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Exner RM, Paisey SJ, Redman JE, Pascu SI. Explorations into Peptide Nucleic Acid Contrast Agents as Emerging Scaffolds for Breakthrough Solutions in Medical Imaging and Diagnosis. ACS OMEGA 2021; 6:28455-28462. [PMID: 34746541 PMCID: PMC8569549 DOI: 10.1021/acsomega.1c03994] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/23/2021] [Indexed: 05/11/2023]
Abstract
Peptide nucleic acids (PNAs, nucleic acid analogues with a peptide backbone rather than a phosphoribosyl backbone) have emerged as promising chemical agents in antigene or antisense therapeutics, as splicing modulators or in gene editing. Their main benefits, compared to DNA or RNA agents, are their biochemical stability and the lack of negative charges throughout the backbone, leading to negligible electrostatic interaction with the strand with which they are hybridizing. As a result, hybridization of PNA strands with DNA or RNA strands leads to higher binding energies and melting temperatures. A lack of natural transporters, however, necessitates the formation of PNA-containing chimeras or the formulation of nanoparticular cell delivery methods. Here, we set out to explore the progress made in using imaging agents based on PNAs in diagnostic applications and highlight selected developments and challenges.
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Affiliation(s)
- Rüdiger M. Exner
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Stephen J. Paisey
- Wales
Research & Diagnostic Positron Emission Tomography Imaging Centre
(PETIC), School of Medicine, Cardiff University,
University Hospital of Wales, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - James E. Redman
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Sofia I. Pascu
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Centre
for Sustainable and Circular Technologies, 1 South, University of Bath, Claverton Down, Bath BA2
7AY, United Kingdom
- Centre
for Therapeutic Innovation, 3 West 2.03, University of Bath, Claverton Down, Bath BA2
7AY, United Kingdom
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2
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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: 31] [Impact Index Per Article: 10.3] [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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3
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Urbanek MO, Krzyzosiak WJ. Discriminating RNA variants with single-molecule allele-specific FISH. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:230-241. [DOI: 10.1016/j.mrrev.2016.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 10/21/2022]
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4
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Cui Y, Liu J, Irudayaraj J. Beyond quantification: in situ analysis of transcriptome and pre-mRNA alternative splicing at the nanoscale. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 9. [PMID: 27813271 DOI: 10.1002/wnan.1443] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/02/2016] [Accepted: 10/02/2016] [Indexed: 11/08/2022]
Abstract
In situ analysis offers a venue for dissecting the complex transcriptome in its natural context to tap into cellular processes that could explain the phenotypic physiology and pathology yet to be understood. Over the past decades, enormous progress has been made to improve the resolution, sensitivity, and specificity of single-cell technologies. The continued efforts in RNA research not only facilitates mechanistic studies of molecular biology but also provides state-of-the-art strategies for diagnostic purposes. The implementation of novel bio-imaging platforms has yielded valuable information for inspecting gene expression, mapping regulatory networks, and classifying cell types. In this article, we discuss the merits and technical challenges in single-molecule in situ RNA profiling. Advanced in situ hybridization methodologies developed for a variety of detection modalities are reviewed. Considering the fact that in mammalian cells the number of protein products immensely exceeds that of the actual coding genes due to pre-mRNA alternative splicing, tools capable of elucidating this process in intact cells are highlighted. To conclude, we point out future directions for in situ transcriptome analysis and expect a plethora of opportunities and discoveries in this field. WIREs Nanomed Nanobiotechnol 2017, 9:e1443. doi: 10.1002/wnan.1443 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Yi Cui
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center and Birck Nanotechnology Center, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA.,Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jing Liu
- Department of Nanoscience and Nanoengineering, South Dakota School of Mines & Technology, Rapid City, SD, USA
| | - Joseph Irudayaraj
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center and Birck Nanotechnology Center, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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5
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Beliveau BJ, Boettiger AN, Avendaño MS, Jungmann R, McCole RB, Joyce EF, Kim-Kiselak C, Bantignies F, Fonseka CY, Erceg J, Hannan MA, Hoang HG, Colognori D, Lee JT, Shih WM, Yin P, Zhuang X, Wu CT. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat Commun 2015; 6:7147. [PMID: 25962338 PMCID: PMC4430122 DOI: 10.1038/ncomms8147] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 04/09/2015] [Indexed: 01/06/2023] Open
Abstract
Fluorescence in situ hybridization (FISH) is a powerful single-cell technique for studying nuclear structure and organization. Here we report two advances in FISH-based imaging. We first describe the in situ visualization of single-copy regions of the genome using two single-molecule super-resolution methodologies. We then introduce a robust and reliable system that harnesses single-nucleotide polymorphisms (SNPs) to visually distinguish the maternal and paternal homologous chromosomes in mammalian and insect systems. Both of these new technologies are enabled by renewable, bioinformatically designed, oligonucleotide-based Oligopaint probes, which we augment with a strategy that uses secondary oligonucleotides (oligos) to produce and enhance fluorescent signals. These advances should substantially expand the capability to query parent-of-origin-specific chromosome positioning and gene expression on a cell-by-cell basis.
