1
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Xiang Z, Lu J, Ming Y, Guo W, Chen X, Sun W. Engineering of a DNA/γPNA Hybrid Nanoreporter for ctDNA Mutation Detection via γPNA Urinalysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2310225. [PMID: 38958527 DOI: 10.1002/advs.202310225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 06/19/2024] [Indexed: 07/04/2024]
Abstract
Detection of circulating tumor DNA (ctDNA) mutations, which are molecular biomarkers present in bodily fluids of cancer patients, can be applied for tumor diagnosis and prognosis monitoring. However, current profiling of ctDNA mutations relies primarily on polymerase chain reaction (PCR) and DNA sequencing and these techniques require preanalytical processing of blood samples, which are time-consuming, expensive, and tedious procedures that increase the risk of sample contamination. To overcome these limitations, here the engineering of a DNA/γPNA (gamma peptide nucleic acid) hybrid nanoreporter is disclosed for ctDNA biosensing via in situ profiling and recording of tumor-specific DNA mutations. The low tolerance of γPNA to single mismatch in base pairing with DNA allows highly selective recognition and recording of ctDNA mutations in peripheral blood. Owing to their remarkable biostability, the detached γPNA strands triggered by mutant ctDNA will be enriched in kidneys and cleared into urine for urinalysis. It is demonstrated that the nanoreporter has high specificity for ctDNA mutation in peripheral blood, and urinalysis of cleared γPNA can provide valuable information for tumor progression and prognosis evaluation. This work demonstrates the potential of the nanoreporter for urinary monitoring of tumor and patient prognosis through in situ biosensing of ctDNA mutations.
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Affiliation(s)
- Zhichu Xiang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore
| | - Jianhua Lu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
| | - Yang Ming
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore
| | - Weisheng Guo
- Department of Minimally Invasive Interventional Radiology, The State Key Laboratory of Respiratory Disease, School of Biomedical Engineering & The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
- Nanomedicine Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Theranostics Center of Excellence (TCE), Yong Loo Lin School of Medicine, National University of Singapore, 11 Biopolis Way, Helios, Singapore, 138667, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Weijian Sun
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
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2
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Aman R, Syed MM, Saleh A, Melliti F, Gundra S, Wang Q, Marsic T, Mahas A, Mahfouz M. Peptide nucleic acid-assisted generation of targeted double-stranded DNA breaks with T7 endonuclease I. Nucleic Acids Res 2024; 52:3469-3482. [PMID: 38421613 PMCID: PMC11014363 DOI: 10.1093/nar/gkae148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/14/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024] Open
Abstract
Gene-editing technologies have revolutionized biotechnology, but current gene editors suffer from several limitations. Here, we harnessed the power of gamma-modified peptide nucleic acids (γPNAs) to facilitate targeted, specific DNA invasion and used T7 endonuclease I (T7EI) to recognize and cleave the γPNA-invaded DNA. Our data show that T7EI can specifically target PNA-invaded linear and circular DNA to introduce double-strand breaks (DSBs). Our PNA-Guided T7EI (PG-T7EI) technology demonstrates that T7EI can be used as a programmable nuclease capable of generating single or multiple specific DSBs in vitro under a broad range of conditions and could be potentially applied for large-scale genomic manipulation. With no protospacer adjacent motif (PAM) constraints and featuring a compact protein size, our PG-T7EI system will facilitate and expand DNA manipulations both in vitro and in vivo, including cloning, large-fragment DNA assembly, and gene editing, with exciting applications in biotechnology, medicine, agriculture, and synthetic biology.
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Affiliation(s)
- Rashid Aman
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Muntjeeb M Syed
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ahmed Saleh
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Firdaws Melliti
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Sivakrishna Rao Gundra
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Qiaochu Wang
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tin Marsic
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ahmed Mahas
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Department of Genetics, Harvard University, Boston, MA 02115, USA
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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3
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Huang SH, Chen SC, Wu TY, Chen CY, Yu CH. Programmable modulation of ribosomal frameshifting by mRNA targeting CRISPR-Cas12a system. iScience 2023; 26:108492. [PMID: 38125012 PMCID: PMC10730746 DOI: 10.1016/j.isci.2023.108492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/13/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Minus 1 programmed ribosomal frameshifting (-1 PRF) is a conserved translational regulation event essential for critical biological processes, including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. Efficient trans-modulation of the structured RNA element crucial to -1 PRF will endow the therapeutic application. Here, we demonstrate that CRISPR RNA can stimulate efficient -1 PRF. Assembled CRISPR-Cas12a, but not CRISPR-Cas9, complex further enhances -1 PRF efficiency through its higher capacity to stall translating ribosomes. We additionally perform CRISPR-Cas12a targeting to impair the SARS-CoV-2 frameshifting pseudoknot structure via a focused screening. We demonstrate that targeting CRISPR-Cas12a results in more than 70% suppression of -1 PRF in vitro and about 50% suppression in mammalian cells. Our results show the expanded function of the CRISPR-Cas12 system in modulating -1 PRF efficiency through stalling ribosomes and deforming frameshifting stimulatory signals, which could serve as a new strategy for future coronavirus pandemics.
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Affiliation(s)
- Shih-Hong Huang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Cheng Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | | | - Cheng-Yao Chen
- YD BioLabs, Inc., Hsinchu, Taiwan
- School of Medical Laboratory Science and Biotechnology, Taipei Medical University, Taipei, Taiwan
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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4
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Oyaghire SN, Quijano E, Perera JDR, Mandl HK, Saltzman WM, Bahal R, Glazer PM. DNA recognition and induced genome modification by a hydroxymethyl-γ tail-clamp peptide nucleic acid. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101635. [PMID: 37920723 PMCID: PMC10621889 DOI: 10.1016/j.xcrp.2023.101635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Peptide nucleic acids (PNAs) can target and stimulate recombination reactions in genomic DNA. We have reported that γPNA oligomers possessing the diethylene glycol γ-substituent show improved efficacy over unmodified PNAs in stimulating recombination-induced gene modification. However, this structural modification poses a challenge because of the inherent racemization risk in O-alkylation of the precursory serine side chain. To circumvent this risk and improve γPNA accessibility, we explore the utility of γPNA oligomers possessing the hydroxymethyl-γ moiety for gene-editing applications. We demonstrate that a γPNA oligomer possessing the hydroxymethyl modification, despite weaker preorganization, retains the ability to form a hybrid with the double-stranded DNA target of comparable stability and with higher affinity than that of the diethylene glycol-γPNA. When formulated into poly(lactic-co-glycolic acid) nanoparticles, the hydroxymethyl-γPNA stimulates higher frequencies (≥ 1.5-fold) of gene modification than the diethylene glycol γPNA in mouse bone marrow cells.
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Affiliation(s)
- Stanley N. Oyaghire
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- These authors contributed equally
| | - Elias Quijano
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- These authors contributed equally
| | - J. Dinithi R. Perera
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hanna K. Mandl
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - W. Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Department of Chemical & Environmental Engineering, Yale University, New Haven, CT 06511, USA
- Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Peter M. Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
- Lead contact
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5
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Argueta-Gonzalez H, Swenson CS, Skowron KJ, Heemstra JM. Elucidating Sequence-Assembly Relationships for Bilingual PNA Biopolymers. ACS OMEGA 2023; 8:37442-37450. [PMID: 37841192 PMCID: PMC10569013 DOI: 10.1021/acsomega.3c05528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023]
Abstract
Nucleic acids and proteins possess encoded "languages" that can be used for information storage or to direct function. However, each biopolymer is limited to encoding its respective "language." Using a peptide nucleic acid (PNA) scaffold, nucleobase and amino acid residues can be installed on a singular backbone, enabling a single biopolymer to encode both languages. Our laboratory previously reported the development of a "bilingual" PNA biopolymer that incorporates a sequence-specific nucleic acid code interspersed with hydrophobic (alanine) and hydrophilic (lysine) amino acid residues at defined positions to produce amphiphilic character. We observed the amphiphilic amino acid residues directing the biopolymer to undergo self-assembly into micelle-like structures, while the nucleic acid recognition was harnessed for disassembly. Herein, we report a series of bilingual PNA sequences having amino acid residues with varying lengths, functional group charges, hydrophobicities, and spacings to elucidate the effect of these parameters on micelle assembly and nucleic acid recognition. Negative charges in the hydrophilic block or increased bulkiness of the hydrophobic side chains led to assembly into similarly sized micelles; however, the negative charge additionally led to increased critical micelle concentration. Upon PNA sequence truncation to decrease the spacing between side chains, the biopolymers remained capable of self-assembling but formed smaller structures. Characterization of disassembly revealed that each variant retained sequence recognition capabilities and stimuli-responsive disassembly. Together, these data show that the amino acid and nucleic acid sequences of amphiphilic bilingual biopolymers can be customized to finely tune the assembly and disassembly properties, which has implications for applications such as the encapsulation and delivery of cargo for therapeutics.
