1
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DʼEste E, Lukinavičius G, Lincoln R, Opazo F, Fornasiero EF. Advancing cell biology with nanoscale fluorescence imaging: essential practical considerations. Trends Cell Biol 2024; 34:671-684. [PMID: 38184400 DOI: 10.1016/j.tcb.2023.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/08/2024]
Abstract
Recently, biologists have gained access to several far-field fluorescence nanoscopy (FN) technologies that allow the observation of cellular components with ~20 nm resolution. FN is revolutionizing cell biology by enabling the visualization of previously inaccessible subcellular details. While technological advances in microscopy are critical to the field, optimal sample preparation and labeling are equally important and often overlooked in FN experiments. In this review, we provide an overview of the methodological and experimental factors that must be considered when performing FN. We present key concepts related to the selection of affinity-based labels, dyes, multiplexing, live cell imaging approaches, and quantitative microscopy. Consideration of these factors greatly enhances the effectiveness of FN, making it an exquisite tool for numerous biological applications.
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Affiliation(s)
- Elisa DʼEste
- Optical Microscopy Facility, Max Planck Institute for Medical Research, Heidelberg 69120, Germany.
| | - Gražvydas Lukinavičius
- Chromatin Labelling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany.
| | - Richard Lincoln
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg 69120, Germany.
| | - Felipe Opazo
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen (UMG), Göttingen 37073, Germany; Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center, Göttingen 37075, Germany; NanoTag Biotechnologies GmbH, Göttingen 37079, Germany.
| | - Eugenio F Fornasiero
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen (UMG), Göttingen 37073, Germany; Department of Life Sciences, University of Trieste, Trieste 34127, Italy.
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2
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Kleene V, Corvaglia V, Chacin E, Forne I, Konrad DB, Khosravani P, Douat C, Kurat CF, Huc I, Imhof A. DNA mimic foldamers affect chromatin composition and disturb cell cycle progression. Nucleic Acids Res 2023; 51:9629-9642. [PMID: 37650653 PMCID: PMC10570015 DOI: 10.1093/nar/gkad681] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023] Open
Abstract
The use of synthetic chemicals to selectively interfere with chromatin and the chromatin-bound proteome represents a great opportunity for pharmacological intervention. Recently, synthetic foldamers that mimic the charge surface of double-stranded DNA have been shown to interfere with selected protein-DNA interactions. However, to better understand their pharmacological potential and to improve their specificity and selectivity, the effect of these molecules on complex chromatin needs to be investigated. We therefore systematically studied the influence of the DNA mimic foldamers on the chromatin-bound proteome using an in vitro chromatin assembly extract. Our studies show that the foldamer efficiently interferes with the chromatin-association of the origin recognition complex in vitro and in vivo, which leads to a disturbance of cell cycle in cells treated with foldamers. This effect is mediated by a strong direct interaction between the foldamers and the origin recognition complex and results in a failure of the complex to organise chromatin around replication origins. Foldamers that mimic double-stranded nucleic acids thus emerge as a powerful tool with designable features to alter chromatin assembly and selectively interfere with biological mechanisms.
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Affiliation(s)
- Vera Kleene
- Department of Molecular Biology, Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians University, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Valentina Corvaglia
- Department of Pharmacy, Institute of Chemical Epigenetics, Ludwig-Maximilians University, Butenandtstraße 5-13, 81377 München, Germany
| | - Erika Chacin
- Department of Molecular Biology, Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians University, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Ignasi Forne
- Protein Analysis Unit, Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians University, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - David B Konrad
- Department of Pharmacy, Institute of Chemical Epigenetics, Ludwig-Maximilians University, Butenandtstraße 5-13, 81377 München, Germany
| | - Pardis Khosravani
- Core Facility Flow Cytometry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Céline Douat
- Department of Pharmacy, Institute of Chemical Epigenetics, Ludwig-Maximilians University, Butenandtstraße 5-13, 81377 München, Germany
| | - Christoph F Kurat
- Department of Molecular Biology, Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians University, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Ivan Huc
- Department of Pharmacy, Institute of Chemical Epigenetics, Ludwig-Maximilians University, Butenandtstraße 5-13, 81377 München, Germany
| | - Axel Imhof
- Department of Molecular Biology, Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians University, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
- Protein Analysis Unit, Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians University, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
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3
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Pradhan S, Apaydin S, Bucevičius J, Gerasimaitė R, Kostiuk G, Lukinavičius G. Sequence-specific DNA labelling for fluorescence microscopy. Biosens Bioelectron 2023; 230:115256. [PMID: 36989663 DOI: 10.1016/j.bios.2023.115256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/04/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
The preservation of nucleus structure during microscopy imaging is a top priority for understanding chromatin organization, genome dynamics, and gene expression regulation. In this review, we summarize the sequence-specific DNA labelling methods that can be used for imaging in fixed and/or living cells without harsh treatment and DNA denaturation: (i) hairpin polyamides, (ii) triplex-forming oligonucleotides, (iii) dCas9 proteins, (iv) transcription activator-like effectors (TALEs) and (v) DNA methyltransferases (MTases). All these techniques are capable of identifying repetitive DNA loci and robust probes are available for telomeres and centromeres, but visualizing single-copy sequences is still challenging. In our futuristic vision, we see gradual replacement of the historically important fluorescence in situ hybridization (FISH) by less invasive and non-destructive methods compatible with live cell imaging. Combined with super-resolution fluorescence microscopy, these methods will open the possibility to look into unperturbed structure and dynamics of chromatin in living cells, tissues and whole organisms.
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4
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Larcombe MR, Hsu S, Polo JM, Knaupp AS. Indirect Mechanisms of Transcription Factor-Mediated Gene Regulation during Cell Fate Changes. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2200015. [PMID: 36911290 PMCID: PMC9993476 DOI: 10.1002/ggn2.202200015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Indexed: 06/18/2023]
Abstract
Transcription factors (TFs) are the master regulators of cellular identity, capable of driving cell fate transitions including differentiations, reprogramming, and transdifferentiations. Pioneer TFs recognize partial motifs exposed on nucleosomal DNA, allowing for TF-mediated activation of repressed chromatin. Moreover, there is evidence suggesting that certain TFs can repress actively expressed genes either directly through interactions with accessible regulatory elements or indirectly through mechanisms that impact the expression, activity, or localization of other regulatory factors. Recent evidence suggests that during reprogramming, the reprogramming TFs initiate opening of chromatin regions rich in somatic TF motifs that are inaccessible in the initial and final cellular states. It is postulated that analogous to a sponge, these transiently accessible regions "soak up" somatic TFs, hence lowering the initial barriers to cell fate changes. This indirect TF-mediated gene regulation event, which is aptly named the "sponge effect," may play an essential role in the silencing of the somatic transcriptional network during different cellular conversions.