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Affiliation(s)
- Brian J. Beliveau
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alistair N. Boettiger
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02138, USA
| | - Maier S. Avendaño
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ralf Jungmann
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ruth B. McCole
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Eric F. Joyce
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Caroline Kim-Kiselak
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Frédéric Bantignies
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Institut de Génétique Humaine, CNRS UPR 1142, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Chamith Y. Fonseka
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mohammed A. Hannan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hien G. Hoang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David Colognori
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Boston, Massachusetts 02114, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Jeannie T. Lee
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Boston, Massachusetts 02114, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - William M. Shih
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xiaowei Zhuang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02138, USA
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Chao-ting Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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Optimized RNA ISH, RNA FISH and protein-RNA double labeling (IF/FISH) in Drosophila ovaries. Nat Protoc 2013; 8:2158-79. [PMID: 24113787 DOI: 10.1038/nprot.2013.136] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In situ hybridization (ISH) is a powerful technique for detecting nucleic acids in cells and tissues. Here we describe three ISH procedures that are optimized for Drosophila ovaries: whole-mount, digoxigenin-labeled RNA ISH; RNA fluorescent ISH (FISH); and protein immunofluorescence (IF)-RNA FISH double labeling (IF/FISH). Each procedure balances conflicting requirements for permeabilization, fixation and preservation of antigenicity to detect RNA and protein expression with high resolution and sensitivity. The ISH protocol uses alkaline phosphatase-conjugated digoxigenin antibodies followed by a color reaction, whereas FISH detection involves tyramide signal amplification (TSA). To simultaneously preserve antigens for protein detection and enable RNA probe penetration for IF/FISH, we perform IF before FISH and use xylenes and detergents to permeabilize the tissue rather than proteinase K, which can damage the antigens. ISH and FISH take 3 d to perform, whereas IF/FISH takes 5 d. Probe generation takes 1 or 2 d to perform.
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Wang Z, Zhang K, Shen Y, Smith J, Bloch S, Achilefu S, Wooley KL, Taylor JS. Imaging mRNA expression levels in living cells with PNA·DNA binary FRET probes delivered by cationic shell-crosslinked nanoparticles. Org Biomol Chem 2013; 11:3159-67. [PMID: 23538604 PMCID: PMC3687806 DOI: 10.1039/c3ob26923j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Optical imaging of gene expression through the use of fluorescent antisense probes targeted to the mRNA has been an area of great interest. The main obstacles to developing highly sensitive antisense fluorescent imaging agents have been the inefficient intracellular delivery of the probes and high background signal from unbound probes. Binary antisense probes have shown great promise as mRNA imaging agents because a signal can only occur if both probes are bound simultaneously to the mRNA target site. Selecting an accessible binding site is made difficult by RNA folding and protein binding in vivo and the need to bind two probes. Even more problematic, has been a lack of methods for efficient cytoplasmic delivery of the probes that would be suitable for eventual applications in vivo in animals. Herein we report the imaging of iNOS mRNA expression in live mouse macrophage cells with PNA·DNA binary FRET probes delivered by a cationic shell crosslinked knedel-like nanoparticle (cSCK). We first demonstrate that FRET can be observed on in vitro transcribed mRNA with both the PNA probes and the PNA·DNA hybrid probes. We then demonstrate that the FRET signal can be observed in live cells when the hybrid probes are transfected with the cSCK, and that the strength of the FRET signal is sequence specific and depends on the mRNA expression level.
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Affiliation(s)
- Zhenghui Wang
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
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8
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Detection of pre-mRNA splicing in vitro by an RNA-templated fluorogenic reaction. Bioorg Med Chem Lett 2012; 22:7248-51. [DOI: 10.1016/j.bmcl.2012.09.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 09/10/2012] [Accepted: 09/11/2012] [Indexed: 11/19/2022]
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9
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Šimková E, Staněk D. Probing nucleic acid interactions and pre-mRNA splicing by Förster Resonance Energy Transfer (FRET) microscopy. Int J Mol Sci 2012; 13:14929-45. [PMID: 23203103 PMCID: PMC3509619 DOI: 10.3390/ijms131114929] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/31/2012] [Accepted: 10/31/2012] [Indexed: 01/11/2023] Open
Abstract
Förster resonance energy transfer (FRET) microscopy is a powerful technique routinely used to monitor interactions between biomolecules. Here, we focus on the techniques that are used for investigating the structure and interactions of nucleic acids (NAs). We present a brief overview of the most commonly used FRET microscopy techniques, their advantages and drawbacks. We list experimental approaches recently used for either in vitro or in vivo studies. Next, we summarize how FRET contributed to the understanding of pre-mRNA splicing and spliceosome assembly.