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Affiliation(s)
| | - Colin S. Swenson
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Kornelia J. Skowron
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United
States
| | - Jennifer M. Heemstra
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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6
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López-Tena M, Farrera-Soler L, Barluenga S, Winssinger N. Pseudo-Complementary G:C Base Pair for Mixed Sequence dsDNA Invasion and Its Applications in Diagnostics (SARS-CoV-2 Detection). JACS AU 2023; 3:449-458. [PMID: 36873687 PMCID: PMC9975836 DOI: 10.1021/jacsau.2c00588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Pseudo-complementary oligonucleotides contain artificial nucleobases designed to reduce duplex formation in the pseudo-complementary pair without compromising duplex formation to targeted (complementary) oligomers. The development of a pseudo-complementary A:T base pair, Us:D, was important in achieving dsDNA invasion. Herein, we report pseudo-complementary analogues of the G:C base pair leveraged on steric and electrostatic repulsion between the cationic phenoxazine analogue of cytosine (G-clamp, C+) and N-7 methyl guanine (G+), which is also cationic. We show that while complementary peptide nucleic acids (PNA) form a much more stable homoduplex than the PNA:DNA heteroduplex, oligomers based on pseudo-C:G complementary PNA favor PNA:DNA hybridization. We show that this enables dsDNA invasion at physiological salt concentration and that stable invasion complexes are obtained with low equivalents of PNAs (2-4 equiv). We harnessed the high yield of dsDNA invasion for the detection of RT-RPA amplicon using a lateral flow assay (LFA) and showed that two strains of SARS-CoV-2 can be discriminated owing to single nucleotide resolution.
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7
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Sarkar S, Colón-Roura G, Pearse A, Armitage BA. Targeting a KRAS i-motif forming sequence by unmodified and gamma-modified peptide nucleic acid oligomers. Biopolymers 2023; 114:e23529. [PMID: 36573547 PMCID: PMC10078108 DOI: 10.1002/bip.23529] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 12/04/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022]
Abstract
Growing interest in i-motif DNA as a transcriptional regulatory element motivates development of synthetic molecules capable of targeting these structures. In this study, we designed unmodified peptide nucleic acid (PNA) and gamma-modified PNA (γPNA) oligomers complementary to an i-motif forming sequence derived from the promoter of the KRAS oncogene. Biophysical techniques such as circular dichroism (CD) spectroscopy, CD melting, and fluorescence spectroscopy demonstrated the successful invasion of the i-motif by PNA and γPNA. Both PNA and γPNA showed very strong binding to the target sequence with high thermal stability of the resulting heteroduplexes. Interestingly fluorescence and CD experiments indicated formation of an intermolecular i-motif structure via the overhangs of target-probe heteroduplexes formed by PNA/γPNA invasion of the intramolecular i-motif. Targeting promoter i-motif forming sequences with high-affinity oligonucleotide mimics like γPNAs may represent a new approach for inhibiting KRAS transcription, thereby representing a potentially useful anti-cancer strategy.
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Affiliation(s)
- Srijani Sarkar
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Gabriela Colón-Roura
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Alexander Pearse
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Bruce A Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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8
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Emehiser RG, Dhuri K, Shepard C, Karmakar S, Bahal R, Hrdlicka PJ. Serine-γPNA, Invader probes, and chimeras thereof: three probe chemistries that enable sequence-unrestricted recognition of double-stranded DNA. Org Biomol Chem 2022; 20:8714-8724. [PMID: 36285843 PMCID: PMC9707317 DOI: 10.1039/d2ob01567f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2023]
Abstract
Three probe chemistries are evaluated with respect to thermal denaturation temperatures, UV-Vis and fluorescence characteristics, recognition of complementary and mismatched DNA hairpin targets, and recognition of chromosomal DNA targets in the context of non-denaturing fluorescence in situ hybridization (nd-FISH) experiments: (i) serine-γPNAs (SγPNAs), i.e., single-stranded peptide nucleic acid (PNA) probes that are modified at the γ-position with (R)-hydroxymethyl moieties, (ii) Invader probes, i.e., DNA duplexes modified with +1 interstrand zippers of 2'-O-(pyren-1-yl)methyl-RNA monomers, a molecular arrangement that results in a violation of the neighbor exclusion principle, and (iii) double-stranded chimeric SγPNAs:Invader probes, i.e., duplexes between complementary SγPNA and Invader strands, which are destabilized due to the poor compatibility between intercalators and PNA:DNA duplexes. Invader probes resulted in efficient, highly specific, albeit comparatively slow recognition of the model DNA hairpin targets. Recognition was equally efficient and faster with the single-stranded SγPNA probes but far less specific, whilst the double-stranded chimeric SγPNAs:Invader probes displayed recognition characteristics that were intermediate of the parent probes. All three probe chemistries demonstrated the capacity to target chromosomal DNA in nd-FISH experiments, with Invader probes resulting in the most favorable and consistent characteristics (signals in >90% of interphase nuclei against a low background and no signal in negative control experiments). These probe chemistries constitute valuable additions to the molecular toolbox needed for DNA-targeting applications.
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Affiliation(s)
| | - Karishma Dhuri
- Pharmaceutical Sciences, University of Connecticut, Storrs, CT-06269, USA
| | - Caroline Shepard
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA.
| | - Saswata Karmakar
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA.
| | - Raman Bahal
- Pharmaceutical Sciences, University of Connecticut, Storrs, CT-06269, USA
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Kostelansky F, Miletin M, Havlinova Z, Szotakova B, Libra A, Kucera R, Novakova V, Zimcik P. Thermal stabilisation of the short DNA duplexes by acridine-4-carboxamide derivatives. Nucleic Acids Res 2022; 50:10212-10229. [PMID: 36156152 PMCID: PMC9561273 DOI: 10.1093/nar/gkac777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/17/2022] [Accepted: 08/29/2022] [Indexed: 11/12/2022] Open
Abstract
The short oligodeoxynucleotide (ODN) probes are suitable for good discrimination of point mutations. However, the probes suffer from low melting temperatures. In this work, the strategy of using acridine-4-carboxamide intercalators to improve thermal stabilisation is investigated. The study of large series of acridines revealed that optimal stabilisation is achieved upon decoration of acridine by secondary carboxamide carrying sterically not demanding basic function bound through a two-carbon linker. Two highly active intercalators were attached to short probes (13 or 18 bases; designed as a part of HFE gene) by click chemistry into positions 7 and/or 13 and proved to increase the melting temperate (Tm) of the duplex by almost 8°C for the best combination. The acridines interact with both single- and double-stranded DNAs with substantially preferred interaction for the latter. The study of interaction suggested higher affinity of the acridines toward the GC- than AT-rich sequences. Good discrimination of two point mutations was shown in practical application with HFE gene (wild type, H63D C > G and S65C A > C mutations). Acridine itself can also serve as a fluorophore and also allows discrimination of the fully matched sequences from those with point mutations in probes labelled only with acridine.
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Affiliation(s)
| | - Miroslav Miletin
- Faculty of Pharmacy in Hradec Králové, Charles University, Ak. Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Zuzana Havlinova
- Generi Biotech, Machkova 587, Hradec Kralove, 500 11, Czech Republic
| | - Barbora Szotakova
- Generi Biotech, Machkova 587, Hradec Kralove, 500 11, Czech Republic
| | - Antonin Libra
- Generi Biotech, Machkova 587, Hradec Kralove, 500 11, Czech Republic
| | - Radim Kucera
- Faculty of Pharmacy in Hradec Králové, Charles University, Ak. Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Veronika Novakova
- Faculty of Pharmacy in Hradec Králové, Charles University, Ak. Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Petr Zimcik
- To whom correspondence should be addressed. Tel: +420 495067257;
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10
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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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11
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Sequence-Specific Recognition of Double-Stranded DNA by Peptide Nucleic Acid Forming Double-Duplex Invasion Complex. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12073677] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Peptide nucleic acid (PNA) is an analog of natural nucleic acids, where the sugar-phosphate backbone of DNA is replaced by an electrostatically neutral N-(2-aminoethyl)glycine backbone. This unique peptide-based backbone enables PNAs to form a very stable duplex with the complementary nucleic acids via Watson–Crick base pairing since there is no electrostatic repulsion between PNA and DNA·RNA. With this high nucleic acid affinity, PNAs have been used in a wide range of fields, from biological applications such as gene targeting, to engineering applications such as probe and sensor developments. In addition to single-stranded DNA, PNA can also recognize double-stranded DNA (dsDNA) through the formation of a double-duplex invasion complex. This double-duplex invasion is hard to achieve with other artificial nucleic acids and is expected to be a promising method to recognize dsDNA in cellula or in vivo since the invasion does not require the prior denaturation of dsDNA. In this paper, we provide basic knowledge of PNA and mainly focus on the research of PNA invasion.
