1
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Hofman CR, Corey DR. Targeting RNA with synthetic oligonucleotides: Clinical success invites new challenges. Cell Chem Biol 2024; 31:125-138. [PMID: 37804835 PMCID: PMC10841528 DOI: 10.1016/j.chembiol.2023.09.005] [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: 07/05/2023] [Revised: 08/27/2023] [Accepted: 09/15/2023] [Indexed: 10/09/2023]
Abstract
Synthetic antisense oligonucleotides (ASOs) and duplex RNAs (dsRNAs) are an increasingly successful strategy for drug development. After a slow start, the pace of success has accelerated since the approval of Spinraza (nusinersen) in 2016 with several drug approvals. These accomplishments have been achieved even though oligonucleotides are large, negatively charged, and have little resemblance to traditional small-molecule drugs-a remarkable achievement of basic and applied science. The goal of this review is to summarize the foundation underlying recent progress and describe ongoing research programs that may increase the scope and impact of oligonucleotide therapeutics.
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Affiliation(s)
- Cristina R Hofman
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - David R Corey
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA.
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2
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Malik S, Pradeep SP, Kumar V, Xiao Y, Deng Y, Fan R, Vasquez JC, Singh V, Bahal R. Antitumor efficacy of a sequence-specific DNA-targeted γPNA-based c-Myc inhibitor. Cell Rep Med 2024; 5:101354. [PMID: 38183981 PMCID: PMC10829792 DOI: 10.1016/j.xcrm.2023.101354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 09/21/2023] [Accepted: 12/11/2023] [Indexed: 01/08/2024]
Abstract
Targeting oncogenes at the genomic DNA level can open new avenues for precision medicine. Significant efforts are ongoing to target oncogenes using RNA-targeted and protein-targeted platforms, but no progress has been made to target genomic DNA for cancer therapy. Here, we introduce a gamma peptide nucleic acid (γPNA)-based genomic DNA-targeted platform to silence oncogenes in vivo. γPNAs efficiently invade the mixed sequences of genomic DNA with high affinity and specificity. As a proof of concept, we establish that γPNA can inhibit c-Myc transcription in multiple cell lines. We evaluate the in vivo efficacy and safety of genomic DNA targeting in three pre-clinical models. We also establish that anti-transcription γPNA in combination with histone deacetylase inhibitors and chemotherapeutic drugs results in robust antitumor activity in cell-line- and patient-derived xenografts. Overall, this strategy offers a unique therapeutic platform to target genomic DNA to inhibit oncogenes for cancer therapy.
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Affiliation(s)
- Shipra Malik
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Sai Pallavi Pradeep
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Vikas Kumar
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Yong Xiao
- Department of Biomedical Engineering, Yale University, New Haven, CT 06510, USA; Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT 06510, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06510, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA; Human and Translational Immunology, Yale School of Medicine, New Haven, CT 06520, USA; Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Juan C Vasquez
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Vijender Singh
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA.
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3
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Bekkouche I, Shishonin AY, Vetcher AA. Recent Development in Biomedical Applications of Oligonucleotides with Triplex-Forming Ability. Polymers (Basel) 2023; 15:polym15040858. [PMID: 36850142 PMCID: PMC9964087 DOI: 10.3390/polym15040858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/12/2023] Open
Abstract
A DNA structure, known as triple-stranded DNA, is made up of three oligonucleotide chains that wind around one another to form a triple helix (TFO). Hoogsteen base pairing describes how triple-stranded DNA may be built at certain conditions by the attachment of the third strand to an RNA, PNA, or DNA, which might all be employed as oligonucleotide chains. In each of these situations, the oligonucleotides can be employed as an anchor, in conjunction with a specific bioactive chemical, or as a messenger that enables switching between transcription and replication through the triplex-forming zone. These data are also considered since various illnesses have been linked to the expansion of triplex-prone sequences. In light of metabolic acidosis and associated symptoms, some consideration is given to the impact of several low-molecular-weight compounds, including pH on triplex production in vivo. The review is focused on the development of biomedical oligonucleotides with triplexes.
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Affiliation(s)
- Incherah Bekkouche
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya Str. 6, Moscow 117198, Russia
| | - Alexander Y. Shishonin
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia
| | - Alexandre A. Vetcher
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya Str. 6, Moscow 117198, Russia
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia
- Correspondence:
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4
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Ivanov GS, Tribulovich VG, Pestov NB, David TI, Amoah AS, Korneenko TV, Barlev NA. Artificial genetic polymers against human pathologies. Biol Direct 2022; 17:39. [PMID: 36474260 PMCID: PMC9727881 DOI: 10.1186/s13062-022-00353-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Originally discovered by Nielsen in 1991, peptide nucleic acids and other artificial genetic polymers have gained a lot of interest from the scientific community. Due to their unique biophysical features these artificial hybrid polymers are now being employed in various areas of theranostics (therapy and diagnostics). The current review provides an overview of their structure, principles of rational design, and biophysical features as well as highlights the areas of their successful implementation in biology and biomedicine. Finally, the review discusses the areas of improvement that would allow their use as a new class of therapeutics in the future.
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Affiliation(s)
- Gleb S Ivanov
- Institute of Cytology, Tikhoretsky Ave 4, Saint Petersburg, Russia, 194064
- St. Petersburg State Technological Institute (Technical University), Saint Petersburg, Russia, 190013
| | - Vyacheslav G Tribulovich
- St. Petersburg State Technological Institute (Technical University), Saint Petersburg, Russia, 190013
| | - Nikolay B Pestov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow, Russia, 108819
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, 117997
- Institute of Biomedical Chemistry, Moscow, Russia, 119121б
| | - Temitope I David
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
| | - Abdul-Saleem Amoah
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
| | - Tatyana V Korneenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, 117997
| | - Nikolai A Barlev
- Institute of Cytology, Tikhoretsky Ave 4, Saint Petersburg, Russia, 194064.
- Institute of Biomedical Chemistry, Moscow, Russia, 119121б.
- School of Medicine, Nazarbayev University, 010000, Astana, Kazakhstan.
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5
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Clausse V, Zheng H, Amarasekara H, Kruhlak M, Appella DH. Thyclotides, tetrahydrofuran-modified peptide nucleic acids that efficiently penetrate cells and inhibit microRNA-21. Nucleic Acids Res 2022; 50:10839-10856. [PMID: 36215040 DOI: 10.1093/nar/gkac864] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/14/2022] [Accepted: 09/26/2022] [Indexed: 11/12/2022] Open
Abstract
Peptide nucleic acids (PNAs) are promising therapeutic molecules for gene modulation; however, they suffer from poor cell uptake. Delivery of PNAs into cells requires conjugation of the PNA to another large molecule, typically a cell-penetrating peptide or nanoparticle. In this study, we describe a new PNA-based molecule with cyclic tetrahydrofuran (THF) backbone modifications that in some cases considerably improve cell uptake. We refer to these THF-PNA oligomers as thyclotides. With THF groups at every position of the oligomer, the cell uptake of thyclotides targeted to miR-21 is enhanced compared with the corresponding unmodified PNA based on an aminoethylglycine backbone. An optimized thyclotide can efficiently enter cells without the use of cell-penetrating peptides, bind miR-21, its designated microRNA target, decrease expression of miR-21 and increase expression of three downstream targets (PTEN, Cdc25a and KRIT1). Using a plasmid with the PTEN-3'UTR coupled with luciferase, we further confirmed that a miR-21-targeted thyclotide prevents miR-21 from binding to its target RNA. Additionally, the thyclotide shows no cytotoxicity when administered at 200 times its active concentration. We propose that thyclotides be further explored as therapeutic candidates to modulate miRNA levels.