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Affiliation(s)
- Eva Šimková
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague, Czech Republic; E-Mail:
| | - David Staněk
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague, Czech Republic; E-Mail:
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Furukawa K, Abe H, Tamura Y, Yoshimoto R, Yoshida M, Tsuneda S, Ito Y. Fluorescence Detection of Intron Lariat RNA with Reduction-Triggered Fluorescent Probes. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201104425] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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11
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Furukawa K, Abe H, Tamura Y, Yoshimoto R, Yoshida M, Tsuneda S, Ito Y. Fluorescence detection of intron lariat RNA with reduction-triggered fluorescent probes. Angew Chem Int Ed Engl 2011; 50:12020-3. [PMID: 22021091 DOI: 10.1002/anie.201104425] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/22/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Kazuhiro Furukawa
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1, Hirosawa, Wako-Shi, Saitama, 351-0198, Japan
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12
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Li X, Yin Y, Yang X, Zhi Z, Zhao XS. Temperature dependence of interaction between double stranded DNA and Cy3 or Cy5. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Higashi M, Yu J, Tsuchiya H, Saito T, Oyama T, Kawana H, Kitagawa M, Tamaru JI, Harigaya K. Visualization of the Activity of Rac1 Small GTPase in a Cell. Acta Histochem Cytochem 2010; 43:163-8. [PMID: 21245983 PMCID: PMC3015054 DOI: 10.1267/ahc.10025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 11/17/2010] [Indexed: 11/22/2022] Open
Abstract
Rho family G proteins including Rac regulate a variety of cellular functions, such as morphology, motility, and gene expression. Here we developed a fluorescence resonance energy transfer-based analysis in which we could monitor the activity of Rac1. To detect fluorescence resonance energy transfer, yellow fluorescent protein fused Rac1 and cyan fluorescent protein fused Cdc42-Rac1-interaction-binding domain of Pak1 protein were used as intermolecular probes of FRET. The fluorophores were separated with linear unmixing method. The fluorescence resonance energy transfer efficiency was measured by acceptor photobleaching assisted assay. With these methods, the Rac1 activity was visualized in a cell. The present findings indicate that this approach is sensitive enough to achieve results similar to those from ratiometric fluorescence resonance energy transfer analysis.
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Affiliation(s)
- Morihiro Higashi
- Department of Pathology, Saitama Medical Center, Saitama Medical University
- Molecular and Tumor Pathology, Chiba University Graduate School of Medicine
| | - Jianyong Yu
- Molecular and Tumor Pathology, Chiba University Graduate School of Medicine
| | - Hiroshi Tsuchiya
- Molecular and Tumor Pathology, Chiba University Graduate School of Medicine
| | - Teruyoshi Saito
- Molecular and Tumor Pathology, Chiba University Graduate School of Medicine
| | - Toshinao Oyama
- Molecular and Tumor Pathology, Chiba University Graduate School of Medicine
| | | | - Motoo Kitagawa
- Molecular and Tumor Pathology, Chiba University Graduate School of Medicine
| | - Jun-ichi Tamaru
- Department of Pathology, Saitama Medical Center, Saitama Medical University
| | - Kenichi Harigaya
- Molecular and Tumor Pathology, Chiba University Graduate School of Medicine
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Blanco AM, Artero R. A practical approach to FRET-based PNA fluorescence in situ hybridization. Methods 2010; 52:343-51. [PMID: 20654719 DOI: 10.1016/j.ymeth.2010.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 07/14/2010] [Accepted: 07/15/2010] [Indexed: 12/01/2022] Open
Abstract
Given the demand for improved methods for detecting and characterizing RNA variants in situ, we developed a quantitative method for detecting RNA alternative splicing variants that combines in situ hybridization of fluorescently labeled peptide nucleic acid (PNA) probes with confocal microscopy Förster resonance energy transfer (FRET). The use of PNA probes complementary to sequences flanking a given splice junction allows to specifically quantify, within the cell, the RNA isoform generating such splice junction as FRET efficiency measure. The FRET-based PNA fluorescence in situ hybridization (FP-FISH) method offers a conceptually new approach for characterizing at the subcellular level not only splice variant isoform structure, location, and dynamics but also potentially a wide variety of close range RNA-RNA interactions. In this paper, we explain the FP-FISH technique workflow for reliable and reproducible results.
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Affiliation(s)
- Ana M Blanco
- Sistemas Genómicos S.L., Parque Tecnológico de Valencia, Ronda G. Marconi 6, Paterna, Spain
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