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Affiliation(s)
- Michael R. Larcombe
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
| | - Sheng Hsu
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
| | - Jose M. Polo
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
- South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical SciencesUniversity of AdelaideAdelaideSouth Australia5005Australia
- Adelaide Centre for Epigenetics, Faculty of Health and Medical SciencesUniversity of AdelaideAdelaideSouth Australia5005Australia
| | - Anja S. Knaupp
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
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5
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Hatanaka J, Hirose Y, Hashiya K, Bando T, Sugiyama H. N‐terminal cationic modification of linear pyrrole−imidazole polyamide improves its binding to DNA. Chembiochem 2022; 23:e202200124. [DOI: 10.1002/cbic.202200124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/18/2022] [Indexed: 11/08/2022]
Affiliation(s)
| | - Yuki Hirose
- Kyoto University - Yoshida Campus: Kyoto Daigaku Chemistry JAPAN
| | - Kaori Hashiya
- Kyoto University - Yoshida Campus: Kyoto Daigaku Chemistry JAPAN
| | - Toshikazu Bando
- Kyoto University - Yoshida Campus: Kyoto Daigaku Chemistry JAPAN
| | - Hiroshi Sugiyama
- Kyoto University Department of Chemistry Kitashirakawa-Oiwakecho 606-8502 Kyoto JAPAN
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6
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Waymack R, Gad M, Wunderlich Z. Molecular competition can shape enhancer activity in the Drosophila embryo. iScience 2021; 24:103034. [PMID: 34568782 PMCID: PMC8449247 DOI: 10.1016/j.isci.2021.103034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/27/2021] [Accepted: 08/20/2021] [Indexed: 01/12/2023] Open
Abstract
Transgenic reporters allow the measurement of regulatory DNA activity in vivo and consequently have long been useful tools for studying enhancers. Despite their utility, few studies have investigated the effects these reporters may have on the expression of other genes. Understanding these effects is required to accurately interpret reporter data and characterize gene regulatory mechanisms. By measuring the expression of Kruppel (Kr) enhancer reporters in live Drosophila embryos, we find reporters inhibit one another's expression and that of a nearby endogenous gene. Using synthetic transcription factor (TF) binding site arrays, we present evidence that competition for TFs is partially responsible for the observed transcriptional inhibition. We develop a simple thermodynamic model that predicts competition of the measured magnitude specifically when TF binding is restricted to distinct nuclear subregions. Our findings underline an unexpected role of the non-homogenous nature of the nucleus in regulating gene expression.
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Affiliation(s)
- Rachel Waymack
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Mario Gad
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Zeba Wunderlich
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
- Department of Biology, Boston University, 610 Commonwealth Ave., Boston, MA 02215, USA
- Biological Design Center, Boston University, 610 Commonwealth Avenue, Boston, MA 02215, USA
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7
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Calabrese DR, Zlotkowski K, Alden S, Hewitt WM, Connelly CM, Wilson RM, Gaikwad S, Chen L, Guha R, Thomas CJ, Mock BA, Schneekloth JS. Characterization of clinically used oral antiseptics as quadruplex-binding ligands. Nucleic Acids Res 2019; 46:2722-2732. [PMID: 29481610 PMCID: PMC5888870 DOI: 10.1093/nar/gky084] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/20/2018] [Indexed: 12/25/2022] Open
Abstract
Approaches to characterize the nucleic acid-binding properties of drugs and druglike small molecules are crucial to understanding the behavior of these compounds in cellular systems. Here, we use a Small Molecule Microarray (SMM) profiling approach to identify the preferential interaction between chlorhexidine, a widely used oral antiseptic, and the G-quadruplex (G4) structure in the KRAS oncogene promoter. The interaction of chlorhexidine and related drugs to the KRAS G4 is evaluated using multiple biophysical methods, including thermal melt, fluorescence titration and surface plasmon resonance (SPR) assays. Chlorhexidine has a specific low micromolar binding interaction with the G4, while related drugs have weaker and/or less specific interactions. Through NMR experiments and docking studies, we propose a plausible binding mode driven by both aromatic stacking and groove binding interactions. Additionally, cancer cell lines harbouring oncogenic mutations in the KRAS gene exhibit increased sensitivity to chlorhexidine. Treatment of breast cancer cells with chlorhexidine decreases KRAS protein levels, while a KRAS gene transiently expressed by a promoter lacking a G4 is not affected. This work confirms that known ligands bind broadly to G4 structures, while other drugs and druglike compounds can have more selective interactions that may be biologically relevant.
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Affiliation(s)
- David R Calabrese
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Katherine Zlotkowski
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Stephanie Alden
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - William M Hewitt
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Colleen M Connelly
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Robert M Wilson
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Snehal Gaikwad
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892-4258, USA
| | - Lu Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Rajarshi Guha
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Beverly A Mock
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892-4258, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
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8
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Kawamoto Y, Bando T, Sugiyama H. Sequence-specific DNA binding Pyrrole-imidazole polyamides and their applications. Bioorg Med Chem 2018; 26:1393-1411. [PMID: 29439914 DOI: 10.1016/j.bmc.2018.01.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/25/2018] [Accepted: 01/28/2018] [Indexed: 12/25/2022]
Abstract
Pyrrole-imidazole polyamides (Py-Im polyamides) are cell-permeable compounds that bind to the minor groove of double-stranded DNA in a sequence-specific manner without causing denaturation of the DNA. These compounds can be used to control gene expression and to stain specific sequences in cells. Here, we review the history, structural variations, and functional investigations of Py-Im polyamides.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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9
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Ali A, Bovilla VR, Mysarla DK, Siripurapu P, Pathak RU, Basu B, Mamillapalli A, Bhattacharya S. Knockdown of Broad-Complex Gene Expression of Bombyx mori by Oligopyrrole Carboxamides Enhances Silk Production. Sci Rep 2017; 7:805. [PMID: 28400559 PMCID: PMC5429751 DOI: 10.1038/s41598-017-00653-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 12/15/2016] [Indexed: 11/09/2022] Open
Abstract
Bombyx mori (B. mori) is important due to its major role in the silk production. Though DNA binding ligands often influence gene expression, no attempt has been made to exploit their use in sericulture. The telomeric heterochromatin of B. mori is enriched with 5'-TTAGG-3' sequences. These sequences were also found to be present in several genes in the euchromatic regions. We examined three synthetic oligopyrrole carboxamides that target 5'-TTAGG-3' sequences in controlling the gene expression in B. mori. The ligands did not show any defect or feeding difference in the larval stage, crucial for silk production. The ligands caused silencing of various isoforms of the broad-complex transcription factor and cuticle proteins which resulted in late pupal developmental defects. Furthermore, treatment with such drugs resulted in statistically enhanced cocoon weight, shell weight, and silk yield. This study shows for the first time use of oligopyrrole carboxamide drugs in controlling gene expression in B. mori and their long term use in enhancing silk production.