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12
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Kabza AM, Kundu N, Zhong W, Sczepanski JT. Integration of chemically modified nucleotides with DNA strand displacement reactions for applications in living systems. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 14:e1743. [PMID: 34328690 DOI: 10.1002/wnan.1743] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/26/2021] [Accepted: 07/06/2021] [Indexed: 01/21/2023]
Abstract
Watson-Crick base pairing rules provide a powerful approach for engineering DNA-based nanodevices with programmable and predictable behaviors. In particular, DNA strand displacement reactions have enabled the development of an impressive repertoire of molecular devices with complex functionalities. By relying on DNA to function, dynamic strand displacement devices represent powerful tools for the interrogation and manipulation of biological systems. Yet, implementation in living systems has been a slow process due to several persistent challenges, including nuclease degradation. To circumvent these issues, researchers are increasingly turning to chemically modified nucleotides as a means to increase device performance and reliability within harsh biological environments. In this review, we summarize recent progress toward the integration of chemically modified nucleotides with DNA strand displacement reactions, highlighting key successes in the development of robust systems and devices that operate in living cells and in vivo. We discuss the advantages and disadvantages of commonly employed modifications as they pertain to DNA strand displacement, as well as considerations that must be taken into account when applying modified oligonucleotide to living cells. Finally, we explore how chemically modified nucleotides fit into the broader goal of bringing dynamic DNA nanotechnology into the cell, and the challenges that remain. This article is categorized under: Diagnostic Tools > In Vivo Nanodiagnostics and Imaging Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Diagnostic Tools > Biosensing.
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Affiliation(s)
- Adam M Kabza
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Nandini Kundu
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Wenrui Zhong
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
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13
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Lyu M, Kong L, Yang Z, Wu Y, McGhee CE, Lu Y. PNA-Assisted DNAzymes to Cleave Double-Stranded DNA for Genetic Engineering with High Sequence Fidelity. J Am Chem Soc 2021; 143:9724-9728. [PMID: 34156847 DOI: 10.1021/jacs.1c03129] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNAzymes have been widely used in many sensing and imaging applications but have rarely been used for genetic engineering since their discovery in 1994, because their substrate scope is mostly limited to single-stranded DNA or RNA, whereas genetic information is stored mostly in double-stranded DNA (dsDNA). To overcome this major limitation, we herein report peptide nucleic acid (PNA)-assisted double-stranded DNA nicking by DNAzymes (PANDA) as the first example to expand DNAzyme activity toward dsDNA. We show that PANDA is programmable in efficiently nicking or causing double strand breaks on target dsDNA, which mimics protein nucleases and can act as restriction enzymes in molecular cloning. In addition to being much smaller than protein enzymes, PANDA has a higher sequence fidelity compared with CRISPR/Cas under the condition we tested, demonstrating its potential as a novel alternative tool for genetic engineering and other biochemical applications.
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14
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Liang X, Liu M, Komiyama M. Recognition of Target Site in Various Forms of DNA and RNA by Peptide Nucleic Acid (PNA): From Fundamentals to Practical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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15
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Meena CL, Singh D, Kizhakeetil B, Prasad M, George M, Tothadi S, Sanjayan GJ. Triazine-Based Janus G-C Nucleobase as a Building Block for Self-Assembly, Peptide Nucleic Acids, and Smart Polymers. J Org Chem 2021; 86:3186-3195. [PMID: 33523657 DOI: 10.1021/acs.joc.0c02530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This communication reports on the utility of a triazine-based self-assembling system, reminiscent of a Janus G-C nucleobase, as a building block for developing (1) supramolecular polymers, (2) peptide nucleic acids (PNAs), and (3) smart polymers. The strategically positioned self-complementary triple H-bonding arrays DDA and AAD facilitate efficient self-assembly, leading to a linear supramolecular polymer.
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Affiliation(s)
- Chhuttan L Meena
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Dharmendra Singh
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Bhavya Kizhakeetil
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Manasa Prasad
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Malini George
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Srinu Tothadi
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
| | - Gangadhar J Sanjayan
- Organic Chemistry Division, Council of Scientific and Industrial Research National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411008, India
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16
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Hsieh WC, Ly DH. A Robust Method for Preparing Optically Pure MiniPEG-Containing Gamma PNA Monomers. Methods Mol Biol 2021; 2105:17-33. [PMID: 32088862 DOI: 10.1007/978-1-0716-0243-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
We report the syntheses of chemical building blocks of a particular class of chiral PNAs, called miniPEG-containing (R)-gamma PNAs (or (R)-MPγPNAs). The strategy involves the application of 9-(4-bromophenyl)-9-fluorenyl as a temporary, safety-catch protecting group for the suppression of racemization in the alkylation and reductive amination steps. The methodology is general and robust, ideally suited for large-scale monomer productions with most synthetic steps providing excellent chemical yields without the need for purification other than a simple workup and precipitation.
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Affiliation(s)
- Wei-Che Hsieh
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, Pittsburgh, PA, USA.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Danith H Ly
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, Pittsburgh, PA, USA. .,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA.
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17
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Investigation of the Characteristics of NLS-PNA: Influence of NLS Location on Invasion Efficiency. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10238663] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Peptide nucleic acid can recognise sequences in double-stranded DNA (dsDNA) through the formation of a double-duplex invasion complex. This double-duplex invasion is a promising method for the recognition of dsDNA in cellula because peptide nucleic acid (PNA) invasion does not require the prior denaturation of dsDNA. To increase its applicability, we developed PNAs modified with a nuclear localisation signal (NLS) peptide. In this study, the characteristics of NLS-modified PNAs were investigated for the future design of novel peptide-modified PNAs.
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18
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Montazersaheb S, Avci ÇB, Bagca BG, Ay NPO, Tarhriz V, Nielsen PE, Charoudeh HN, Hejazi MS. Targeting TdT gene expression in Molt-4 cells by PNA-octaarginine conjugates. Int J Biol Macromol 2020; 164:4583-4590. [PMID: 32941907 DOI: 10.1016/j.ijbiomac.2020.09.081] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 12/11/2022]
Abstract
Peptide nucleic acid (PNA) is an amide based structural nucleic acid mimic with potential applications in gene therapeutic drug discovery. In the present study, we evaluated and compared the effects on gene expression, cell viability and apoptosis of two antisense PNA-d-octaarginine conjugates, targeting sequences at the AUG translation start site or the 5'-UTR of the TdT (terminal deoxynucleotidyl transferase) gene, as well as a sense oligomer corresponding to the 5'-UTR-antisense, in Molt-4 cells. The protein level of TdT was determined by flow cytometry, and qPCR was used for mRNA expression analysis. Mismatch PNAs were used as control to address the sequence/target spcifity of the biological effects. The results showed that treatment with the AUG- and to slightly lesser extent with the 5'-UTR-antisense PNAs reduced the TdT mRNA as wel as the protein level, whereas only very low effect was observed for the 5'-UTR-sense PNA. A parallel effect was observed on reduced cell survival and increased rate of apoptosis. Our findings suggest that antisense PNAs can inhibit expression of the TdT gene and induce apoptosis in Molt-4 cells.
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Affiliation(s)
- Soheila Montazersaheb
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Çığır Biray Avci
- Faculty of Medicine, Department of Medical Biology, Ege University, Izmir, Turkey
| | - Bakiye Goker Bagca
- Faculty of Medicine, Department of Medical Biology, Ege University, Izmir, Turkey
| | | | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | | | - Mohammad Saeid Hejazi
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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19
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Muangkaew P, Vilaivan T. Modulation of DNA and RNA by PNA. Bioorg Med Chem Lett 2020; 30:127064. [PMID: 32147357 DOI: 10.1016/j.bmcl.2020.127064] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 02/08/2023]
Abstract
Peptide nucleic acid (PNA), a synthetic DNA mimic that is devoid of the (deoxy)ribose-phosphate backbone yet still perfectly retains the ability to recognize natural nucleic acids in a sequence-specific fashion, can be employed as a tool to modulate gene expressions via several different mechanisms. The unique strength of PNA compared to other oligonucleotide analogs is its ability to bind to nucleic acid targets with secondary structures such as double-stranded and quadruplex DNA as well as RNA. This digest aims to introduce general readers to the advancement in the area of modulation of DNA/RNA functions by PNA, its current status and future research opportunities, with emphasis on recent progress in new targeting modes of structured DNA/RNA by PNA and PNA-mediated gene editing.