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Affiliation(s)
- Victor Clausse
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hongchao Zheng
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Harsha Amarasekara
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Kruhlak
- Microscopy Core Facility, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
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6
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Brodyagin N, Kataoka Y, Kumpina I, McGee DW, Rozners E. Cellular uptake of 2-aminopyridine-modified peptide nucleic acids conjugated with cell-penetrating peptides. Biopolymers 2021; 113:e23484. [PMID: 34914092 DOI: 10.1002/bip.23484] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 01/31/2023]
Abstract
Cell-penetrating peptides (CPPs) have been extensively used to deliver peptide nucleic acid (PNA) in cells. We have previously found that replacement of cytosine in triplex-forming PNAs with 2-aminopyridine (M) not only enhanced RNA binding, but also improved cellular uptake of PNAs. In this study, we used confocal fluorescence microscopy to evaluate the ability of CPPs to further improve cellular uptake of M-modified PNAs. We found that PNAs conjugated with Tat and octa-arginine peptides were effectively taken up in MCF7 cells when supplied in cell media at 1 μM. Remarkably, M-modified PNA without any CPP conjugation also showed strong uptake when the concentration was increased to 5 μM. Majority of PNA conjugates remained localized in distinct cytoplasmic vesicles, as judged by dot-like fluorescence patterns. However, M-modified PNAs conjugated with Tat, octa-arginine, and even a simple tri-lysine peptide also showed dispersed fluorescence in cytoplasm and were taken up in nuclei where they localized in larger vesicles, most likely nucleoli. Endosomolytic peptides or chemicals (chloroquine and CaCl2 ) did not release the conjugates from cytosolic vesicles, which suggested that the PNAs were not entrapped in endosomes. We hypothesize that M-modified PNAs escape endosomes and accumulate in cellular compartments rich in RNA, such as nucleoli, stress granules, and P-bodies.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York, USA
| | - Yuka Kataoka
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York, USA
| | - Ilze Kumpina
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York, USA
| | - Dennis W McGee
- Department of Biological Sciences, Binghamton University, The State University of New York, Binghamton, New York, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York, USA
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7
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Extracellular vesicles mediated exocytosis of antisense peptide nucleic acids. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:302-315. [PMID: 34458012 PMCID: PMC8379631 DOI: 10.1016/j.omtn.2021.07.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/27/2021] [Indexed: 12/19/2022]
Abstract
Peptide nucleic acids (PNAs), a synthetic DNA mimic, have been extensively utilized for antisense- and antigene-based biomedical applications. Significant efforts have been made to increase the cellular uptake of PNAs, but here we examined relatively unexplored aspects of intracellular trafficking and endocytic recycling of PNAs. For proof-of-concept, we used anti-microRNA (miR) PNA targeting miR-155. The sub-cellular localization of PNA was studied via confocal and flow-cytometry-based assays in HeLa cells. A comprehensive characterization of PNA-containing extracellular vesicles revealed spherical morphology, negative surface charge density, and the presence of tetraspanin markers. Most importantly, we investigated rab11a and rab27b GTPases' role in regulating the exocytosis of PNAs. Organelle staining, followed by confocal imaging, showed higher localization of PNA in lysosomes. Gene-expression analysis established the enhanced functional activity of PNA after inhibition of endocytic recycling. Multiple studies report the exocytosis of single-stranded oligonucleotides, short interfering RNAs (siRNAs), and nanocarriers. To our knowledge, this is the first mechanistic study to establish that PNA undergoes endocytic recycling and exocytosis out of tumor cells. The results presented here can serve as a platform to develop and optimize strategies for improving the therapeutic efficacy of PNAs by avoiding the recycling pathways.
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8
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Brodyagin N, Katkevics M, Kotikam V, Ryan CA, Rozners E. Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications. Beilstein J Org Chem 2021; 17:1641-1688. [PMID: 34367346 PMCID: PMC8313981 DOI: 10.3762/bjoc.17.116] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/28/2021] [Indexed: 12/23/2022] Open
Abstract
Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA's chemistry, optimization of structure and function, applications as probes and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA's binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA therapeutics. While many modifications have improved on PNA's binding affinity and specificity, solubility and other biophysical properties, the original PNA is still most frequently used in diagnostic and other in vitro applications. Development of therapeutics and other in vivo applications of PNA has notably lagged behind and is still limited by insufficient bioavailability and difficulties with tissue specific delivery. Relatively high doses are required to overcome poor cellular uptake and endosomal entrapment, which increases the risk of toxicity. These limitations remain unsolved problems waiting for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Venubabu Kotikam
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Christopher A Ryan
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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9
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Perera JDR, Carufe KEW, Glazer PM. Peptide nucleic acids and their role in gene regulation and editing. Biopolymers 2021; 112:e23460. [PMID: 34129732 DOI: 10.1002/bip.23460] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/19/2022]
Abstract
The unique properties of peptide nucleic acid (PNA) makes it a desirable candidate to be used in therapeutic and biotechnological interventions. It has been broadly utilized for numerous applications, with a major focus in regulation of gene expression, and more recently in gene editing. While the classic PNA design has mainly been employed to date, chemical modifications of the PNA backbone and nucleobases provide an avenue to advance the technology further. This review aims to discuss the recent developments in PNA based gene manipulation techniques and the use of novel chemical modifications to improve the current state of PNA mediated gene targeting.
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Affiliation(s)
- J Dinithi R Perera
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kelly E W Carufe
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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10
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Krissanaprasit A, Key CM, Froehlich K, Pontula S, Mihalko E, Dupont DM, Andersen ES, Kjems J, Brown AC, LaBean TH. Multivalent Aptamer-Functionalized Single-Strand RNA Origami as Effective, Target-Specific Anticoagulants with Corresponding Reversal Agents. Adv Healthc Mater 2021; 10:e2001826. [PMID: 33882195 DOI: 10.1002/adhm.202001826] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/23/2021] [Indexed: 12/15/2022]
Abstract
Anticoagulants are commonly utilized during surgeries and to treat thrombotic diseases like stroke and deep vein thrombosis. However, conventional anticoagulants have serious side-effects, narrow therapeutic windows, and lack safe reversal agents (antidotes). Here, an alternative RNA origami displaying RNA aptamers as target-specific anticoagulant is described. Improved design and construction techniques for self-folding, single-molecule RNA origami as a platform for displaying pre-selected RNA aptamers with precise orientational and spatial control are reported. Nuclease resistance is added using 2'-fluoro-modified pyrimidines during in vitro transcription. When four aptamers are displayed on the RNA origami platform, the measured thrombin inhibition and anticoagulation activity is higher than observed for free aptamers, ssRNA-linked RNA aptamers, and RNA origami displaying fewer aptamers. Importantly, thrombin inhibition is immediately switched off by addition of specific reversal agents. Results for single-stranded DNA (ssDNA) and single-stranded peptide nucleic acid (PNA) antidotes show restoration of 63% and 95% coagulation activity, respectively. To demonstrate potential for practical, long-term storage for clinical use, RNA origami is freeze-dried, and stored at room temperature. Freshly produced and freeze-dried RNA show identical levels of activity in coagulation assays. Compared to current commercial intravenous anticoagulants, RNA origami-based molecules show promise as safer alternatives with rapid activity switching for future therapeutic applications.