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Affiliation(s)
- Asfa Ali
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560 012, India
| | - Venugopal Reddy Bovilla
- Department of Biotechnology, GITAM Institute of Science, GITAM University, Visakhapatnam, 530 045, India
| | - Danti Kumari Mysarla
- Department of Biotechnology, GITAM Institute of Science, GITAM University, Visakhapatnam, 530 045, India
| | - Prasanthi Siripurapu
- Department of Biotechnology, GITAM Institute of Science, GITAM University, Visakhapatnam, 530 045, India
| | - Rashmi U Pathak
- Centre for Cellular and Molecular Biology, Hyderabad, 500 007, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India
| | - Anitha Mamillapalli
- Department of Biotechnology, GITAM Institute of Science, GITAM University, Visakhapatnam, 530 045, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560 012, India. .,Director's Research Unit, and Technical Research Centre, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, West Bengal, 700 032, India.
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10
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Kemme CA, Nguyen D, Chattopadhyay A, Iwahara J. Regulation of transcription factors via natural decoys in genomic DNA. Transcription 2016; 7:115-20. [PMID: 27384377 PMCID: PMC4984682 DOI: 10.1080/21541264.2016.1188873] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/05/2016] [Accepted: 05/06/2016] [Indexed: 01/24/2023] Open
Abstract
Eukaryotic genomic DNA contains numerous high-affinity sites for transcription factors. Only a small fraction of these sites directly regulates target genes. Other high-affinity sites can serve as naturally present decoys that sequester transcription factors. Such natural decoys in genomic DNA may provide novel regulatory mechanisms for transcription factors.
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Affiliation(s)
- Catherine A. Kemme
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Dan Nguyen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Abhijnan Chattopadhyay
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
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11
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Sawatani Y, Kashiwazaki G, Chandran A, Asamitsu S, Guo C, Sato S, Hashiya K, Bando T, Sugiyama H. Sequence-specific DNA binding by long hairpin pyrrole-imidazole polyamides containing an 8-amino-3,6-dioxaoctanoic acid unit. Bioorg Med Chem 2016; 24:3603-11. [PMID: 27301681 DOI: 10.1016/j.bmc.2016.05.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 05/28/2016] [Accepted: 05/30/2016] [Indexed: 12/13/2022]
Abstract
With the aim of improving aqueous solubility, we designed and synthesized five N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides capable of recognizing 9-bp sequences. Their DNA-binding affinities and sequence specificities were evaluated by SPR and Bind-n-Seq analyses. The design of polyamide 1 was based on a conventional model, with three consecutive Py or Im rings separated by a β-alanine to match the curvature and twist of long DNA helices. Polyamides 2 and 3 contained an 8-amino-3,6-dioxaoctanoic acid (AO) unit, which has previously only been used as a linker within linear Py-Im polyamides or between Py-Im hairpin motifs for tandem hairpin. It is demonstrated herein that AO also functions as a linker element that can extend to 2-bp in hairpin motifs. Notably, although the AO-containing unit can fail to bind the expected sequence, polyamide 4, which has two AO units facing each other in a hairpin form, successfully showed the expected motif and a KD value of 16nM was recorded. Polyamide 5, containing a β-alanine-β-alanine unit instead of the AO of polyamide 2, was synthesized for comparison. The aqueous solubilities and nuclear localization of three of the polyamides were also examined. The results suggest the possibility of applying the AO unit in the core of Py-Im polyamide compounds.
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Affiliation(s)
- Yoshito Sawatani
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Anandhakumar Chandran
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Sefan Asamitsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Chuanxin Guo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiyacho, Sakyo, Kyoto 606-8501, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiyacho, Sakyo, Kyoto 606-8501, Japan.
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12
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Guenther DC, Anderson GH, Karmakar S, Anderson BA, Didion BA, Guo W, Verstegen JP, Hrdlicka PJ. Invader probes: Harnessing the energy of intercalation to facilitate recognition of chromosomal DNA for diagnostic applications. Chem Sci 2015; 6:5006-5015. [PMID: 26240741 PMCID: PMC4521421 DOI: 10.1039/c5sc01238d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/10/2015] [Indexed: 01/01/2023] Open
Abstract
Development of probes capable of recognizing specific regions of chromosomal DNA has been a long-standing goal for chemical biologists. Current strategies such as PNA, triplex-forming oligonucleotides, and polyamides are subject to target choice limitations and/or necessitate non-physiological conditions, leaving a need for alternative approaches. Toward this end, we have recently introduced double-stranded oligonucleotide probes that are energetically activated for DNA recognition through modification with +1 interstrand zippers of intercalator-functionalized nucleotide monomers. Here, probes with different chemistries and architectures - varying in the position, number, and distance between the intercalator zippers - are studied with respect to hybridization energetics and DNA-targeting properties. Experiments with model DNA targets demonstrate that optimized probes enable efficient (C50 < 1 μM), fast (t50 < 3h), kinetically stable (> 24h), and single nucleotide specific recognition of DNA targets at physiologically relevant ionic strengths. Optimized probes were used in non-denaturing fluorescence in situ hybridization experiments for detection of gender-specific mixed-sequence chromosomal DNA target regions. These probes present themselves as a promising strategy for recognition of chromosomal DNA, which will enable development of new tools for applications in molecular biology, genomic engineering and nanotechnology.
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Affiliation(s)
- Dale C. Guenther
- Department of Chemistry , University of Idaho , 875 Perimeter Dr , Moscow , ID 83844-2343 , USA .
| | - Grace H. Anderson
- Department of Chemistry , University of Idaho , 875 Perimeter Dr , Moscow , ID 83844-2343 , USA .
- Department of Biological Sciences , Montana Tech of the University of Montana , 1300 W Park St , Butte , MT 59701-8997 , USA
| | - Saswata Karmakar
- Department of Chemistry , University of Idaho , 875 Perimeter Dr , Moscow , ID 83844-2343 , USA .
| | - Brooke A. Anderson
- Department of Chemistry , University of Idaho , 875 Perimeter Dr , Moscow , ID 83844-2343 , USA .
| | | | - Wei Guo
- MoFA , PO Box 930187, 419 Venture Ct. , Verona , WI 53593 , USA
| | | | - Patrick J. Hrdlicka
- Department of Chemistry , University of Idaho , 875 Perimeter Dr , Moscow , ID 83844-2343 , USA .