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Affiliation(s)
- Penthip Muangkaew
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
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20
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Swenson CS, Heemstra JM. Peptide nucleic acids harness dual information codes in a single molecule. Chem Commun (Camb) 2020; 56:1926-1935. [PMID: 32009137 DOI: 10.1039/c9cc09905k] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nature encodes the information required for life in two fundamental biopolymers: nucleic acids and proteins. Peptide nucleic acid (PNA), a synthetic analog comprised of nucleobases arrayed along a pseudopeptide backbone, has the ability to combine the power of nucleic acids to encode information with the versatility of amino acids to encode structure and function. Historically, PNA has been perceived as a simple nucleic acid mimic having desirable properties such as high biostability and strong affinity for complementary nucleic acids. In this feature article, we aim to adjust this perception by highlighting the ability of PNA to act as a peptide mimic and showing the largely untapped potential to encode information in the amino acid sequence. First, we provide an introduction to PNA and discuss the use of conjugation to impart tunable properties to the biopolymer. Next, we describe the integration of functional groups directly into the PNA backbone to impart specific physical properties. Lastly, we highlight the use of these integrated amino acid side chains to encode peptide-like sequences in the PNA backbone, imparting novel activity and function and demonstrating the ability of PNA to simultaneously mimic both a peptide and a nucleic acid.
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Affiliation(s)
- Colin S Swenson
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA.
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21
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Bartl JD, Scarbolo P, Brandalise D, Stutzmann M, Tornow M, Selmi L, Cattani-Scholz A. Role of Different Receptor-Surface Binding Modes in the Morphological and Electrochemical Properties of Peptide-Nucleic-Acid-Based Sensing Platforms. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:3272-3283. [PMID: 30735621 DOI: 10.1021/acs.langmuir.8b03968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Label-free detection of charged biomolecules, such as DNA, has experienced an increase in research activity in recent years, mainly to obviate the need for elaborate and expensive pretreatments for labeling target biomolecules. A promising label-free approach is based on the detection of changes in the electrical surface potential on biofunctionalized silicon field-effect devices. These devices require a reliable and selective immobilization of charged biomolecules on the device surface. In this work, self-assembled monolayers of phosphonic acids are used to prepare organic interfaces with a high density of peptide nucleic acid (PNA) bioreceptors, which are a synthetic analogue to DNA, covalently bound either in a multidentate (∥PNA) or monodentate (⊥PNA) fashion to the underlying silicon native oxide surface. The impact of the PNA bioreceptor orientation on the sensing platform's surface properties is characterized in detail by water contact angle measurements, atomic force microscopy, X-ray photoelectron spectroscopy, cyclic voltammetry, and electrochemical impedance spectroscopy. Our results suggest that the multidentate binding of the bioreceptor via attachment groups at the γ-points along the PNA backbone leads to the formation of an extended, protruding, and netlike three-dimensional metastructure. Typical "mesh" sizes are on the order of 8 ± 2.5 nm in diameter, with no preferential spatial orientation relative to the underlying surface. Contrarily, the monodentate binding provides a spatially more oriented metastructure comprising cylindrical features, of a typical size of 62 ± 23 × 12 ± 2 nm2. Additional cyclic voltammetry measurements in a redox buffer solution containing a small and highly mobile Ru-based complex reveal strikingly different insulating properties (ion diffusion kinetics) of these two PNA systems. Investigation by electrochemical impedance spectroscopy confirms that the binding mode has a significant impact on the electrochemical properties of the functional PNA layers represented by detectable changes of the conductance and capacitance of the underlying silicon substrate in the range of 30-50% depending on the surface organization of the bioreceptors in different bias potential regimes.
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Affiliation(s)
- Johannes D Bartl
- Walter Schottky Institute (WSI) and Physics Department , Technische Universität München , Am Coulombwall 4 , 85748 Garching bei München , Germany
| | - Paolo Scarbolo
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA) , Università degli Studi di Udine , Via delle Scienze 206 , 33100 Udine , Italy
| | - Denis Brandalise
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA) , Università degli Studi di Udine , Via delle Scienze 206 , 33100 Udine , Italy
- Dipartimento di Ingegneria "Enzo Ferrari" , Università degli Studi di Modena e Reggio Emilia , Via Vivarelli 10 , 41125 Modena , Italy
| | - Martin Stutzmann
- Walter Schottky Institute (WSI) and Physics Department , Technische Universität München , Am Coulombwall 4 , 85748 Garching bei München , Germany
| | - Marc Tornow
- Molecular Electronics, Department of Electrical and Computer Engineering , Technische Universität München , Theresienstr. 90 , 80333 München , Germany
- Fraunhofer Research Institution for Microsystems and Solid State Technologies (EMFT) , Hansastr. 27d , 80686 München , Germany
- Center for Nanoscience (CeNS) , Ludwig-Maximilians-Universität München , Geschwister-Scholl-Platz 1 , 80539 München , Germany
| | - Luca Selmi
- Dipartimento di Ingegneria "Enzo Ferrari" , Università degli Studi di Modena e Reggio Emilia , Via Vivarelli 10 , 41125 Modena , Italy
| | - Anna Cattani-Scholz
- Walter Schottky Institute (WSI) and Physics Department , Technische Universität München , Am Coulombwall 4 , 85748 Garching bei München , Germany
- Center for Nanoscience (CeNS) , Ludwig-Maximilians-Universität München , Geschwister-Scholl-Platz 1 , 80539 München , Germany
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22
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Shigi N, Mizuno Y, Kunifuda H, Matsumura K, Komiyama M. Promotion of Single-Strand Invasion of PNA to Double-Stranded DNA by Pseudo-Complementary Base Pairing. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Narumi Shigi
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yuki Mizuno
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Department of Materials Science & Engineering, Shibaura Institute of Technology, 3-7-5 Toyosu, Koto-ku, Tokyo 135-8548, Japan
| | - Hiroko Kunifuda
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Kazunari Matsumura
- Department of Materials Science & Engineering, Shibaura Institute of Technology, 3-7-5 Toyosu, Koto-ku, Tokyo 135-8548, Japan
| | - Makoto Komiyama
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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23
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Komiyama M, Yoshimoto K, Sisido M, Ariga K. Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170156] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Makoto Komiyama
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8577
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902
| | - Masahiko Sisido
- Professor Emeritus, Research Core for Interdisciplinary Sciences, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530
| | - Katsuhiko Ariga
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0827
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24
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Gupta A, Quijano E, Liu Y, Bahal R, Scanlon SE, Song E, Hsieh WC, Braddock DE, Ly DH, Saltzman WM, Glazer PM. Anti-tumor Activity of miniPEG-γ-Modified PNAs to Inhibit MicroRNA-210 for Cancer Therapy. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 9:111-119. [PMID: 29246289 PMCID: PMC5633812 DOI: 10.1016/j.omtn.2017.09.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 11/30/2022]
Abstract
MicroRNAs (miRs) are frequently overexpressed in human cancers. In particular, miR-210 is induced in hypoxic cells and acts to orchestrate the adaptation of tumor cells to hypoxia. Silencing oncogenic miRs such as miR-210 may therefore offer a promising approach to anticancer therapy. We have developed a miR-210 inhibition strategy based on a new class of conformationally preorganized antisense γ peptide nucleic acids (γPNAs) that possess vastly superior RNA-binding affinity, improved solubility, and favorable biocompatibility. For cellular delivery, we encapsulated the γPNAs in poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs). Our results show that γPNAs targeting miR-210 cause significant delay in growth of a human tumor xenograft in mice compared to conventional PNAs. Further, histopathological analyses show considerable necrosis, fibrosis, and reduced cell proliferation in γPNA-treated tumors compared to controls. Overall, our work provides a chemical framework for a novel anti-miR therapeutic approach using γPNAs that should facilitate rational design of agents to potently inhibit oncogenic microRNAs.