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Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering College of Engineering North Carolina State University Raleigh NC 27695 USA
| | - Carson M. Key
- Department of Materials Science and Engineering College of Engineering North Carolina State University Raleigh NC 27695 USA
| | - Kristen Froehlich
- Joint Department of Biomedical Engineering College of Engineering North Carolina State University and University of North Carolina – Chapel Hill Raleigh NC 27695 USA
| | | | - Emily Mihalko
- Joint Department of Biomedical Engineering College of Engineering North Carolina State University and University of North Carolina – Chapel Hill Raleigh NC 27695 USA
| | - Daniel M. Dupont
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Aarhus C Aarhus 8000 Denmark
| | - Ebbe S. Andersen
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Aarhus C Aarhus 8000 Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Aarhus C Aarhus 8000 Denmark
| | - Ashley C. Brown
- Joint Department of Biomedical Engineering College of Engineering North Carolina State University and University of North Carolina – Chapel Hill Raleigh NC 27695 USA
- Comparative Medicine Institute North Carolina State University and University of North Carolina – Chapel Hill Raleigh NC 27695 USA
| | - Thomas H. LaBean
- Department of Materials Science and Engineering College of Engineering North Carolina State University Raleigh NC 27695 USA
- Comparative Medicine Institute North Carolina State University and University of North Carolina – Chapel Hill Raleigh NC 27695 USA
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11
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Brodyagin N, Kumpina I, Applegate J, Katkevics M, Rozners E. Pyridazine Nucleobase in Triplex-Forming PNA Improves Recognition of Cytosine Interruptions of Polypurine Tracts in RNA. ACS Chem Biol 2021; 16:872-881. [PMID: 33881836 DOI: 10.1021/acschembio.1c00044] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sequence specific recognition of regulatory noncoding RNAs would open new possibilities for fundamental science and medicine. However, molecular recognition of such complex double-stranded RNA (dsRNA) structures remains a formidable problem. Recently, we discovered that peptide nucleic acids (PNAs) form an unusually stable and sequence-specific triple helix with dsRNA. Triplex-forming PNAs could become universal tools for recognition of noncoding dsRNAs but are limited by the requirement of polypurine tracts in target RNAs as only purines form stable Hoogsteen hydrogen bonded base triplets. Herein, we systematically surveyed simple nitrogen heterocycles PN as modified nucleobases for recognition of cytosine in PN*C-G triplets. We found that a 3-pyridazinyl nucleobase formed significantly more stable PN*C-G triplets than other heterocycles including the pyrimidin-2-one previously used by us and others for recognition of cytosine interruptions in polypurine tracts of PNA-dsRNA triplexes. Our results improve triple helical recognition of dsRNA and provide insights for future development of new nucleobases to expand the sequence scope of noncoding dsRNAs that can be targeted by triplex-forming PNAs.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Ilze Kumpina
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Justin Applegate
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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12
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Shiraishi T, Ghavami M, Nielsen PE. In Vitro Cellular Delivery of Peptide Nucleic Acid (PNA). Methods Mol Biol 2021; 2105:173-185. [PMID: 32088870 DOI: 10.1007/978-1-0716-0243-0_10] [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
Cellular delivery methods are a prerequisite for cellular studies with PNA. This chapter describes PNA cellular delivery using cell-penetrating peptide (CPP)-PNA conjugates and transfection of PNA-ligand conjugates mediated by cationic lipids. Furthermore, two endosomolytic procedures employing chloroquine treatment or photochemical internalization (PCI) for significantly improving PNA delivery efficacy are described.
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Affiliation(s)
- Takehiko Shiraishi
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Mahdi Ghavami
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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13
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Volpi S, Cancelli U, Neri M, Corradini R. Multifunctional Delivery Systems for Peptide Nucleic Acids. Pharmaceuticals (Basel) 2020; 14:14. [PMID: 33375595 PMCID: PMC7823687 DOI: 10.3390/ph14010014] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023] Open
Abstract
The number of applications of peptide nucleic acids (PNAs)-oligonucleotide analogs with a polyamide backbone-is continuously increasing in both in vitro and cellular systems and, parallel to this, delivery systems able to bring PNAs to their targets have been developed. This review is intended to give to the readers an overview on the available carriers for these oligonucleotide mimics, with a particular emphasis on newly developed multi-component- and multifunctional vehicles which boosted PNA research in recent years. The following approaches will be discussed: (a) conjugation with carrier molecules and peptides; (b) liposome formulations; (c) polymer nanoparticles; (d) inorganic porous nanoparticles; (e) carbon based nanocarriers; and (f) self-assembled and supramolecular systems. New therapeutic strategies enabled by the combination of PNA and proper delivery systems are discussed.
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Affiliation(s)
| | | | | | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.V.); (U.C.); (M.N.)
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14
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Ryan C, Rozners E. Impact of Chirality and Position of Lysine Conjugation in Triplex-Forming Peptide Nucleic Acids. ACS OMEGA 2020; 5:28722-28729. [PMID: 33195925 PMCID: PMC7659144 DOI: 10.1021/acsomega.0c04021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
Conjugation with cationic lysine residues improves the biophysical and biological properties of peptide nucleic acids (PNAs). A single lysine is routinely used to improve the solubility and prevent aggregation of the neutral and hydrophobic amide backbone of PNA. Literature precedents include the attachment of lysine at either the N- or the C-terminus. Moreover, conjugation with short lysine peptides (four to eight residues) improves the cellular uptake of PNA akin to more complex cell-penetrating peptides. Herein, we report a systematic study of the effect of lysine location (N- vs C-terminus) and chirality (d- vs l-) on triple-helical binding of PNA to double-stranded RNA and DNA (dsRNA and dsDNA). The results confirmed our earlier findings that conjugation with lysine significantly increased the stability of PNA-dsRNA and PNA-dsDNA triplexes and that PNA affinity for dsRNA was about an order of magnitude higher than for the same sequence of dsDNA. In contrast, conjugation of PNA with noncharged amino acids decreased the affinity of PNA. Surprisingly, neither the location nor the chirality of lysine had significant impact on PNA affinity for either dsRNA or dsDNA. The results are consistent with the lack of chiral preorganization of single-stranded PNAs, even after conjugation with four d- or l-amino acids. Instead, the positive charge of lysine appears to be the main driving force behind the increased affinity.
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Affiliation(s)
- Christopher
A. Ryan
- Department of Chemistry, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
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15
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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: 20] [Impact Index Per Article: 5.0] [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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16
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Abstract
Antibacterial agents are a group of materials that selectively destroy bacteria by interfering with bacterial growth or survival. With the emergence of resistance phenomenon of bacterial pathogens to current antibiotics, new drugs are frequently entering into the market along with the existing drugs, and the alternative compounds with antibacterial functions are being explored. Due to the advantages of their inherent biochemical and biophysical properties including precise targeting ability, biocompatibility, biodegradability, long blood circulation time, and low cytotoxicity, biomolecules such as peptides, carbohydrates, and nucleic acids have huge potential for the antimicrobial application and have been extensively studied in recent years. In this review, antimicrobial therapeutic agents composed of three kinds of functional biological molecules were summarized. In addition, the research progress of antibacterial mechanism, chemical modification, and nanoparticle coupling of those biomolecules were also discussed.
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17
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Indumathi K, Abiram A, Praveena G. Effect of peptidic backbone on the nucleic acid dimeric strands. Mol Phys 2020. [DOI: 10.1080/00268976.2019.1584682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- K. Indumathi
- Department of Physics, PSGR Krishnammal College for Women, Coimbatore, India
| | - A. Abiram
- Department of Physics, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - G. Praveena
- Department of Physics, PSGR Krishnammal College for Women, Coimbatore, India
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18
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Ong AAL, Tan J, Bhadra M, Dezanet C, Patil KM, Chong MS, Kierzek R, Decout JL, Roca X, Chen G. RNA Secondary Structure-Based Design of Antisense Peptide Nucleic Acids for Modulating Disease-Associated Aberrant Tau Pre-mRNA Alternative Splicing. Molecules 2019; 24:molecules24163020. [PMID: 31434312 PMCID: PMC6720520 DOI: 10.3390/molecules24163020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 12/18/2022] Open
Abstract
Alternative splicing of tau pre-mRNA is regulated by a 5' splice site (5'ss) hairpin present at the exon 10-intron 10 junction. Single mutations within the hairpin sequence alter hairpin structural stability and/or the binding of splicing factors, resulting in disease-causing aberrant splicing of exon 10. The hairpin structure contains about seven stably formed base pairs and thus may be suitable for targeting through antisense strands. Here, we used antisense peptide nucleic acids (asPNAs) to probe and target the tau pre-mRNA exon 10 5'ss hairpin structure through strand invasion. We characterized by electrophoretic mobility shift assay the binding of the designed asPNAs to model tau splice site hairpins. The relatively short (10-15 mer) asPNAs showed nanomolar binding to wild-type hairpins as well as a disease-causing mutant hairpin C+19G, albeit with reduced binding strength. Thus, the structural stabilizing effect of C+19G mutation could be revealed by asPNA binding. In addition, our cell culture minigene splicing assay data revealed that application of an asPNA targeting the 3' arm of the hairpin resulted in an increased exon 10 inclusion level for the disease-associated mutant C+19G, probably by exposing the 5'ss as well as inhibiting the binding of protein factors to the intronic spicing silencer. On the contrary, the application of asPNAs targeting the 5' arm of the hairpin caused an increased exon 10 exclusion for a disease-associated mutant C+14U, mainly by blocking the 5'ss. PNAs could enter cells through conjugation with amino sugar neamine or by cotransfection with minigene plasmids using a commercially available transfection reagent.