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13
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Koeller KJ, Harris GD, Aston K, He G, Castaneda CH, Thornton MA, Edwards TG, Wang S, Nanjunda R, Wilson WD, Fisher C, Bashkin JK. DNA Binding Polyamides and the Importance of DNA Recognition in their use as Gene-Specific and Antiviral Agents. Med Chem 2014; 4:338-344. [PMID: 24839583 DOI: 10.4172/2161-0444.1000162] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is a long history for the bioorganic and biomedical use of N-methyl-pyrrole-derived polyamides (PAs) that are higher homologs of natural products such as distamycin A and netropsin. This work has been pursued by many groups, with the Dervan and Sugiyama groups responsible for many breakthroughs. We have studied PAs since about 1999, partly in industry and partly in academia. Early in this program, we reported methods to control cellular uptake of polyamides in cancer cell lines and other cells likely to have multidrug resistance efflux pumps induced. We went on to discover antiviral polyamides active against HPV31, where SAR showed that a minimum binding size of about 10 bp of DNA was necessary for activity. Subsequently we discovered polyamides active against two additional high-risk HPVs, HPV16 and 18, a subset of which showed broad spectrum activity against HPV16, 18 and 31. Aspects of our results presented here are incompatible with reported DNA recognition rules. For example, molecules with the same cognate DNA recognition properties varied from active to inactive against HPVs. We have since pursued the mechanism of action of antiviral polyamides, and polyamides in general, with collaborators at NanoVir, the University of Missouri-St. Louis, and Georgia State University. We describe dramatic consequences of β-alanine positioning even in relatively small, 8-ring polyamides; these results contrast sharply with prior reports. This paper was originally presented by JKB as a Keynote Lecture in the 2nd International Conference on Medicinal Chemistry and Computer Aided Drug Design Conference in Las Vegas, NV, October 2013.
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Affiliation(s)
- Kevin J Koeller
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St.Louis, MO 63121, USA
| | - G Davis Harris
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St.Louis, MO 63121, USA
| | - Karl Aston
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St.Louis, MO 63121, USA
| | - Gaofei He
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St.Louis, MO 63121, USA
| | - Carlos H Castaneda
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St.Louis, MO 63121, USA
| | - Melissa A Thornton
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St.Louis, MO 63121, USA
| | | | - Shuo Wang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Rupesh Nanjunda
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | | | - James K Bashkin
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St.Louis, MO 63121, USA ; NanoVir, LLC, Kalamazoo, MI 49008, USA
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Didion BA, Karmakar S, Guenther DC, Sau SP, Verstegen JP, Hrdlicka PJ. Invaders: Recognition of Double-Stranded DNA by Using Duplexes Modified with Interstrand Zippers of 2'-O-(Pyren-1-yl)methyl-ribonucleotides. Chembiochem 2013; 14:1534-1538. [PMID: 24038876 PMCID: PMC3838861 DOI: 10.1002/cbic.201300414] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Indexed: 12/23/2022]
Abstract
The invasion has begun: Invaders are shown to recognize DNA hairpins in cell-free assays and chromosomal DNA during non-denaturing fluorescence in situ hybridization (nd-FISH) experiments. As Invaders are devoid of inherent sequence limitations, many previously inaccessible DNA targets could become accessible to exogenous control with important ramifications for karyotyping, in vivo imaging, and gene regulation.
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Affiliation(s)
- Bradley A Didion
- Minitube of America, Inc. PO Box 930187, 419 Venture Ct., Verona, WI 53593 (USA)
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15
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Blackledge MS, Melander C. Programmable DNA-binding small molecules. Bioorg Med Chem 2013; 21:6101-14. [PMID: 23665141 DOI: 10.1016/j.bmc.2013.04.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/29/2013] [Accepted: 04/05/2013] [Indexed: 10/26/2022]
Abstract
Aberrant gene expression is responsible for a myriad of human diseases from infectious diseases to cancer. Precise regulation of these genes via specific interactions with the DNA double helix could pave the way for novel therapeutics. Pyrrole-imidazole polyamides are small molecules capable of binding to pre-determined DNA sequences up to 16 base pairs with affinity and specificity comparable to natural transcription factors. In the three decades since their development, great strides have been made relating to synthetic accessibility and improved sequence specificity and binding affinity. This perspective presents a brief history of early seminal developments in the field and highlights recent reports of the utility of polyamides as both genetic modulators and molecular probes.
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Affiliation(s)
- Meghan S Blackledge
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8024, United States
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16
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Meier JL, Yu AS, Korf I, Segal DJ, Dervan PB. Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing. J Am Chem Soc 2012; 134:17814-22. [PMID: 23013524 PMCID: PMC3483022 DOI: 10.1021/ja308888c] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Genomic applications of DNA-binding molecules require
an unbiased
knowledge of their high affinity sites. We report the high-throughput
analysis of pyrrole-imidazole polyamide DNA-binding specificity in
a 1012-member DNA sequence library using affinity purification
coupled with massively parallel sequencing. We find that even within
this broad context, the canonical pairing rules are remarkably predictive
of polyamide DNA-binding specificity. However, this approach also
allows identification of unanticipated high affinity DNA-binding sites
in the reverse orientation for polyamides containing β/Im pairs.
These insights allow the redesign of hairpin polyamides with different
turn units capable of distinguishing 5′-WCGCGW-3′ from
5′-WGCGCW-3′. Overall, this study displays the power
of high-throughput methods to aid the optimal targeting of sequence-specific
minor groove binding molecules, an essential underpinning for biological
and nanotechnological applications.
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Affiliation(s)
- Jordan L Meier
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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17
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Vaijayanthi T, Bando T, Pandian GN, Sugiyama H. Progress and prospects of pyrrole-imidazole polyamide-fluorophore conjugates as sequence-selective DNA probes. Chembiochem 2012; 13:2170-85. [PMID: 23023993 DOI: 10.1002/cbic.201200451] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Indexed: 12/24/2022]
Abstract
Recently, the versatility of N-methylpyrrole (Py)-N-methylimidazole (Im) polyamide conjugates, which have been developed from the DNA-binding antibiotics distamycin A and netropsin, has been shown. These synthetic small molecules can permeate cells to bind with duplex DNA in a sequence-specific manner, and hence can influence gene expression in vivo. Accordingly, several reports demonstrating the sequence specificity and biological activity of Py-Im polyamides have accumulated. However, the benefits of Py-Im polyamides, in particular those conjugated with fluorophores, has been overlooked. Moreover, clear directions for the employment of these attractive artificial small molecules have not yet been shown. Here, we present a detailed overview of the current and prospective applications of Py-Im polyamide-fluorophore conjugates, including sequence-specific recognition with fluorescence emission properties, and their potential roles in biological imaging.