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Affiliation(s)
- Anisha Gupta
- Department of Therapeutic Radiology, Yale University, New Haven, CT 06510, USA
| | - Elias Quijano
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Yanfeng Liu
- Department of Therapeutic Radiology, Yale University, New Haven, CT 06510, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Susan E Scanlon
- Department of Therapeutic Radiology, Yale University, New Haven, CT 06510, USA
| | - Eric Song
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Wei-Che Hsieh
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | | | - Danith H Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - W Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University, New Haven, CT 06510, USA; Department of Genetics, Yale University, New Haven, CT 06510, USA.
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25
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Verona MD, Verdolino V, Palazzesi F, Corradini R. Focus on PNA Flexibility and RNA Binding using Molecular Dynamics and Metadynamics. Sci Rep 2017; 7:42799. [PMID: 28211525 PMCID: PMC5314342 DOI: 10.1038/srep42799] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/13/2017] [Indexed: 12/20/2022] Open
Abstract
Peptide Nucleic Acids (PNAs) can efficiently target DNA or RNA acting as chemical tools for gene regulation. Their backbone modification and functionalization is often used to increase the affinity for a particular sequence improving selectivity. The understanding of the trading forces that lead the single strand PNA to bind the DNA or RNA sequence is preparatory for any further rational design, but a clear and unique description of this process is still not complete. In this paper we report further insights into this subject, by a computational investigation aiming at the characterization of the conformations of a single strand PNA and how these can be correlated to its capability in binding DNA/RNA. Employing Metadynamics we were able to better define conformational pre-organizations of the single strand PNA and γ-modified PNA otherwise unrevealed through classical molecular dynamics. Our simulations driven on backbone modified PNAs lead to the conclusion that this γ-functionalization affects the single strand preorganization and targeting properties to the DNA/RNA, in agreement with circular dichroism (CD) spectra obtained for this class of compounds. MD simulations on PNA:RNA dissociation and association mechanisms allowed to reveal the critical role of central bases and preorganization in the binding process.
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Affiliation(s)
| | - Vincenzo Verdolino
- Department of Chemistry and Applied Biosciences, ETH Zurich, c/o Università della Svizzera Italiana Campus, 6900 Lugano, Switzerland
- Facoltà di Informatica, Instituto di Scienze Computazionali, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Ferruccio Palazzesi
- Department of Chemistry and Applied Biosciences, ETH Zurich, c/o Università della Svizzera Italiana Campus, 6900 Lugano, Switzerland
- Facoltà di Informatica, Instituto di Scienze Computazionali, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Roberto Corradini
- Dipartimento di Chimica, University of Parma, Italy, 43124, Italy
- National Institute for Biostructures and Biosystems (INBB)-Viale delle Medaglie d’Oro, 305, 00136 Roma, Italy
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26
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Bolarinwa O, Nimmagadda A, Su M, Cai J. Structure and Function of AApeptides. Biochemistry 2017; 56:445-457. [PMID: 28029249 DOI: 10.1021/acs.biochem.6b01132] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The intrinsic drawbacks encountered in bioactive peptides in chemical biology and biomedical sciences have diverted research efforts to the development of sequence-specific peptidomimetics that are capable of mimicking the structure and function of peptides and proteins. Modifications in the backbone and/or the side chain of peptides have been explored to develop biomimetic molecular probes or drug leads for biologically important targets. To expand the family of oligomeric peptidomimetics to facilitate their further application, we recently developed a new class of peptidomimetics, AApeptides based on a chiral peptide nucleic acid backbone. AApeptides are resistant to proteolytic degradation and amenable to enormous chemical diversification. Moreover, they could mimic the primary structure of peptides and also fold into discrete secondary structure such as helices and turn-like structures. Furthermore, they have started to show promise in applications in material and biomedical sciences. Herein, we highlight the structural design and some function of AApeptides and present our perspective on their future development.
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Affiliation(s)
- Olapeju Bolarinwa
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Alekhya Nimmagadda
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Ma Su
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, Tampa, Florida 33620, United States
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27
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Bergquist H, Rocha CSJ, Álvarez-Asencio R, Nguyen CH, Rutland MW, Smith CIE, Good L, Nielsen PE, Zain R. Disruption of Higher Order DNA Structures in Friedreich's Ataxia (GAA)n Repeats by PNA or LNA Targeting. PLoS One 2016; 11:e0165788. [PMID: 27846236 PMCID: PMC5112992 DOI: 10.1371/journal.pone.0165788] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/07/2016] [Indexed: 01/08/2023] Open
Abstract
Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigenetic modifications. With the aim of interfering with higher order H-DNA (like) DNA structures within pathological (GAA)n expansions, we examined sequence-specific interaction of peptide nucleic acid (PNA) with (GAA)n repeats of different lengths (short: n=9, medium: n=75 or long: n=115) by chemical probing of triple helical and single stranded regions. We found that a triplex structure (H-DNA) forms at GAA repeats of different lengths; however, single stranded regions were not detected within the medium size pathological repeat, suggesting the presence of a more complex structure. Furthermore, (GAA)4-PNA binding of the repeat abolished all detectable triplex DNA structures, whereas (CTT)5-PNA did not. We present evidence that (GAA)4-PNA can invade the DNA at the repeat region by binding the DNA CTT strand, thereby preventing non-canonical-DNA formation, and that triplex invasion complexes by (CTT)5-PNA form at the GAA repeats. Locked nucleic acid (LNA) oligonucleotides also inhibited triplex formation at GAA repeat expansions, and atomic force microscopy analysis showed significant relaxation of plasmid morphology in the presence of GAA-LNA. Thus, by inhibiting disease related higher order DNA structures in the Frataxin gene, such PNA and LNA oligomers may have potential for discovery of drugs aiming at recovering Frataxin expression.
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Affiliation(s)
- Helen Bergquist
- Department of Medical Biochemistry and Microbiology, Microbiology-Immunology, Uppsala University, Uppsala, Sweden
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Sweden
| | - Cristina S. J. Rocha
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Sweden
| | - Rubén Álvarez-Asencio
- KTH Royal Institute of Technology, School of Chemical Science and Engineering, Department of Chemistry, Stockholm, Sweden
| | - Chi-Hung Nguyen
- Laboratoire de Pharmacochimie, Institut Curie, PSL Research University, UMR 9187 – U 1196 CNRS-Institut Curie, INSERM, Centre Universitaire, Orsay, France
| | - Mark. W. Rutland
- KTH Royal Institute of Technology, School of Chemical Science and Engineering, Department of Chemistry, Stockholm, Sweden
| | - C. I. Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Sweden
| | - Liam Good
- Department of Pathology and Infectious Diseases, Royal Veterinary College, University of London, United Kingdom
| | - Peter E. Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, The Panum Institute, Copenhagen, Denmark
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Sweden
- Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
- * E-mail:
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Manicardi A, Bertucci A, Rozzi A, Corradini R. A Bifunctional Monomer for On-Resin Synthesis of Polyfunctional PNAs and Tailored Induced-Fit Switching Probes. Org Lett 2016; 18:5452-5455. [PMID: 27768299 DOI: 10.1021/acs.orglett.6b02363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A synthetic strategy for the production of polyfunctional PNAs bearing substituent groups both on the nucleobase and on the backbone C5 carbon of the same monomer is described; this is based on the use of a tris-orthogonally protected monomer and subsequent solid-phase selective functionalization. This strategy can be used for synthesizing PNAs that are not readily accessible by use of preformed modified monomers. As an example, a PNA-based probe that undergoes a switch in its fluorescence emission upon hybridization with a target oligonucleotide, induced by tailor-made movement of two pyrene substituent groups, was synthesized.
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Affiliation(s)
- Alex Manicardi
- Department of Chemistry, University of Parma , Parco Area delle Scienze 17/A, Parma 43123, Italy
| | - Alessandro Bertucci
- Department of Chemistry, University of Parma , Parco Area delle Scienze 17/A, Parma 43123, Italy
| | - Andrea Rozzi
- Department of Chemistry, University of Parma , Parco Area delle Scienze 17/A, Parma 43123, Italy
| | - Roberto Corradini
- Department of Chemistry, University of Parma , Parco Area delle Scienze 17/A, Parma 43123, Italy.,I.N.B.B. Consortium , Viale delle Medaglie D'Oro, 305, 00136 Roma, Italy
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29
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Asanuma H, Niwa R, Akahane M, Murayama K, Kashida H, Kamiya Y. Strand-invading linear probe combined with unmodified PNA. Bioorg Med Chem 2016; 24:4129-4137. [PMID: 27394693 DOI: 10.1016/j.bmc.2016.06.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/23/2016] [Accepted: 06/29/2016] [Indexed: 11/19/2022]
Abstract
Efficient strand invasion by a linear probe to fluorescently label double-stranded DNA has been implemented by employing a probe and unmodified PNA. As a fluorophore, we utilized ethynylperylene. Multiple ethynylperylene residues were incorporated into the DNA probe via a d-threoninol scaffold. The ethynylperylene did not significantly disrupt hybridization with complementary DNA. The linear probe self-quenched in the absence of target DNA and did not hybridize with PNA. A gel-shift assay revealed that linear probe and PNA combination invaded the central region of double-stranded DNA upon heat-shock treatment to form a double duplex. To further suppress the background emission and increase the stability of the probe/DNA duplex, a probe containing anthraquinones as well as ethynylperylene was synthesized. This probe and PNA invader pair detected an internal sequence in a double-stranded DNA with high sensitivity when heat shock treatment was used. The probe and PNA pair was able to invade at the terminus of a long double-stranded DNA at 40°C at 100mM NaCl concentration.