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Affiliation(s)
- Alan Ann Lerk Ong
- NTU Institute for Health Technologies (HeathTech NTU), Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553, Singapore
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Jiazi Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Malini Bhadra
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Clément Dezanet
- University Grenoble Alpes/CNRS, Département de Pharmacochimie Moléculaire, ICMG FR 2607, UMR 5063, 470 Rue de la Chimie, F-38041 Grenoble, France
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Mei Sian Chong
- Geriatic Education & Research Institute, 2 Yishun Central 2, Singapore 768024, Singapore
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Jean-Luc Decout
- University Grenoble Alpes/CNRS, Département de Pharmacochimie Moléculaire, ICMG FR 2607, UMR 5063, 470 Rue de la Chimie, F-38041 Grenoble, France
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore.
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19
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Efficient cell penetration and delivery of peptide nucleic acids by an argininocalix[4]arene. Sci Rep 2019; 9:3036. [PMID: 30816154 PMCID: PMC6395679 DOI: 10.1038/s41598-019-39211-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/03/2019] [Indexed: 01/25/2023] Open
Abstract
The application of Peptide Nucleic Acids (PNAs), mimics of DNA lacking the sugar-phosphate backbone, for antisense/anti-gene therapy and gene editing is limited by their low uptake by cells. Currently, no simple and efficient delivery systems and methods are available to solve this open issue. One of the most promising approach is the modification of the PNA structure through the covalent linkage of poliarginine tails, but this means that every PNA intended to be internalized must be modified. Herein we report the results relative to the delivery ability of a macrocyclic multivalent tetraargininocalix[4]arene (1) used as non-covalent vector for anti-miR-221-3p PNAs. High delivery efficiency, low cytotoxicity, maintenance of the PNA biological activity and ease preparation of the transfection formulation, simply attained by mixing PNA and calixarene, candidate this vector as universal delivery system for this class of nucleic acid analogues.
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20
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Kesy J, Patil KM, Kumar SR, Shu Z, Yong HY, Zimmermann L, Ong AAL, Toh DFK, Krishna MS, Yang L, Decout JL, Luo D, Prabakaran M, Chen G, Kierzek E. A Short Chemically Modified dsRNA-Binding PNA (dbPNA) Inhibits Influenza Viral Replication by Targeting Viral RNA Panhandle Structure. Bioconjug Chem 2019; 30:931-943. [PMID: 30721034 DOI: 10.1021/acs.bioconjchem.9b00039] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNAs play critical roles in diverse catalytic and regulatory biological processes and are emerging as important disease biomarkers and therapeutic targets. Thus, developing chemical compounds for targeting any desired RNA structures has great potential in biomedical applications. The viral and cellular RNA sequence and structure databases lay the groundwork for developing RNA-binding chemical ligands through the recognition of both RNA sequence and RNA structure. Influenza A virion consists of eight segments of negative-strand viral RNA (vRNA), all of which contain a highly conserved panhandle duplex structure formed between the first 13 nucleotides at the 5' end and the last 12 nucleotides at the 3' end. Here, we report our binding and cell culture anti-influenza assays of a short 10-mer chemically modified double-stranded RNA (dsRNA)-binding peptide nucleic acid (PNA) designed to bind to the panhandle duplex structure through novel major-groove PNA·RNA2 triplex formation. We demonstrated that incorporation of chemically modified PNA residues thio-pseudoisocytosine (L) and guanidine-modified 5-methyl cytosine (Q) previously developed by us facilitates the sequence-specific recognition of Watson-Crick G-C and C-G pairs, respectively, at physiologically relevant conditions. Significantly, the chemically modified dsRNA-binding PNA (dbPNA) shows selective binding to the dsRNA region in panhandle structure over a single-stranded RNA (ssRNA) and a dsDNA containing the same sequence. The panhandle structure is not accessible to traditional antisense DNA or RNA with a similar length. Conjugation of the dbPNA with an aminosugar neamine enhances the cellular uptake. We observed that 2-5 μM dbPNA-neamine conjugate results in a significant reduction of viral replication. In addition, the 10-mer dbPNA inhibits innate immune receptor RIG-I binding to panhandle structure and thus RIG-I ATPase activity. These findings would provide the foundation for developing novel dbPNAs for the detection of influenza viral RNAs and therapeutics with optimal antiviral and immunomodulatory activities.
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Affiliation(s)
- Julita Kesy
- Institute of Bioorganic Chemistry, Polish Academy of Sciences , Noskowskiego 12/14 , 61-704 Poznan , Poland
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | | | - Zhiyu Shu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Hui Yee Yong
- Lee Kong Chian School of Medicine , Nanyang Technological University , EMB 03-07, 59 Nanyang Drive , 636921 , Singapore.,NTU Institute of Structural Biology , Nanyang Technological University , EMB 06-01, 59 Nanyang Drive , 636921 , Singapore.,School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , 636921 , Singapore
| | - Louis Zimmermann
- Département de Pharmacochimie Moléculaire , University Grenoble Alpes, CNRS, ICMG FR 2607, UMR 5063 , 470 Rue de la Chimie , F-38041 Grenoble , France
| | - Alan Ann Lerk Ong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Lixia Yang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Jean-Luc Decout
- Département de Pharmacochimie Moléculaire , University Grenoble Alpes, CNRS, ICMG FR 2607, UMR 5063 , 470 Rue de la Chimie , F-38041 Grenoble , France
| | - Dahai Luo
- Lee Kong Chian School of Medicine , Nanyang Technological University , EMB 03-07, 59 Nanyang Drive , 636921 , Singapore.,NTU Institute of Structural Biology , Nanyang Technological University , EMB 06-01, 59 Nanyang Drive , 636921 , Singapore
| | - Mookkan Prabakaran
- Temasek Life Science Laboratory, 1 Research Link , National University of Singapore , 117604 , Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences , Noskowskiego 12/14 , 61-704 Poznan , Poland
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21
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Montazersaheb S, Hejazi MS, Nozad Charoudeh H. Potential of Peptide Nucleic Acids in Future Therapeutic Applications. Adv Pharm Bull 2018; 8:551-563. [PMID: 30607328 PMCID: PMC6311635 DOI: 10.15171/apb.2018.064] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 12/11/2022] Open
Abstract
Peptide nucleic acids (PNA) are synthetic analog of DNA with a repeating N-(2-aminoethyl)-glycine peptide backbone connected to purine and pyrimidine nucleobases via a linker. Considering the unique properties of PNA, including resistance to enzymatic digestion, higher biostability combined with great hybridization affinity toward DNA and RNA, it has attracted great attention toward PNA- based technology as a promising approach for gene alteration. However, an important challenge in utilizing PNA is poor intracellular uptake. Therefore, some strategies have been developed to enhance the delivery of PNA in order to reach cognate site. Although PNAs primarily demonstrated to act as an antisense and antigene agents for inhibition of transcription and translation of target genes, more therapeutic applications such as splicing modulation and gene editing are also used to produce specific genome modifications. Hence, several approaches based on PNAs technology have been designed for these purposes. This review briefly presents the properties and characteristics of PNA as well as different gene modulation mechanisms. Thereafter, current status of successful therapeutic applications of PNA as gene therapeutic intervention in different research areas with special interest in medical application in particular, anti-cancer therapy are discussed. Then it focuses on possible use of PNA as anti-mir agent and PNA-based strategies against clinically important bacteria.