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Affiliation(s)
- Thangavel Vaijayanthi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa oiwakecho, Kyoto 606-8502, Japan
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18
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Bashkin JK, Aston K, Ramos JP, Koeller KJ, Nanjunda R, He G, Dupureur CM, David Wilson W. Promoter scanning of the human COX-2 gene with 8-ring polyamides: unexpected weakening of polyamide-DNA binding and selectivity by replacing an internal N-Me-pyrrole with β-alanine. Biochimie 2012; 95:271-9. [PMID: 23023196 DOI: 10.1016/j.biochi.2012.09.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 09/18/2012] [Indexed: 12/16/2022]
Abstract
Rules for polyamide-DNA recognition have proved invaluable for the design of sequence-selective DNA binding agents in cell-free systems. However, these rules are not fully transferrable to predicting activity in cells, tissues or animals, and additional refinements to our understanding of DNA recognition would help biomedical studies. Similar complexities are encountered when using internal β-alanines as polyamide building blocks in place of N-methylpyrrole; β-alanines were introduced in polyamide designs to maintain good hydrogen bonding registry with the target DNA, especially for long polyamides or those with several GC bp (P.B. Dervan, A.R. Urbach, Essays Contemp. Chem. (2001) 327-339). Thus, to clarify important subtleties of molecular recognition, we studied the effects of replacing a single pyrrole with β-alanine in 8-ring polyamides designed against the Ets-1 transcription factor. Replacement of a single internal N-methylpyrrole with β-alanine to generate a β/Im pairing in two 8-ring polyamides causes a decrease in DNA binding affinity by two orders of magnitude and decreases DNA binding selectivity, contrary to expectations based on the literature. Measurements were made by fluorescence spectroscopy, quantitative DNA footprinting and surface plasmon resonance, with these vastly different techniques showing excellent agreement. Furthermore, results were validated for a range of DNA substrates from small hairpins to long dsDNA sequences. Docking studies helped show that β-alanine does not make efficient hydrophobic contacts with the rest of the polyamide or nearby DNA, in contrast to pyrrole. These results help refine design principles and expectations for polyamide-DNA recognition.
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Affiliation(s)
- James K Bashkin
- Department of Chemistry & Biochemistry, Center for Nanoscience, University of Missouri-St. Louis, One University Blvd., St. Louis, MO 63121, USA.
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Chromatin Organization by Repetitive Elements (CORE): A Genomic Principle for the Higher-Order Structure of Chromosomes. Genes (Basel) 2011; 2:502-15. [PMID: 24710208 PMCID: PMC3927610 DOI: 10.3390/genes2030502] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 07/21/2011] [Accepted: 07/25/2011] [Indexed: 12/01/2022] Open
Abstract
Eukaryotic genomes contain a large amount of DNA repeats (also known as repetitive DNA, repetitive elements, and repetitive sequences). Here, I propose a role of repetitive DNA in the formation of higher-order structures of chromosomes. The central idea of this theory is that chromatin regions with repetitive sequences pair with regions harboring homologous repeats and that such somatic repeat pairing (RP) assembles repetitive DNA chromatin into compact chromosomal domains that specify chromatin folding in a site-directed manner. According to this theory, DNA repeats are not randomly distributed in the genome. Instead, they form a core framework that coordinates the architecture of chromosomes. In contrast to the viewpoint that DNA repeats are genomic ‘junk’, this theory advocates that repetitive sequences are chromatin organizer modules that determine chromatin-chromatin contact points within chromosomes. This novel concept, if correct, would suggest that DNA repeats in the linear genome encode a blueprint for higher-order chromosomal organization.
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20
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Pazos E, Mosquera J, Vázquez ME, Mascareñas JL. DNA Recognition by Synthetic Constructs. Chembiochem 2011; 12:1958-73. [DOI: 10.1002/cbic.201100247] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Indexed: 12/29/2022]
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21
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Abstract
The term epigenetic landscape was coined by CH Waddington to describe how cell fates were established in development, visualized as valleys and ridges directing the irreversibility of cell type differentiation. It is now clear that normal differentiation control breaks down during tumor development and that all tumor types show aberrant regulation of the epigenetic code, including changes in DNA methylation, histone modification and microRNAs. This has led to much interest in the development of epigenetic cancer therapies to target this aberrant epigenetic regulation. Histone deacetylase and DNA methyltransferase inhibitors are now used in the treatment of certain hematological malignancies. However, their more general applicability to solid tumors may be limited by lack of specificity and delivery challenges. Approaches to overcome these limitations and how to develop more specific drugs are discussed. The use of RNAi in the context of genome regulation as well as the possibility to use polyamides and engineered zinc fingers to target master regulators in the future is examined. Ultimately, improved specificity of epigenetic therapies will require increased mapping of the aberrant epigenetic landscape in cancer and cancer-specific target validation using chemical epigenetic approaches.
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22
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Kelly BL, Singh G, Aiyar A. Molecular and cellular characterization of an AT-hook protein from Leishmania. PLoS One 2011; 6:e21412. [PMID: 21731738 PMCID: PMC3121789 DOI: 10.1371/journal.pone.0021412] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 05/27/2011] [Indexed: 11/26/2022] Open
Abstract
AT-rich DNA, and the proteins that bind it (AT-hook proteins), modulate chromosome structure and function in most eukaryotes. Unlike other trypanosomatids, the genome of Leishmania species is unusually GC-rich, and the regulation of Leishmania chromosome structure, replication, partitioning is not fully understood. Because AT-hook proteins modulate these functions in other eukaryotes, we examined whether AT-hook proteins are encoded in the Leishmania genome, to test their potential functions. Several Leishmania ORFs predicted to be AT-hook proteins were identified using in silico approaches based on sequences shared between eukaryotic AT-hook proteins. We have used biochemical, molecular and cellular techniques to characterize the L. amazonensis ortholog of the L. major protein LmjF06.0720, a potential AT-hook protein that is highly conserved in Leishmania species. Using a novel fusion between the AT-hook domain encoded by LmjF06.0720 and a herpesviral protein, we have demonstrated that LmjF06.0720 functions as an AT-hook protein in mammalian cells. Further, as observed for mammalian and viral AT-hook proteins, the AT-hook domains of LmjF06.0720 bind specific regions of condensed mammalian metaphase chromosomes, and support the licensed replication of DNA in mammalian cells. LmjF06.0720 is nuclear in Leishmania, and this localization is disrupted upon exposure to drugs that displace AT-hook proteins from AT-rich DNA. Coincidentally, these drugs dramatically alter the cellular physiology of Leishmania promastigotes. Finally, we have devised a novel peptido-mimetic agent derived from the sequence of LmjF06.0720 that blocks the proliferation of Leishmania promastigotes, and lowers amastigote parasitic burden in infected macrophages. Our results indicate that AT-hook proteins are critical for the normal biology of Leishmania. In addition, we have described a simple technique to examine the function of Leishmania chromatin-binding proteins in a eukaryotic context amenable to studying chromosome structure and function. Lastly, we demonstrate the therapeutic potential of compounds directed against AT-hook proteins in Leishmania.