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Affiliation(s)
- Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
| | - Rie Niwa
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Mariko Akahane
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yukiko Kamiya
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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30
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Duplex DNA-Invading γ-Modified Peptide Nucleic Acids Enable Rapid Identification of Bloodstream Infections in Whole Blood. mBio 2016; 7:e00345-16. [PMID: 27094328 PMCID: PMC4850259 DOI: 10.1128/mbio.00345-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bloodstream infections are a leading cause of morbidity and mortality. Early and targeted antimicrobial intervention is lifesaving, yet current diagnostic approaches fail to provide actionable information within a clinically viable time frame due to their reliance on blood culturing. Here, we present a novel pathogen identification (PID) platform that features the use of duplex DNA-invading γ-modified peptide nucleic acids (γPNAs) for the rapid identification of bacterial and fungal pathogens directly from blood, without culturing. The PID platform provides species-level information in under 2.5 hours while reaching single-CFU-per-milliliter sensitivity across the entire 21-pathogen panel. The clinical utility of the PID platform was demonstrated through assessment of 61 clinical specimens, which showed >95% sensitivity and >90% overall correlation to blood culture findings. This rapid γPNA-based platform promises to improve patient care by enabling the administration of a targeted first-line antimicrobial intervention. Bloodstream infections continue to be a major cause of death for hospitalized patients, despite significant improvements in both the availability of treatment options as well their application. Since early and targeted antimicrobial intervention is one of the prime determinants of patient outcome, the rapid identification of the pathogen can be lifesaving. Unfortunately, current diagnostic approaches for identifying these infections all rely on time-consuming blood culture, which precludes immediate intervention with a targeted antimicrobial. To address this, we have developed and characterized a new and comprehensive methodology, from patient specimen to result, for the rapid identification of both bacterial and fungal pathogens without the need for culturing. We anticipate broad interest in our work, given the novelty of our technical approach combined with an immense unmet need.
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31
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Bohländer PR, Vilaivan T, Wagenknecht HA. Strand displacement and duplex invasion into double-stranded DNA by pyrrolidinyl peptide nucleic acids. Org Biomol Chem 2015. [PMID: 26223770 DOI: 10.1039/c5ob01273b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The so-called acpcPNA system bears a peptide backbone consisting of 4'-substituted proline units with (2'R,4'R) configuration in an alternating combination with (2S)-amino-cyclopentane-(1S)-carboxylic acids. acpcPNA forms exceptionally stable hybrids with complementary DNA. We demonstrate herein (i) strand displacements by single-stranded DNA from acpcPNA-DNA hybrids, and by acpcPNA strands from DNA duplexes, and (ii) strand invasions by acpcPNA into double-stranded DNA. These processes were studied in vitro using synthetic oligonucleotides and by means of our concept of wavelength-shifting fluorescent nucleic acid probes, including fluorescence lifetime measurements that allow quantifying energy transfer efficiencies. The strand displacements of preannealed 14mer acpcPNA-7mer DNA hybrids consecutively by 10mer and 14mer DNA strands occur with rather slow kinetics but yield high fluorescence color ratios (blue : yellow or blue : red), fluorescence intensity enhancements, and energy transfer efficiencies. Furthermore, 14mer acpcPNA strands are able to invade into 30mer double-stranded DNA, remarkably with quantitative efficiency in all studied cases. These processes can also be quantified by means of fluorescence. This remarkable behavior corroborates the extraordinary versatile properties of acpcPNA. In contrast to conventional PNA systems which require 3 or more equivalents PNA, only 1.5 equivalents acpcPNA are sufficient to get efficient double duplex invasion. Invasions also take place even in the presence of 250 mM NaCl which represents an ionic strength nearly twice as high as the physiological ion concentration. These remarkable results corroborate the extraordinary properties of acpcPNA, and thus acpcPNA represents an eligible tool for biological analytics and antigene applications.
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Affiliation(s)
- Peggy R Bohländer
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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32
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Sacui I, Hsieh WC, Manna A, Sahu B, Ly DH. Gamma Peptide Nucleic Acids: As Orthogonal Nucleic Acid Recognition Codes for Organizing Molecular Self-Assembly. J Am Chem Soc 2015; 137:8603-10. [PMID: 26079820 DOI: 10.1021/jacs.5b04566] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nucleic acids are an attractive platform for organizing molecular self-assembly because of their specific nucleobase interactions and defined length scale. Routinely employed in the organization and assembly of materials in vitro, however, they have rarely been exploited in vivo, due to the concerns for enzymatic degradation and cross-hybridization with the host's genetic materials. Herein we report the development of a tight-binding, orthogonal, synthetically versatile, and informationally interfaced nucleic acid platform for programming molecular interactions, with implications for in vivo molecular assembly and computing. The system consists of three molecular entities: the right-handed and left-handed conformers and a nonhelical domain. The first two are orthogonal to each other in recognition, while the third is capable of binding to both, providing a means for interfacing the two conformers as well as the natural nucleic acid biopolymers (i.e., DNA and RNA). The three molecular entities are prepared from the same monomeric chemical scaffold, with the exception of the stereochemistry or lack thereof at the γ-backbone that determines if the corresponding oligo adopts a right-handed or left-handed helix, or a nonhelical motif. These conformers hybridize to each other with exquisite affinity, sequence selectivity, and level of orthogonality. Recognition modules as short as five nucleotides in length are capable of organizing molecular assembly.
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Affiliation(s)
- Iulia Sacui
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Wei-Che Hsieh
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Arunava Manna
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Bichismita Sahu
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Danith H Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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33
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Komiyama M. Chemical modifications of artificial restriction DNA cutter (ARCUT) to promote its in vivo and in vitro applications. ARTIFICIAL DNA, PNA & XNA 2014; 5:e1112457. [PMID: 26744220 PMCID: PMC5329899 DOI: 10.1080/1949095x.2015.1112457] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 05/10/2023]
Abstract
Recently, completely chemistry-based tools for site-selective scission of DNA (ARCUT) have been prepared by combining 2 strands of pseudo-complementary PNA (pcPNA: site-selective activator) and a Ce(IV)-EDTA complex (molecular scissors). Its site-specificity is sufficient to cut the whole human genome at one predetermined site. In this first-generation ARCUT, however, there still remain several problems to be solved for wider applications. This review presents recent approaches to solve these problems. They are divided into (i) covalent modification of pcPNA with other functional groups and (ii) new strategies using conventional PNA, in place of pcPNA, as site-selective activator. Among various chemical modifications, conjugation with positively-charged nuclear localization signal peptide is especially effective. Furthermore, unimolecular activators, a single strand of which successfully activates the target site in DNA for site-selective scission, have been also developed. As the result of these modifications, the site-selective scission by Ce(IV)-EDTA was achieved promptly even under high salt conditions which are otherwise unfavourable for double-duplex invasion. Furthermore, it has been shown that "molecular crowding effect," which characterizes the inside of living cells, enormously promotes the invasion, and thus the invasion seems to proceed effectively and spontaneously in the cells. Strong potential of pcPNA for further applications in vivo and in vitro has been confirmed.
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Affiliation(s)
- Makoto Komiyama
- Life Science Center of Tsukuba Advanced Research Alliance; University of Tsukuba; Tsukuba, Ibaraki, Japan
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34
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Moccia M, Adamo MFA, Saviano M. Insights on chiral, backbone modified peptide nucleic acids: Properties and biological activity. ARTIFICIAL DNA, PNA & XNA 2014; 5:e1107176. [PMID: 26752710 PMCID: PMC5329900 DOI: 10.1080/1949095x.2015.1107176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 10/02/2015] [Accepted: 10/07/2015] [Indexed: 12/14/2022]
Abstract
PNAs are emerging as useful synthetic devices targeting natural miRNAs. In particular 3 classes of structurally modified PNAs analogs are herein described, namely α, β and γ, which differ by their backbone modification. Their mode and binding affinity for natural nucleic acids and their use in medicinal chemistry as potential miRNA binders is discussed.