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Affiliation(s)
- Soheila Montazersaheb
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Saeid Hejazi
- Molecular Medicine Research Center, 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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22
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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23
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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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24
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Hnedzko D, McGee DW, Karamitas YA, Rozners E. Sequence-selective recognition of double-stranded RNA and enhanced cellular uptake of cationic nucleobase and backbone-modified peptide nucleic acids. RNA (NEW YORK, N.Y.) 2017; 23:58-69. [PMID: 27742909 PMCID: PMC5159649 DOI: 10.1261/rna.058362.116] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/08/2016] [Indexed: 05/07/2023]
Abstract
Sequence-selective recognition of complex RNAs in live cells could find broad applications in biology, biomedical research, and biotechnology. However, specific recognition of structured RNA is challenging, and generally applicable and effective methods are lacking. Recently, we found that peptide nucleic acids (PNAs) were unusually well-suited ligands for recognition of double-stranded RNAs. Herein, we report that 2-aminopyridine (M) modified PNAs and their conjugates with lysine and arginine tripeptides form strong (Ka = 9.4 to 17 × 107 M-1) and sequence-selective triple helices with RNA hairpins at physiological pH and salt concentration. The affinity of PNA-peptide conjugates for the matched RNA hairpins was unusually high compared to the much lower affinity for DNA hairpins of the same sequence (Ka = 0.05 to 1.1 × 107 M-1). The binding of double-stranded RNA by M-modified PNA-peptide conjugates was a relatively fast process (kon = 2.9 × 104 M-1 sec-1) compared to the notoriously slow triple helix formation by oligodeoxynucleotides (kon ∼ 103 M-1 sec-1). M-modified PNA-peptide conjugates were not cytotoxic and were efficiently delivered in the cytosol of HEK293 cells at 10 µM. Surprisingly, M-modified PNAs without peptide conjugation were also taken up by HEK293 cells, which, to the best of our knowledge, is the first example of heterocyclic base modification that enhances the cellular uptake of PNA. Our results suggest that M-modified PNA-peptide conjugates are promising probes for sequence-selective recognition of double-stranded RNA in live cells and other biological systems.
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Affiliation(s)
- Dziyana Hnedzko
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, USA
| | - Dennis W McGee
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, New York 13902, USA
| | - Yannis A Karamitas
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, USA
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25
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Sabale PM, Srivatsan SG. Responsive Fluorescent PNA Analogue as a Tool for Detecting G-quadruplex Motifs of Oncogenes and Activity of Toxic Ribosome-Inactivating Proteins. Chembiochem 2016; 17:1665-73. [PMID: 27271025 DOI: 10.1002/cbic.201600192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 12/13/2022]
Abstract
Fluorescent oligomers that are resistant to enzymatic degradation and report their binding to target oligonucleotides (ONs) by changes in fluorescence properties are highly useful in developing nucleic-acid-based diagnostic tools and therapeutic strategies. Here, we describe the synthesis and photophysical characterization of fluorescent peptide nucleic acid (PNA) building blocks made of microenvironment-sensitive 5-(benzofuran-2-yl)- and 5-(benzothiophen-2-yl)-uracil cores. The emissive monomers, when incorporated into PNA oligomers and hybridized to complementary ONs, are minimally perturbing and are highly sensitive to their neighboring base environment. In particular, benzothiophene-modified PNA reports the hybridization process with significant enhancement in fluorescence intensity, even when placed in the vicinity of guanine residues, which often quench fluorescence. This feature was used in the turn-on detection of G-quadruplex-forming promoter DNA sequences of human proto-oncogenes (c-myc and c-kit). Furthermore, the ability of benzothiophene-modified PNA oligomer to report the presence of an abasic site in RNA enabled us to develop a simple fluorescence hybridization assay to detect and estimate the depurination activity of ribosome-inactivating protein toxins. Our results demonstrate that this approach with responsive PNA probes will provide new opportunities to develop robust tools to study nucleic acids.
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Affiliation(s)
- Pramod M Sabale
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.
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26
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Gupta A, Bahal R, Gupta M, Glazer PM, Saltzman WM. Nanotechnology for delivery of peptide nucleic acids (PNAs). J Control Release 2016; 240:302-311. [PMID: 26776051 DOI: 10.1016/j.jconrel.2016.01.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 12/10/2015] [Accepted: 01/04/2016] [Indexed: 12/22/2022]
Abstract
Over the past three decades, peptide nucleic acids have been employed in numerous chemical and biological applications. Peptide nucleic acids possess enormous potential because of their superior biophysical properties, compared to other oligonucleotide chemistries. However, for therapeutic applications, intracellular delivery of peptide nucleic acids remains a challenge. In this review, we summarize the progress that has been made in delivering peptide nucleic acids to intracellular targets. In addition, we emphasize recent nanoparticle-based strategies for efficient delivery of conventional and chemically-modified peptides nucleic acids.
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Affiliation(s)
- Anisha Gupta
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Raman Bahal
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Meera Gupta
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Department of Chemical Engineering, Indian Institute of Technology-Delhi, New Delhi, India
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA; Department of Genetics, Yale University, New Haven, CT, USA.
| | - W Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
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27
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Zhao XL, Chen BC, Han JC, Wei L, Pan XB. Delivery of cell-penetrating peptide-peptide nucleic acid conjugates by assembly on an oligonucleotide scaffold. Sci Rep 2015; 5:17640. [PMID: 26612536 PMCID: PMC4661726 DOI: 10.1038/srep17640] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 11/03/2015] [Indexed: 01/01/2023] Open
Abstract
Delivery to intracellular target sites is still one of the main obstacles in the development of peptide nucleic acids (PNAs) as antisense-antigene therapeutics. Here, we designed a self-assembled oligonucleotide scaffold that included a central complementary region for self-assembly and lateral regions complementing the PNAs. Assembly of cell-penetrating peptide (CPP)-PNAs on the scaffold significantly promoted endocytosis of PNAs by at least 10-fold in cell cultures, particularly for scaffolds in which the central complementary region was assembled by poly(guanine) and poly(cytosine). The antisense activity of CPP-PNAs increased by assembly on the scaffold and was further enhanced after co-assembly with endosomolytic peptide (EP)-PNA. This synergistic effect was also observed following the assembly of antigene CPP-PNAs\EP-PNAs on the scaffold. However, antigene activity was only observed by targeting episomal viral DNA or transfected plasmids, but not the chromosome in the cell cultures. In conclusion, assembly on oligonucleotide scaffolds significantly enhanced the antisense-antigene activity of PNAs by promoting endocytosis and endosomal escape. This oligonucleotide scaffold provided a simple strategy for assembly of multiple functional peptide-PNA conjugates, expanding the applications of PNAs and demonstrating the potential of PNAs as antiviral therapeutics.
