such as the 4-O(2)NC(6)H(4)- or 1-methylpyridinium-4-yl substituent, preferentially facilitate the intermolecular cytosine complexation with large binding constants.
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Affiliation(s)
- Chia-Hui Chien
- Department of Chemistry, National Taiwan University, Taipei, Taiwan 106, Republic of China
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37
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Holmes SC, Arzumanov AA, Gait MJ. Steric inhibition of human immunodeficiency virus type-1 Tat-dependent trans-activation in vitro and in cells by oligonucleotides containing 2'-O-methyl G-clamp ribonucleoside analogues. Nucleic Acids Res 2003; 31:2759-68. [PMID: 12771202 PMCID: PMC156719 DOI: 10.1093/nar/gkg384] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report the synthesis of a novel 2'-O-methyl (OMe) riboside phosphoramidite derivative of the G-clamp tricyclic base and incorporation into a series of small steric blocking OMe oligonucleotides targeting the apical stem-loop region of human immunodeficiency virus type 1 (HIV-1) trans- activation-responsive (TAR) RNA. Binding to TAR RNA is substantially enhanced for certain single site substitutions in the centre of the oligonucleotide, and doubly substituted anti-TAR OMe 9mers or 12mers exhibit remarkably low binding constants of <0.1 nM. G-clamp-containing oligomers achieved 50% inhibition of Tat-dependent in vitro transcription at approximately 25 nM, 4-fold lower than for a TAR 12mer OMe oligonucleotide and better than found for any other oligonucleotide tested to date. Addition of one or two OMe G-clamps did not impart cellular trans-activation inhibition activity to cellularly inactive OMe oligonucleotides. Addition of an OMe G-clamp to a 12mer OMe-locked nucleic acid chimera maintained, but did not enhance, inhibition of Tat-dependent in vitro transcription and cellular trans-activation in HeLa cells. The results demonstrate clearly that an OMe G-clamp has remarkable RNA-binding enhancement ability, but that oligonucleotide effectiveness in steric block inhibition of Tat-dependent trans-activation both in vitro and in cells is governed by factors more complex than RNA-binding strength alone.
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Affiliation(s)
- Stephen C Holmes
- Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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