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Affiliation(s)
- Maria Moccia
- Consiglio Nazionale delle Ricerche-Institute of Cristallography; Bari, Italy
| | - Mauro F A Adamo
- Centre for Synthesis and Chemical Biology (CSCB); Department of Pharmaceutical & Medicinal Chemistry; Royal College of Surgeons in Ireland; Dublin, Ireland
| | - Michele Saviano
- Consiglio Nazionale delle Ricerche-Institute of Cristallography; Bari, Italy
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35
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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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36
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Kuhn H, Sahu B, Rapireddy S, Ly DH, Frank-Kamenetskii MD. Sequence specificity at targeting double-stranded DNA with a γ-PNA oligomer modified with guanidinium G-clamp nucleobases. ARTIFICIAL DNA, PNA & XNA 2014; 1:45-53. [PMID: 21687526 DOI: 10.4161/adna.1.1.12444] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Revised: 05/19/2010] [Accepted: 05/24/2010] [Indexed: 11/19/2022]
Abstract
γ-PNA, a new class of peptide nucleic acids, promises to overcome previous sequence limitations of double-stranded DNA (dsDNA) targeting with PNA. To check the potential of γ-PNA, we have synthesized a biotinylated, pentadecameric γ-PNA of mixed sequence carrying three guanidinium G-clamp nucleobases. We have found that strand invasion reactions of the γ-PNA oligomer to its fully complementary target within dsDNA occurs with significantly higher binding rates than to targets containing single mismatches. Association of the PNA oligomer to mismatched targets does not go to completion but instead reaches a stationary level at or below 60%, even at conditions of very low ionic strength. Initial binding rates to both matched and mismatched targets experience a steep decrease with increasing salt concentration. We demonstrate that a linear DNA target fragment with the correct target sequence can be purified from DNA mixtures containing mismatched target or unrelated genomic DNA by affinity capture with streptavidin-coated magnetic beads. Similarly, supercoiled plasmid DNA is obtained with high purity from an initial sample mixture that included a linear DNA fragment with the fully complementary sequence. Based on the results obtained in this study we believe that γ-PNA has a great potential for specific targeting of chosen duplex DNA sites in a sequence-unrestricted fashion.
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Affiliation(s)
- Heiko Kuhn
- Center for Advanced Biotechnology; Department of Biomedical Engineering; Boston University; Boston, MA USA
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37
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Abstract
Chiral open-chain PNAs have been shown to have improved properties in terms of control of helical handedness, DNA affinity, sequence selectivity, and cellular uptake. They can be synthesized either using preformed chiral monomers or by means of a submonomeric strategy. The former is preferred when only a stereogenic center is present at C-5, whereas for PNA-bearing substituents at C-2, the submonomeric approach is preferred, since racemization, generally occurring during the solid-phase synthesis, can be minimized by this procedure. Here we describe the protocols for the synthesis of PNA oligomers containing C-2- or C-5- (or both) modified monomers and a GC method for checking the optical purity of C-2-modified PNAs.
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38
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Xia X, Piao X, Bong D. Bifacial peptide nucleic acid as an allosteric switch for aptamer and ribozyme function. J Am Chem Soc 2014; 136:7265-8. [PMID: 24796374 DOI: 10.1021/ja5032584] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We demonstrate herein that bifacial peptide nucleic acid (bPNA) hybrid triplexes functionally substitute for duplex DNA or RNA. Structure-function loss in three non-coding nucleic acids was inflicted by replacement of a duplex stem with unstructured oligo-T/U strands, which are bPNA binding sites. Functional rescue was observed on refolding of the oligo-T/U strands into bPNA triplex hybrid stems. Bifacial PNA binding was thus used to allosterically switch-on protein and small-molecule binding in DNA and RNA aptamers, as well as catalytic bond scission in a ribozyme. Duplex stems that support the catalytic site of a minimal type I hammerhead ribozyme were replaced with oligo-U loops, severely crippling or ablating the native RNA splicing function. Refolding of the U-loops into bPNA triplex stems completely restored splicing function in the hybrid system. These studies indicate that bPNA may have general utility as an allosteric trigger for a wide range of functions in non-coding nucleic acids.
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Affiliation(s)
- Xin Xia
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
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39
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Bahal R, McNeer NA, Ly DH, Saltzman WM, Glazer PM. Nanoparticle for delivery of antisense γPNA oligomers targeting CCR5. ARTIFICIAL DNA, PNA & XNA 2014; 4:49-57. [PMID: 23954968 DOI: 10.4161/adna.25628] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The development of a new class of peptide nucleic acids (PNAs), i.e., gamma PNAs (γPNAs), creates the need for a general and effective method for its delivery into cells for regulating gene expression in mammalian cells. Here we report the antisense activity of a recently developed hydrophilic and biocompatible diethylene glycol (miniPEG)-based gamma peptide nucleic acid called MPγPNAs via its delivery by poly(lactide-co-glycolide) (PLGA)-based nanoparticle system. We show that MPγPNA oligomers designed to bind to the selective region of chemokine receptor 5 (CC R5) transcript, induce potent and sequence-specific antisense effects as compared with regular PNA oligomers. In addition, PLGA nanoparticle delivery of MPγPNAs is not toxic to the cells. The findings reported in this study provide a combination of γPNA technology and PLGA-based nanoparticle delivery method for regulating gene expression in live cells via the antisense mechanism.
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40
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Rapid Access to Multiple Classes of Peptidomimetics from Common γ-AApeptide Building Blocks. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301841] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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41
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Gambari R. Peptide nucleic acids: a review on recent patents and technology transfer. Expert Opin Ther Pat 2014; 24:267-94. [PMID: 24405414 DOI: 10.1517/13543776.2014.863874] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION DNA/RNA-based drugs are considered of major interest in molecular diagnosis and nonviral gene therapy. In this field, peptide nucleic acids (PNAs, DNA analogs in which the sugar-phosphate backbone is replaced by N-(2-aminoethyl)glycine units or similar building blocks) have been demonstrated to be excellent candidates as diagnostic reagents and biodrugs. AREAS COVERED Recent (2002 - 2013) patents based on studies on development of PNA analogs, delivery systems for PNAs, applications of PNAs in molecular diagnosis, and use of PNA for innovative therapeutic protocols. EXPERT OPINION PNAs are unique reagents in molecular diagnosis and have been proven to be very active and specific for alteration of gene expression, despite the fact that solubility and uptake by target cells can be limiting factors. Accordingly, patents on PNAs have taken in great consideration delivery strategies. PNAs have been proven stable and effective in vivo, despite the fact that possible long-term toxicity should be considered. For possible clinical applications, the use of PNA molecules in combination with drugs already employed in therapy has been suggested. Considering the patents available and the results on in vivo testing on animal models, we expect in the near future relevant PNA-based clinical trials.
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Affiliation(s)
- Roberto Gambari
- University of Ferrara, Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section , Via Fossato di Mortara n.74, 44100 Ferrara , Italy +39 532 974443 ; +39 532 974500 ;
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42
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Abstract
Peptide nucleic acids (PNAs) are attractive, as compared to other classes of oligonucleotides that have been developed to date, in that they are relatively easy to synthesize and modify, hybridize to DNA and RNA with high affinity and sequence selectivity, and are resistant to enzymatic degradation by proteases and nucleases; however, the downside is that they are only moderately soluble in aqueous solution. Herein we describe the protocols for synthesizing the second-generation γPNAs, both the monomers and oligomers, containing MiniPEG side chain with considerable improvements in water solubility, biocompatibility, and hybridization properties.
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Affiliation(s)
- Arunava Manna
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, USA
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43
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Wu H, Li Y, Bai G, Niu Y, Qiao Q, Tipton JD, Cao C, Cai J. γ-AApeptide-based small-molecule ligands that inhibit Aβ aggregation. Chem Commun (Camb) 2013; 50:5206-8. [PMID: 24158240 DOI: 10.1039/c3cc46685j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report the design, synthesis, characterization and evaluation of a novel class of γ-AApeptide one-bead-one-compound (OBOC) library, from which a small γ-AApeptide was identified to effectively prevent and disassemble Aβ aggregation.
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Affiliation(s)
- Haifan Wu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA.