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Affiliation(s)
- Xing-Liang Zhao
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases; Beijing 100044, P.R. China
| | - Bi-Cheng Chen
- Zhejiang Provincial Top Key Discipline in Surgery, Wenzhou Key Laboratory of Surgery; Department of Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325200, P.R. China
| | - Jin-Chao Han
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases; Beijing 100044, P.R. China
| | - Lai Wei
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases; Beijing 100044, P.R. China
| | - Xiao-Ben Pan
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases; Beijing 100044, P.R. China
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28
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Ellipilli S, vasudeva Murthy R, Ganesh KN. Perfluoroalkylchain conjugation as a new tactic for enhancing cell permeability of peptide nucleic acids (PNAs) via reducing the nanoparticle size. Chem Commun (Camb) 2015; 52:521-4. [PMID: 26535419 DOI: 10.1039/c5cc05342k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Perfluoro undecanoyl chain conjugated peptide nucleic acids (PNAs) show 2.5 to 3 fold higher cellular uptake efficiency in NIH 3T3 and HeLa cells compared to simple undecanoyl PNAs. Fluorination of PNAs leads to the formation of lower size (∼100-250 nm) nanoparticles compared to larger size (∼500 nm) nanoparticles from non-fluorinated PNAs, thereby improving the efficiency of cell penetration.
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Affiliation(s)
- Satheesh Ellipilli
- Chemical Biology Unit, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pune 411008, Maharashtra, India
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29
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Canady TD, Telmer CA, Oyaghire SN, Armitage BA, Bruchez MP. In Vitro Reversible Translation Control Using γPNA Probes. J Am Chem Soc 2015; 137:10268-75. [PMID: 26241615 DOI: 10.1021/jacs.5b05351] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
On-demand regulation of gene expression in living cells is a central goal of chemical biology and antisense therapeutic development. While significant advances have allowed regulatory modulation through inserted genetic elements, on-demand control of the expression/translation state of a given native gene by complementary sequence interactions remains a technical challenge. Toward this objective, we demonstrate the reversible suppression of a luciferase gene in cell-free translation using Watson-Crick base pairing between the mRNA and a complementary γ-modified peptide nucleic acid (γPNA) sequence with a noncomplementary toehold. Exploiting the favorable thermodynamics of γPNA-γPNA interactions, the antisense sequence can be removed by hybridization of a second, fully complementary γPNA, through a strand displacement reaction, allowing translation to proceed. Complementary RNA is also shown to displace the bound antisense γPNA, opening up possibilities of in vivo regulation by native gene expression.
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Affiliation(s)
- Taylor D Canady
- †Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Cheryl A Telmer
- †Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Stanley N Oyaghire
- †Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Bruce A Armitage
- †Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Marcel P Bruchez
- †Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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30
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Watanabe T, Hoshida T, Sakyo J, Kishi M, Tanabe S, Matsuura J, Akiyama S, Nakata M, Tanabe Y, Suzuki AZ, Watanabe S, Furuta T. Synthesis of nucleobase-caged peptide nucleic acids having improved photochemical properties. Org Biomol Chem 2015; 12:5089-93. [PMID: 24921960 DOI: 10.1039/c4ob00418c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A nucleobase-caged peptide nucleic acid (PNA) having a (6-bromo-7-methoxycoumarin)-4-ylmethoxycarbonyl (Bmcmoc) caging group was newly synthesized. The Bmcmoc-caged PNAs were photolyzed to produce parent PNAs with a high photochemical efficiency. Introduction of a single Bmcmoc group was sufficient to suppress polymerase chain reaction (PCR) clamping activity and triplex invasion complex formation. Photo-mediated restoration of the PCR clamping activity was also demonstrated.
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Affiliation(s)
- Takayoshi Watanabe
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.
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31
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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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32
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Shiraishi T, Nielsen PE. Cellular delivery of peptide nucleic acids (PNAs). Methods Mol Biol 2014; 1050:193-205. [PMID: 24297361 DOI: 10.1007/978-1-62703-553-8_16] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cellular delivery methods are a prerequisite for cellular studies with PNA. This chapter describes PNA cellular delivery using cell-penetrating peptide (CPP)-PNA conjugates and transfection of PNA-ligand conjugates mediated by cationic lipids. Furthermore, two endosomolytic procedures employing chloroquine treatment or photochemical internalization (PCI) for significantly improving PNA delivery efficacy are described.
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Affiliation(s)
- Takehiko Shiraishi
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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33
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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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34
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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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35
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Gupta A, Lee LL, Roy S, Tanious FA, Wilson WD, Ly DH, Armitage BA. Strand invasion of DNA quadruplexes by PNA: comparison of homologous and complementary hybridization. Chembiochem 2013; 14:1476-84. [PMID: 23868291 PMCID: PMC3856695 DOI: 10.1002/cbic.201300263] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Indexed: 12/18/2022]
Abstract
Molecular recognition of DNA quadruplex structures is envisioned to be a strategy for regulating gene expression at the transcriptional level and for in situ analysis of telomere structure and function. The recognition of DNA quadruplexes by peptide nucleic acid (PNA) oligomers is presented here, with a focus on comparing complementary, heteroduplex-forming and homologous, heteroquadruplex-forming PNAs. Surface plasmon resonance and optical spectroscopy experiments demonstrated that the efficacy of a recognition mode depended strongly on the target. Homologous PNA readily invades a quadruplex derived from the promoter regulatory region found upstream of the MYC proto-oncogene to form a heteroquadruplex at high potassium concentration mimicking the intracellular environment, whereas complementary PNA exhibits virtually no hybridization. In contrast, complementary PNA is superior to the homologous in hybridizing to a quadruplex modeled on the human telomere sequence. The results are discussed in terms of the different structural morphologies of the quadruplex targets and the implications for in vivo recognition of quadruplexes by PNAs.
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Affiliation(s)
- Anisha Gupta
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Ling-Ling Lee
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Subhadeep Roy
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Farial A. Tanious
- Department of Chemistry, Georgia State University, Atlanta, GA 30303
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303
| | - Danith H. Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Bruce A. Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
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36
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Muse O, Zengeya T, Mwaura J, Hnedzko D, McGee DW, Grewer CT, Rozners E. Sequence selective recognition of double-stranded RNA at physiologically relevant conditions using PNA-peptide conjugates. ACS Chem Biol 2013; 8:1683-6. [PMID: 23721369 DOI: 10.1021/cb400144x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Conjugation of short peptide nucleic acids (PNA) with tetralysine peptides strongly enhanced triple helical binding to RNA at physiologically relevant conditions. The PNA hexamers and heptamers carrying cationic nucleobase and tetralysine modifications displayed high binding affinity for complementary double-stranded RNA without compromising sequence selectivity. The PNA-peptide conjugates had unique preference for binding double-stranded RNA, while having little, if any, affinity for double-stranded DNA. The cationic PNAs were efficiently taken up by HEK293 cells, whereas little uptake was observed for unmodified PNA.
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Affiliation(s)
- Oluwatoyosi Muse
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Thomas Zengeya
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Juddy Mwaura
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Dziyana Hnedzko
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Dennis W. McGee
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Christof T. Grewer
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Eriks Rozners
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
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37
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Shen Y, Shrestha R, Ibricevic A, Gunsten SP, Welch MJ, Wooley KL, Brody SL, Taylor JSA, Liu Y. Antisense peptide nucleic acid-functionalized cationic nanocomplex for in vivo mRNA detection. Interface Focus 2013; 3:20120059. [PMID: 24427537 PMCID: PMC3638413 DOI: 10.1098/rsfs.2012.0059] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Acute lung injury (ALI) is a complex syndrome with many aetiologies, resulting in the upregulation of inflammatory mediators in the host, followed by dyspnoea, hypoxemia and pulmonary oedema. A central mediator is inducible nitric oxide synthase (iNOS) that drives the production of NO and continued inflammation. Thus, it is useful to have diagnostic and therapeutic agents for targeting iNOS expression. One general approach is to target the precursor iNOS mRNA with antisense nucleic acids. Peptide nucleic acids (PNAs) have many advantages that make them an ideal platform for development of antisense theranostic agents. Their membrane impermeability, however, limits biological applications. Here, we report the preparation of an iNOS imaging probe through electrostatic complexation between a radiolabelled antisense PNA-YR9 · oligodeoxynucleotide (ODN) hybrid and a cationic shell-cross-linked knedel-like nanoparticle (cSCK). The Y (tyrosine) residue was used for (123)I radiolabelling, whereas the R9 (arginine9) peptide was included to facilitate cell exit of untargeted PNA. Complete binding of the antisense PNA-YR9 · ODN hybrid to the cSCK was achieved at an 8 : 1 cSCK amine to ODN phosphate (N/P) ratio by a gel retardation assay. The antisense PNA-YR9 · ODN · cSCK nanocomplexes efficiently entered RAW264.7 cells, whereas the PNA-YR9 · ODN alone was not taken up. Low concentrations of (123)I-labelled antisense PNA-YR9 · ODN complexed with cSCK showed significantly higher retention of radioactivity when iNOS was induced in lipopolysaccharide+interferon-γ-activated RAW264.7 cells when compared with a mismatched PNA. Moreover, statistically, greater retention of radioactivity from the antisense complex was also observed in vivo in an iNOS-induced mouse lung after intratracheal administration of the nanocomplexes. This study demonstrates the specificity and sensitivity by which the radiolabelled nanocomplexes can detect iNOS mRNA in vitro and in vivo and their potential for early diagnosis of ALI.