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Affiliation(s)
- Ben L. Kelly
- Department of Microbiology, Immunology and Parasitology, Lousiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Gyanendra Singh
- Stanley S. Scott Cancer Center, Lousiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Ashok Aiyar
- Department of Microbiology, Immunology and Parasitology, Lousiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
- Stanley S. Scott Cancer Center, Lousiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
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23
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Baron RM, Lopez-Guzman S, Riascos DF, Macias AA, Layne MD, Cheng G, Harris C, Chung SW, Reeves R, von Andrian UH, Perrella MA. Distamycin A inhibits HMGA1-binding to the P-selectin promoter and attenuates lung and liver inflammation during murine endotoxemia. PLoS One 2010; 5:e10656. [PMID: 20498830 PMCID: PMC2871042 DOI: 10.1371/journal.pone.0010656] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 04/17/2010] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The architectural transcription factor High Mobility Group-A1 (HMGA1) binds to the minor groove of AT-rich DNA and forms transcription factor complexes ("enhanceosomes") that upregulate expression of select genes within the inflammatory cascade during critical illness syndromes such as acute lung injury (ALI). AT-rich regions of DNA surround transcription factor binding sites in genes critical for the inflammatory response. Minor groove binding drugs (MGBs), such as Distamycin A (Dist A), interfere with AT-rich region DNA binding in a sequence and conformation-specific manner, and HMGA1 is one of the few transcription factors whose binding is inhibited by MGBs. OBJECTIVES To determine whether MGBs exert beneficial effects during endotoxemia through attenuating tissue inflammation via interfering with HMGA1-DNA binding and modulating expression of adhesion molecules. METHODOLOGY/PRINCIPAL FINDINGS Administration of Dist A significantly decreased lung and liver inflammation during murine endotoxemia. In intravital microscopy studies, Dist A attenuated neutrophil-endothelial interactions in vivo following an inflammatory stimulus. Endotoxin induction of P-selectin expression in lung and liver tissue and promoter activity in endothelial cells was significantly reduced by Dist A, while E-selectin induction was not significantly affected. Moreover, Dist A disrupted formation of an inducible complex containing NF-kappaB that binds an AT-rich region of the P-selectin promoter. Transfection studies demonstrated a critical role for HMGA1 in facilitating cytokine and NF-kappaB induction of P-selectin promoter activity, and Dist A inhibited binding of HMGA1 to this AT-rich region of the P-selectin promoter in vivo. CONCLUSIONS/SIGNIFICANCE We describe a novel targeted approach in modulating lung and liver inflammation in vivo during murine endotoxemia through decreasing binding of HMGA1 to a distinct AT-rich region of the P-selectin promoter. These studies highlight the ability of MGBs to function as molecular tools for dissecting transcriptional mechanisms in vivo and suggest alternative treatment approaches for critical illness.
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Affiliation(s)
- Rebecca M Baron
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.
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24
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Ledesma A, Zinczuk J, López González J, Ben Altabef A, Brandán S. Structural and vibrational study of 4-(2′-furyl)-1-methylimidazole. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.01.058] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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25
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Chou CJ, Farkas ME, Tsai SM, Alvarez D, Dervan PB, Gottesfeld JM. Small molecules targeting histone H4 as potential therapeutics for chronic myelogenous leukemia. Mol Cancer Ther 2008; 7:769-78. [PMID: 18413791 DOI: 10.1158/1535-7163.mct-08-0130] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We recently identified a polyamide-chlorambucil conjugate, 1R-Chl, which alkylates and down-regulates transcription of the human histone H4c gene and inhibits the growth of several cancer cell lines in vitro and in a murine SW620 xenograft model, without apparent animal toxicity. In this study, we analyzed the effects of 1R-Chl in the chronic myelogenous leukemia cell line K562 and identified another polyamide conjugate, 6R-Chl, which targets H4 genes and elicits a similar cellular response. Other polyamide conjugates that do not target the H4 gene do not elicit this response. In a murine model, both 1R-Chl and 6R-Chl were found to be highly effective in blocking K562 xenograft growth with high-dose tolerance. Unlike conventional and distamycin-based alkylators, little or no cytotoxicities and animal toxicities were observed in mg/kg dosage ranges. These results suggest that these polyamide alkylators may be a viable treatment alternative for chronic myelogenous leukemia.
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Affiliation(s)
- C James Chou
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
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26
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Gottesfeld JM. Small molecules affecting transcription in Friedreich ataxia. Pharmacol Ther 2007; 116:236-48. [PMID: 17826840 PMCID: PMC2080619 DOI: 10.1016/j.pharmthera.2007.06.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Accepted: 06/25/2007] [Indexed: 12/21/2022]
Abstract
This review concerns the development of small molecule therapeutics for the inherited neurodegenerative disease Friedreich ataxia (FRDA). FRDA is caused by transcriptional repression of the nuclear FXN gene, encoding the essential mitochondrial protein frataxin and accompanying loss of frataxin protein. Frataxin insufficiency leads to mitochrondrial dysfunction and progressive neurodegeneration, along with scoliosis, diabetes and cardiomyopathy. Individuals with FRDA generally die in early adulthood from the associated heart disease, the most common cause of death in FRDA. While antioxidants and iron chelators have shown promise in ameliorating the symptoms of the disease, there is no effective therapy for FRDA that addresses the cause of the disease, the loss of frataxin protein. Gene therapy and protein replacement strategies for FRDA are promising approaches; however, current technology is not sufficiently advanced to envisage treatments for FRDA coming from these approaches in the near future. Since the FXN mutation in FRDA, expanded GAA.TTC triplets in an intron, does not alter the amino acid sequence of frataxin protein, gene reactivation would be of therapeutic benefit. Thus, a number of laboratories have focused on small molecule activators of FXN gene expression as potential therapeutics, and this review summarizes the current status of these efforts, as well as the molecular basis for gene silencing in FRDA.
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Affiliation(s)
- Joel M Gottesfeld
- Department of Molecular Biology, MB-27, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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27
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Abstract
A protein-DNA dimerizer constructed from a DNA-binding pyrrole-imidazole polyamide and the peptide FYPWMK facilitates binding of the natural transcription factor Exd to an adjacent DNA site. Previous dimerizers have been constructed with the peptide attached to an internal pyrrole monomer in an overall branched oligomer. Linear oligomers constructed by attaching the peptide to the polyamide C-terminus expand the range of protein-DNA dimerization to six additional DNA sites. Replacing the FYPWMK hexapeptide with a WM dipeptide, which was previously functional in branched compounds, does not lead to a functional linear dimerizer. Instead, inserting an additional lysine generates a minimal, linear WMK tripeptide conjugate that maintains the activity of the larger FYPWMK dimerizers in a single DNA-binding site orientation. These studies provide insight into the importance of linker length and composition, binding site spacing and orientation, and the protein-binding domain content that are important for the optimization of protein-DNA dimerizers suitable for biological experiments.