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44
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Kameshima W, Ishizuka T, Minoshima M, Yamamoto M, Sugiyama H, Xu Y, Komiyama M. Conjugation of peptide nucleic acid with a pyrrole/imidazole polyamide to specifically recognize and cleave DNA. Angew Chem Int Ed Engl 2013; 52:13681-4. [PMID: 24155125 DOI: 10.1002/anie.201305489] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/03/2013] [Indexed: 11/06/2022]
Abstract
Cut loose: A pseudocomplementary peptide nucleic acid was tethered to a pyrrole/imidazole hairpin polyamide, and was used to selectively target a specific DNA sequence. Binding even occurs under high salt conditions. Furthermore, the conjugate facilitated sequence-specific scission of long dsDNA. This simple approach promises to resolve the technical difficulties in targeting DNA sequences with PNA.
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Affiliation(s)
- Wataru Kameshima
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904 (Japan)
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45
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Kameshima W, Ishizuka T, Minoshima M, Yamamoto M, Sugiyama H, Xu Y, Komiyama M. Conjugation of Peptide Nucleic Acid with a Pyrrole/Imidazole Polyamide to Specifically Recognize and Cleave DNA. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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46
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Yaroslavsky AI, Smolina IV. Fluorescence imaging of single-copy DNA sequences within the human genome using PNA-directed padlock probe assembly. ACTA ACUST UNITED AC 2013; 20:445-53. [PMID: 23521801 DOI: 10.1016/j.chembiol.2013.02.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 12/24/2012] [Accepted: 02/07/2013] [Indexed: 01/07/2023]
Abstract
We present an approach for fluorescent in situ detection of short, single-copy sequences within genomic DNA in human cells. The single-copy sensitivity and single-base specificity of our method is achieved due to the combination of three components. First, a peptide nucleic acid (PNA) probe locally opens a chosen target site, which allows a padlock DNA probe to access the site and become ligated. Second, rolling circle amplification (RCA) generates thousands of single-stranded copies of the target sequence. Finally, fluorescent in situ hybridization (FISH) is used to visualize the amplified DNA. We validate this technique by successfully detecting six single-copy target sites on human mitochondrial and autosomal DNA. We also demonstrate the high selectivity of this method by detecting X- and Y-specific sequences on human sex chromosomes and by simultaneously detecting three sequence-specific target sites. Finally, we discriminate two target sites that differ by 2 nt. The PNA-RCA-FISH approach is a distinctive in situ hybridization method capable of multitarget visualization within human chromosomes and nuclei that does not require DNA denaturation and is extremely sequence specific.
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De A, Souchelnytskyi S, van den Berg A, Carlen ET. Peptide nucleic acid (PNA)-DNA duplexes: comparison of hybridization affinity between vertically and horizontally tethered PNA probes. ACS APPLIED MATERIALS & INTERFACES 2013; 5:4607-4612. [PMID: 23668364 DOI: 10.1021/am4011429] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We compare the PNA-DNA duplex hybridization characteristics of vertically tethered and new horizontally tethered PNA probes on solid surfaces. The horizontal 15-mer PNA probe has been synthesized with linker molecules attached at three locations (γ-points) positioned along the PNA backbone that provides covalent attachment of the probe with the backbone aligned parallel to the surface, which is important for DNA hybridization assays that use electric field effect sensors for detection. A radioactive labeled assay and real-time surface plasmon resonance (SPR) biosensor are used to assess the probe surface density, nonspecific binding, and DNA hybridization affinity, respectively, of the new PNA probe configuration. The estimated equilibrium dissociation constants of the horizontally tethered duplex and the vertically tethered duplex are of the same order of magnitude (KD ≈ 5 nM), which indicates a sufficient hybridization affinity for many electronic biosensors that benefit from the horizontal alignment, which minimizes the effects of counterion screening.
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De Costa NTS, Heemstra JM. Evaluating the effect of ionic strength on duplex stability for PNA having negatively or positively charged side chains. PLoS One 2013; 8:e58670. [PMID: 23484047 PMCID: PMC3590165 DOI: 10.1371/journal.pone.0058670] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 02/06/2013] [Indexed: 11/19/2022] Open
Abstract
The enhanced thermodynamic stability of PNA:DNA and PNA:RNA duplexes compared with DNA:DNA and DNA:RNA duplexes has been attributed in part to the lack of electrostatic repulsion between the uncharged PNA backbone and negatively charged DNA or RNA backbone. However, there are no previously reported studies that systematically evaluate the effect of ionic strength on duplex stability for PNA having a charged backbone. Here we investigate the role of charge repulsion in PNA binding by synthesizing PNA strands having negatively or positively charged side chains, then measuring their duplex stability with DNA or RNA at varying salt concentrations. At low salt concentrations, positively charged PNA binds more strongly to DNA and RNA than does negatively charged PNA. However, at medium to high salt concentrations, this trend is reversed, and negatively charged PNA shows higher affinity for DNA and RNA than does positively charged PNA. These results show that charge screening by counterions in solution enables negatively charged side chains to be incorporated into the PNA backbone without reducing duplex stability with DNA and RNA. This research provides new insight into the role of electrostatics in PNA binding, and demonstrates that introduction of negatively charged side chains is not significantly detrimental to PNA binding affinity at physiological ionic strength. The ability to incorporate negative charge without sacrificing binding affinity is anticipated to enable the development of PNA therapeutics that take advantage of both the inherent benefits of PNA and the multitude of charge-based delivery technologies currently being developed for DNA and RNA.
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Affiliation(s)
- N. Tilani S. De Costa
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, United States of America
| | - Jennifer M. Heemstra
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, United States of America
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Moreno PMD, Geny S, Pabon YV, Bergquist H, Zaghloul EM, Rocha CSJ, Oprea II, Bestas B, Andaloussi SE, Jørgensen PT, Pedersen EB, Lundin KE, Zain R, Wengel J, Smith CIE. Development of bis-locked nucleic acid (bisLNA) oligonucleotides for efficient invasion of supercoiled duplex DNA. Nucleic Acids Res 2013; 41:3257-73. [PMID: 23345620 PMCID: PMC3597675 DOI: 10.1093/nar/gkt007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In spite of the many developments in synthetic oligonucleotide (ON) chemistry and design, invasion into double-stranded DNA (DSI) under physiological salt and pH conditions remains a challenge. In this work, we provide a new ON tool based on locked nucleic acids (LNAs), designed for strand invasion into duplex DNA (DSI). We thus report on the development of a clamp type of LNA ON—bisLNA—with capacity to bind and invade into supercoiled double-stranded DNA. The bisLNA links a triplex-forming, Hoogsteen-binding, targeting arm with a strand-invading Watson–Crick binding arm. Optimization was carried out by varying the number and location of LNA nucleotides and the length of the triplex-forming versus strand-invading arms. Single-strand regions in target duplex DNA were mapped using chemical probing. By combining design and increase in LNA content, it was possible to achieve a 100-fold increase in potency with 30% DSI at 450 nM using a bisLNA to plasmid ratio of only 21:1. Although this first conceptual report does not address the utility of bisLNA for the targeting of DNA in a chromosomal context, it shows bisLNA as a promising candidate for interfering also with cellular genes.
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Affiliation(s)
- Pedro M D Moreno
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, 141 86 Huddinge, Stockholm, Sweden
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Sugiyama T, Kittaka A. Chiral peptide nucleic acids with a substituent in the N-(2-aminoethy)glycine backbone. Molecules 2012; 18:287-310. [PMID: 23271467 PMCID: PMC6269907 DOI: 10.3390/molecules18010287] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 12/19/2012] [Accepted: 12/19/2012] [Indexed: 11/16/2022] Open
Abstract
A peptide nucleic acid (PNA) is a synthetic nucleic acid mimic in which the sugar-phosphate backbone is replaced by a peptide backbone. PNAs hybridize to complementary DNA and RNA with higher affinity and superior sequence selectivity compared to DNA. PNAs are resistant to nucleases and proteases and have a low affinity for proteins. These properties make PNAs an attractive agent for biological and medical applications. To improve the antisense and antigene properties of PNAs, many backbone modifications of PNAs have been explored under the concept of preorganization. This review focuses on chiral PNAs bearing a substituent in the N-(2-aminoethyl)glycine backbone. Syntheses, properties, and applications of chiral PNAs are described.
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Affiliation(s)
- Toru Sugiyama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
- Author to whom correspondence should be addressed; E-Mail: ; Tel./Fax: +81-3-5465-8743
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Kaga, Itabashi-ku, Tokyo 173-8605, Japan; E-Mail:
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