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Affiliation(s)
- Yuefei Shen
- Department of Chemistry, Washington University, St Louis, MO 63130, USA
| | - Ritu Shrestha
- Department of Chemistry and Chemical Engineering, Texas A&M University, PO Box 30012, College Station, TX 77842-3012, USA
| | - Aida Ibricevic
- Department of Medicine, Washington University, St Louis, MO 63110, USA
| | - Sean P. Gunsten
- Department of Medicine, Washington University, St Louis, MO 63110, USA
| | - Michael J. Welch
- Department of Radiology, Washington University, St Louis, MO 63110, USA
| | - Karen L. Wooley
- Department of Chemistry and Chemical Engineering, Texas A&M University, PO Box 30012, College Station, TX 77842-3012, USA
| | - Steven L. Brody
- Department of Medicine, Washington University, St Louis, MO 63110, USA
- Department of Radiology, Washington University, St Louis, MO 63110, USA
| | | | - Yongjian Liu
- Department of Radiology, Washington University, St Louis, MO 63110, USA
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38
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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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39
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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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40
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Ding C, Wang N, Zhang J, Wang Z. Rolling circle amplification combined with nanoparticle aggregates for highly sensitive identification of DNA and cancer cells. Biosens Bioelectron 2012; 42:486-91. [PMID: 23238323 DOI: 10.1016/j.bios.2012.10.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 09/21/2012] [Accepted: 10/03/2012] [Indexed: 11/29/2022]
Abstract
An electrochemical biosensor based on rolling circle amplification (RCA) and nanoparticle aggregates for highly sensitive identification of DNA and cancer cells were established in this work. First, a "sandwich-type" DNA complexes containing target DNA was constructed on the surface of the magnetic beads. Second, one part of the primer in the "sandwich-type" DNA complexes induced the RCA in the system. Then the long RCA products were digested to construct another "sandwich-type" DNA complex for the electrochemical detection. Differential pulse voltammetry (DPV) peaks with high signal intensity were obtained, and the signal intensities were found to be dependent on the amount of Fc, which is related to the concentration of target DNA. Under the optimum conditions, the electrochemical signal intensity was increased with the increase of the concentration of target DNA. A detection limit of 2.8×10⁻¹⁸ M of target DNA was achieved. Combined with aptamers technology, the proposed signal amplification strategy was also used for the identification of cancer cells with the detection limit of 100 Ramos cells mL⁻¹.
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Affiliation(s)
- Caifeng Ding
- State Key Laboratory Base of Eco-chemical Engineering, Key Laboratory of Biochemical Analysis, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China.
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41
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Recent advances in chemical modification of Peptide nucleic acids. J Nucleic Acids 2012; 2012:518162. [PMID: 22991652 PMCID: PMC3443988 DOI: 10.1155/2012/518162] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Revised: 07/12/2012] [Accepted: 07/20/2012] [Indexed: 12/14/2022] Open
Abstract
Peptide nucleic acid (PNA) has become an extremely powerful tool in chemistry and biology. Although PNA recognizes single-stranded nucleic acids with exceptionally high affinity and sequence selectivity, there is considerable ongoing effort to further improve properties of PNA for both fundamental science and practical applications. The present paper discusses selected recent studies that improve on cellular uptake and binding of PNA to double-stranded DNA and RNA. The focus is on chemical modifications of PNA's backbone and heterocyclic nucleobases. The paper selects representative recent studies and does not attempt to provide comprehensive coverage of the broad and vibrant field of PNA modification.
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42
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Panyutin IG, Onyshchenko MI, Englund EA, Appella DH, Neumann RD. Targeting DNA G-quadruplex structures with peptide nucleic acids. Curr Pharm Des 2012; 18:1984-91. [PMID: 22376112 DOI: 10.2174/138161212799958440] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 11/28/2011] [Indexed: 11/22/2022]
Abstract
Regulation of genetic functions based on targeting DNA or RNA sequences with complementary oligonucleotides is especially attractive in the post-genome era. Oligonucleotides can be rationally designed to bind their targets based on simple nucleic acid base pairing rules. However, the use of natural DNA and RNA oligonucleotides as targeting probes can cause numerous off-target effects. In addition, natural nucleic acids are prone to degradation in vivo by various nucleases. To address these problems, nucleic acid mimics such as peptide nucleic acids (PNA) have been developed. They are more stable, show less off-target effects, and, in general, have better binding affinity to their targets. However, their high affinity to DNA can reduce their sequence-specificity. The formation of alternative DNA secondary structures, such as the G-quadruplex, provides an extra level of specificity as targets for PNA oligomers. PNA probes can target the loops of G-quadruplex, invade the core by forming PNA-DNA guanine-tetrads, or bind to the open bases on the complementary cytosine-rich strand. Not only could the development of such G-quadruplex-specific probes allow regulation of gene expression, but it will also provide a means to clarify the biological roles G-quadruplex structures may possess.
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43
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Järver P, Coursindel T, Andaloussi SEL, Godfrey C, Wood MJA, Gait MJ. Peptide-mediated Cell and In Vivo Delivery of Antisense Oligonucleotides and siRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2012; 1:e27. [PMID: 23344079 PMCID: PMC3390225 DOI: 10.1038/mtna.2012.18] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 04/26/2012] [Accepted: 04/26/2012] [Indexed: 12/22/2022]
Affiliation(s)
- Peter Järver
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Samir EL Andaloussi
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
- Department of Laboratory Medicine, Karolinska Institute, Hudidnge, Sweden
| | - Caroline Godfrey
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Matthew JA Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Michael J Gait
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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44
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Smith AR, Ikkanda BA, Holman GG, Iverson BL. Subtle recognition of 14-base pair DNA sequences via threading polyintercalation. Biochemistry 2012; 51:4445-52. [PMID: 22554127 PMCID: PMC3369501 DOI: 10.1021/bi300317n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small molecules that bind DNA in a sequence-specific manner could act as antibiotic, antiviral, or anticancer agents because of their potential ability to manipulate gene expression. Our laboratory has developed threading polyintercalators based on 1,4,5,8-naphthalene diimide (NDI) units connected in a head-to-tail fashion by flexible peptide linkers. Previously, a threading tetraintercalator composed of alternating minor-major-minor groove-binding modules was shown to bind specifically to a 14 bp DNA sequence with a dissociation half-life of 16 days [Holman, G. G., et al. (2011) Nat. Chem. 3, 875-881]. Herein are described new NDI-based tetraintercalators with a different major groove-binding module and a reversed N to C directionality of one of the minor groove-binding modules. DNase I footprinting and kinetic analyses revealed that these new tetraintercalators are able to discriminate, by as much as 30-fold, 14 bp DNA binding sites that differ by 1 or 2 bp. Relative affinities were found to correlate strongly with dissociation rates, while overall C(2) symmetry in the DNA-binding molecule appeared to contribute to enhanced association rates.