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Affiliation(s)
- Ryan L Stafford
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
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28
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Liu X, Wu B, Szary J, Kofoed EM, Schaufele F. Functional sequestration of transcription factor activity by repetitive DNA. J Biol Chem 2007; 282:20868-76. [PMID: 17526489 PMCID: PMC3812952 DOI: 10.1074/jbc.m702547200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Higher eukaryote genomes contain repetitive DNAs, often concentrated in transcriptionally inactive heterochromatin. Although repetitive DNAs are not typically considered as regulatory elements that directly affect transcription, they can contain binding sites for some transcription factors. Here, we demonstrate that binding of the transcription factor CCAAT/enhancer-binding protein alpha (C/EBPalpha) to the mouse major alpha-satellite repetitive DNA sequesters C/EBPalpha in the transcriptionally inert pericentromeric heterochromatin. We find that this sequestration reduces the transcriptional capacity of C/EBPalpha. Functional sequestration of C/EBPalpha was demonstrated by experimentally reducing C/EBPalpha binding to the major alpha-satellite DNA, which elevated the concentration of C/EBPalpha in the non-heterochromatic subcompartment of the cell nucleus. The reduction in C/EBPalpha binding to alpha-satellite DNA was induced by the co-expression of the transcription factor Pit-1, which removes C/EBPalpha from the heterochromatic compartment, and by the introduction of an altered-specificity mutation into C/EBPalpha that reduces binding to alpha-satellite DNA but permits normal binding to sites in some gene promoters. In both cases the loss of alpha-satellite DNA binding coincided with an elevation in the binding of C/EBPalpha to a promoter and an increased transcriptional output from that promoter. Thus, the binding of C/EBPalpha to this highly repetitive DNA reduced the amount of C/EBPalpha available for binding to and regulation of this promoter. The functional sequestration of some transcription factors through binding to repetitive DNAs may represent an underappreciated mechanism controlling transcription output.
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Affiliation(s)
- Xiaowei Liu
- Diabetes Center and Department of Medicine, University of California San Francisco, San Francisco, California 94143
| | - Bo Wu
- Diabetes Center and Department of Medicine, University of California San Francisco, San Francisco, California 94143
| | - Jaroslaw Szary
- Diabetes Center and Department of Medicine, University of California San Francisco, San Francisco, California 94143
| | - Eric M. Kofoed
- Diabetes Center and Department of Medicine, University of California San Francisco, San Francisco, California 94143
| | - Fred Schaufele
- Diabetes Center and Department of Medicine, University of California San Francisco, San Francisco, California 94143
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29
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Stafford RL, Arndt HD, Brezinski ML, Ansari AZ, Dervan PB. Minimization of a protein-DNA dimerizer. J Am Chem Soc 2007; 129:2660-8. [PMID: 17290996 PMCID: PMC3064071 DOI: 10.1021/ja067971k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A protein-DNA dimerizer constructed from a DNA-binding polyamide and the peptide FYPWMKG facilitates the binding of a natural transcription factor Exd to an adjacent DNA site. The Exd binding domain can be reduced to a dipeptide WM attached to the polyamide through an epsilon-aminohexanoic acid linker with retention of protein-DNA dimerizer activity. Screening a library of analogues indicated that the tryptophan indole moiety is more important than methionine's side chain or the N-terminal acetamide. Remarkably, switching the stereochemistry of the tryptophan residue (l to d) stabilizes the dimerizer*Exd*DNA ternary complex at 37 degrees C. These observations provide design principles for artificial transcription factors that may function in concert with the cellular regulatory circuitry.
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30
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Ghosh I, Stains CI, Ooi AT, Segal DJ. Direct detection of double-stranded DNA: Molecular methods and applications for DNA diagnostics. MOLECULAR BIOSYSTEMS 2006; 2:551-60. [PMID: 17216036 DOI: 10.1039/b611169f] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methodologies to detect DNA sequences with high sensitivity and specificity have tremendous potential as molecular diagnostic agents. Most current methods exploit the ability of single-stranded DNA (ssDNA) to base pair with high specificity to a complementary molecule. However, recent advances in robust techniques for recognition of DNA in the major and minor groove have made possible the direct detection of double-stranded DNA (dsDNA), without the need for denaturation, renaturation, or hybridization. This review will describe the progress in adapting polyamides, triplex DNA, and engineered zinc finger DNA-binding proteins as dsDNA diagnostic systems. In particular, the sequence-enabled reassembly (SEER) method, involving the use of custom zinc finger proteins, offers the potential for direct detection of dsDNA in cells, with implications for cell-based diagnostics and therapeutics.
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Affiliation(s)
- Indraneel Ghosh
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA.
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Burnett R, Melander C, Puckett JW, Son LS, Wells RD, Dervan PB, Gottesfeld JM. DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA.TTC repeats in Friedreich's ataxia. Proc Natl Acad Sci U S A 2006; 103:11497-502. [PMID: 16857735 PMCID: PMC1544198 DOI: 10.1073/pnas.0604939103] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The DNA abnormality found in 98% of Friedreich's ataxia (FRDA) patients is the unstable hyperexpansion of a GAA.TTC triplet repeat in the first intron of the frataxin gene. Expanded GAA.TTC repeats result in decreased transcription and reduced levels of frataxin protein in affected individuals. Beta-alanine-linked pyrrole-imidazole polyamides bind GAA.TTC tracts with high affinity and disrupt the intramolecular DNA.DNA-associated region of the sticky-DNA conformation formed by long GAA.TTC repeats. Fluorescent polyamide-Bodipy conjugates localize in the nucleus of a lymphoid cell line derived from a FRDA patient. The synthetic ligands increase transcription of the frataxin gene in cell culture, resulting in increased levels of frataxin protein. DNA microarray analyses indicate that a limited number of genes are significantly affected in FRDA cells. Polyamides may increase transcription by altering the DNA conformation of genes harboring long GAA.TTC repeats or by chromatin opening.
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Affiliation(s)
- Ryan Burnett
- *Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Christian Melander
- *Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - James W. Puckett
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
| | - Leslie S. Son
- Center for Genome Research, Institute for Biosciences and Technology, Texas A&M University System Health Science Center, 2121 West Holcombe Boulevard, Houston, TX 77030
| | - Robert D. Wells
- Center for Genome Research, Institute for Biosciences and Technology, Texas A&M University System Health Science Center, 2121 West Holcombe Boulevard, Houston, TX 77030
| | - Peter B. Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
| | - Joel M. Gottesfeld
- *Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
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32
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Liu Y, Deng Y, Zheng R, Zhang P, Zhai H, Zhu C. Synthesis and cellular effect of a novel conjugate of polyamide and phospholipid. Chem Pharm Bull (Tokyo) 2006; 54:832-5. [PMID: 16755053 DOI: 10.1248/cpb.54.832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In order to improve the cell penetration of polyamide and its movement toward nucleic DNA we synthesized a conjugate of polyamide and phospholipid, which showed a significantly reduced cytotoxicity and effective apoptosis when comparing with the native polyamide.