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Affiliation(s)
- Amy Rhoden Smith
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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45
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Avitabile C, Saviano M, D'Andrea L, Bianchi N, Fabbri E, Brognara E, Gambari R, Romanelli A. Targeting pre-miRNA by peptide nucleic acids: a new strategy to interfere in the miRNA maturation. ARTIFICIAL DNA, PNA & XNA 2012; 3:88-96. [PMID: 22699795 PMCID: PMC3429535 DOI: 10.4161/adna.20911] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
PNAs conjugated to carrier peptides have been employed for the targeting of miRNA precursor, with the aim to develop molecules able to interfere in the pre-miRNA processing. The capability of the molecules to bind pre-miRNA has been tested in vitro by fluorescence assayes on Thiazole Orange labeled molecules and in vivo, in K562 cells, evaluating the amount of miRNA produced after treatment of cells with two amounts of PNAs.
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Affiliation(s)
- Concetta Avitabile
- Dipartimento delle Scienze Biologiche, Università di Napoli "Federico II", Napoli, Italy
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46
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Liu Y, Chai Y, Kumar A, Tidwell RR, Boykin DW, Wilson WD. Designed compounds for recognition of 10 base pairs of DNA with two at binding sites. J Am Chem Soc 2012; 134:5290-9. [PMID: 22369366 DOI: 10.1021/ja211628j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Short AT base pair sequences that are separated by a small number of GCs are common in eukaryotic parasite genomes. Cell-permeable compounds that bind effectively and selectively to such sequences present an attractive therapeutic approach. Compounds with linked, one or two amidine-benzimidazole-phenyl (ABP) motifs were designed, synthesized, and evaluated for binding to adjacent AT sites by biosensor-surface plasmon resonance (SPR). A surprising feature of the linked ABP motifs is that a set of six similar compounds has three different minor groove binding modes with the target sequences. Compounds with one ABP bind independently to two separated AT sites. Unexpectedly, compounds with two ABP motifs can bind strongly either as monomers or as cooperative dimers to the full site. The results are supported by mass spectrometry and circular dichroism, and models to explain the different binding modes are presented.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, United States
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47
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Abstract
A brief historical introduction describes early attempts to silence specific genes using the antisense oligonucleotides that flourished in the 1980s. Early aspirations for therapeutic applications were almost extinguished by the unexpected complexity of oligonucleotide pharmacology. Once the biochemistry and molecular biology behind some of the pharmacology was worked out, new approaches became apparent for using oligonucleotides to treat disease. The biochemistry of small nucleic acids is outlined in Section 2. Various approaches employing oligonucleotides to control cellular functions are reviewed in Section 3. These include antisense oligonucleotides and siRNA that bind to RNA, antigene oligonucleotides that bind to DNA, and aptamers, decoys, and CpG oligonucleotides that bind to proteins.
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MESH Headings
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/pharmacology
- Aptamers, Nucleotide/therapeutic use
- Communicable Diseases/drug therapy
- Communicable Diseases/pathology
- CpG Islands
- DNA/chemistry
- DNA/metabolism
- DNA, Catalytic/chemistry
- DNA, Catalytic/pharmacology
- DNA, Catalytic/therapeutic use
- Diabetes Mellitus/drug therapy
- Diabetes Mellitus/pathology
- Humans
- MicroRNAs/chemistry
- MicroRNAs/pharmacology
- MicroRNAs/therapeutic use
- Molecular Targeted Therapy/methods
- Neoplasms/drug therapy
- Neoplasms/pathology
- Neurodegenerative Diseases/drug therapy
- Neurodegenerative Diseases/pathology
- Nucleic Acid Hybridization
- Oligonucleotides/chemistry
- Oligonucleotides/pharmacology
- Oligonucleotides/therapeutic use
- Oligonucleotides, Antisense/chemistry
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- RNA, Catalytic/chemistry
- RNA, Catalytic/pharmacology
- RNA, Catalytic/therapeutic use
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/pharmacology
- RNA, Small Interfering/therapeutic use
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Affiliation(s)
- John Goodchild
- Department of Chemistry, Worcester State University, Worcester, MA 01602-2597, USA.
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48
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Li D, Yang Z, Long Y, Zhao G, Lv B, Hiew S, Ng MTT, Guo J, Tan H, Zhang H, Yuan W, Su H, Li T. Precise engineering and visualization of signs and magnitudes of DNA writhe on the basis of PNA invasion. Chem Commun (Camb) 2011; 47:10695-7. [PMID: 21892494 DOI: 10.1039/c1cc13158c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
It is demonstrated that the right and left handedness of DNA supercoils can be engineered precisely and readily at the molecular level in vitro through utilization of the invading property of peptide nucleic acid.
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Affiliation(s)
- Dawei Li
- RecDivision of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore
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49
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Targeted gene modification of hematopoietic progenitor cells in mice following systemic administration of a PNA-peptide conjugate. Mol Ther 2011; 20:109-18. [PMID: 21829173 DOI: 10.1038/mt.2011.163] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hematopoietic stem cell (HSC) gene therapy offers promise for the development of new treatments for a variety of hematologic disorders. However, efficient in vivo modification of HSCs has proved challenging, thus imposing constraints on the therapeutic potential of this approach. Herein, we provide a gene-targeting strategy that allows site-specific in vivo gene modification in the HSCs of mice. Through conjugation of a triplex-forming peptide nucleic acid (PNA) to the transport peptide, antennapedia (Antp), we achieved successful in vivo chromosomal genomic modification of hematopoietic progenitor cells, while still retaining intact differentiation capabilities. Following systemic administration of PNA-Antp conjugates, sequence-specific gene modification was observed in multiple somatic tissues as well as within multiple compartments of the hematopoietic system, including erythroid, myeloid, and lymphoid cell lineages. As a true functional measure of gene targeting in a long-term renewable HSC, we also demonstrate preserved genomic modification in the bone marrow and spleen of primary recipient mice following transplantation of bone marrow from PNA-Antp-treated donor mice. Our approach offers a minimally invasive alternative to ex vivo gene therapy, by eliminating the need for the complex steps of stem cell mobilization and harvesting, ex vivo manipulation, and transplantation of stem cells. Therefore, our approach may provide new options for individualized therapies in the treatment of monogenic hematologic diseases such as sickle cell anemia and thalassemia.
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50
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Gagnon KT, Watts JK, Pendergraff HM, Montaillier C, Thai D, Potier P, Corey DR. Antisense and antigene inhibition of gene expression by cell-permeable oligonucleotide-oligospermine conjugates. J Am Chem Soc 2011; 133:8404-7. [PMID: 21539318 PMCID: PMC3106116 DOI: 10.1021/ja200312y] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Oligonucleotides and their derivatives are a proven chemical strategy for modulating gene expression. However, their negative charge remains a challenge for delivery and target recognition inside cells. Here we show that oligonucleotide-oligospermine conjugates (Zip nucleic acids or ZNAs) can help overcome these shortcomings by serving as effective antisense and antigene agents. Conjugates containing DNA and locked nucleic acid (LNA) oligonucleotides are active, and oligospermine conjugation facilitates carrier-free cell uptake at nanomolar concentrations. Conjugates targeting the CAG triplet repeat within huntingtin (HTT) mRNA selectively inhibit expression of the mutant huntingtin protein. Conjugates targeting the promoter of the progesterone receptor (PR) function as antigene agents to block PR expression. These observations support further investigation of ZNA conjugates as gene silencing agents.
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Affiliation(s)
- Keith T. Gagnon
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Jonathan K. Watts
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Hannah M. Pendergraff
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | | | - Danielle Thai
- SIGMA Custom Products, Genopole Campus 1, 5 rue Desbruères, 91030 Evry Cedex, France
| | - Pierre Potier
- SIGMA Custom Products, Genopole Campus 1, 5 rue Desbruères, 91030 Evry Cedex, France
| | - David R. Corey
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
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