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Affiliation(s)
- Yi Liu
- Department of Applied Chemistry, Beijing Institute of Technology, 100081 Beijing, China
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33
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Blattes R, Monod C, Susbielle G, Cuvier O, Wu JH, Hsieh TS, Laemmli UK, Käs E. Displacement of D1, HP1 and topoisomerase II from satellite heterochromatin by a specific polyamide. EMBO J 2006; 25:2397-408. [PMID: 16675949 PMCID: PMC1478169 DOI: 10.1038/sj.emboj.7601125] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Accepted: 04/11/2006] [Indexed: 11/09/2022] Open
Abstract
The functions of DNA satellites of centric heterochromatin are difficult to assess with classical molecular biology tools. Using a chemical approach, we demonstrate that synthetic polyamides that specifically target AT-rich satellite repeats of Drosophila melanogaster can be used to study the function of these sequences. The P9 polyamide, which binds the X-chromosome 1.688 g/cm3 satellite III (SAT III), displaces the D1 protein. This displacement in turn results in a selective loss of HP1 and topoisomerase II from SAT III, while these proteins remain bound to the adjacent rDNA repeats and to other regions not targeted by P9. Conversely, targeting of (AAGAG)n satellite V repeats by the P31 polyamide results in the displacement of HP1 from these sequences, indicating that HP1 interactions with chromatin are sensitive to DNA-binding ligands. P9 fed to larvae suppresses the position-effect variegation phenotype of white-mottled adult flies. We propose that this effect is due to displacement of the heterochromatin proteins D1, HP1 and topoisomerase II from SAT III, hence resulting in stochastic chromatin opening and desilencing of the nearby white gene.
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Affiliation(s)
- Roxane Blattes
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099 CNRS-Université Paul Sabatier, Toulouse Cedex, France
| | - Caroline Monod
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099 CNRS-Université Paul Sabatier, Toulouse Cedex, France
| | - Guillaume Susbielle
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099 CNRS-Université Paul Sabatier, Toulouse Cedex, France
| | - Olivier Cuvier
- Institut de Génétique Humaine, CNRS UPR 1142, Montpellier Cedex, France
| | - Jian-hong Wu
- Department of Biochemistry, Nanaline H Duke Building, Duke University Medical Center, Durham, NC, USA
| | - Tao-shih Hsieh
- Department of Biochemistry, Nanaline H Duke Building, Duke University Medical Center, Durham, NC, USA
| | - Ulrich K Laemmli
- Département de Biologie Moléculaire, Université de Genève, Sciences II, Geneva, Switzerland
| | - Emmanuel Käs
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099 CNRS-Université Paul Sabatier, Toulouse Cedex, France
- LBME, UMR5099, IBCG, 118 route de Narbonne, 31062 Toulouse Cedex 9, France. Tel.: +33 561 335959; Fax: +33 561 335886; E-mail:
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34
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Belikov SV, Grokhovsky SL, Isaguliants MG, Surovaya AN, Gursky GV. Sequence-Specific Minor Groove Binding Ligands as Potential Regulators of Gene Expression in Xenopus Laevis Oocytes. J Biomol Struct Dyn 2005; 23:193-202. [PMID: 16060693 DOI: 10.1080/07391102.2005.10507059] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The mouse mammary tumor virus (MMTV) promoter is induced by glucocorticoid hormone. A robust hormone- and receptor-dependent gene activation could be reproduced in Xenopus laevis oocytes. The homogeneous response in this system allowed a detailed analysis of the DNA-protein interactions following hormone activation. The strategy of artificial regulating of gene activity by sequence-specific minor groove binding ligands is very attractive. We have synthesized and studied the interaction with DNA of bis-linked netropsin derivatives in which two monomers are attached via short linkers in head-to-head and tail-to-tail manners. We have found that cis-diammine-platinum bridged bis-netropsin added to Xenopus oocytes media penetrates cellular and nuclear membrane and binds selectively to the MMTV promoter at the DNA segment that partly overlaps with the site recognized by glucocorticoid receptor. DNase I footprinting studies demonstrate that there are more stronger binding sites for cis-diammine-platinum bridged bis-netropsin on the naked MMTV DNA which are found to be inaccessible for its binding in oocytes.
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Affiliation(s)
- S V Belikov
- Department of Cell and Molecular Biology, The Medical Nobel Institute, Karolinska Institute, SE 17177, Stockholm, Sweden
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35
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Vinson C. A rationally designed small molecule that inhibits the HIF-1alpha-ARNT heterodimer from binding to DNA in vivo. Sci Signal 2005; 2005:pe23. [PMID: 15900031 DOI: 10.1126/stke.2842005pe23] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Modern drug development is focused on two steps: the identification of new molecular targets and the development of drugs that affect these targets. A molecular target can be an enzymatic activity or a macromolecular interface that is important in a disease pathway. Current drugs on the market are biased toward targeting cell surface receptors and intracellular enzymatic activities. However, macromolecular interfaces can also serve as potential molecular targets. A recent paper from Kaelin and Dervan's groups examined an underused molecular target-transcription factor DNA binding. To specifically disrupt transcriptional activation, they used a rationally designed small molecule that binds specifically in the minor groove of a DNA sequence that in vivo is bound by a bHLH heterodimer transcription factor.
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Affiliation(s)
- Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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36
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Dickinson LA, Burnett R, Melander C, Edelson BS, Arora PS, Dervan PB, Gottesfeld JM. Arresting Cancer Proliferation by Small-Molecule Gene Regulation. ACTA ACUST UNITED AC 2004; 11:1583-94. [PMID: 15556009 DOI: 10.1016/j.chembiol.2004.09.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2004] [Revised: 09/03/2004] [Accepted: 09/09/2004] [Indexed: 12/31/2022]
Abstract
A small library of pyrrole-imidazole polyamide-DNA alkylator (chlorambucil) conjugates was screened for effects on morphology and growth characteristics of a human colon carcinoma cell line, and a compound was identified that causes cells to arrest in the G2/M stage of the cell cycle. Microarray analysis indicates that the histone H4c gene is significantly downregulated by this polyamide. RT-PCR and Western blotting experiments confirm this result, and siRNA to H4c mRNA yields the same cellular response. Strikingly, reduction of H4 protein by >50% does not lead to widespread changes in global gene expression. Sequence-specific alkylation within the coding region of the H4c gene in cell culture was confirmed by LM-PCR. The compound is active in a wide range of cancer cell lines, and treated cells do not form tumors in nude mice. The compound is also active in vivo, blocking tumor growth in mice, without obvious animal toxicity.
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Affiliation(s)
- Liliane A Dickinson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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37
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Melander C, Burnett R, Gottesfeld JM. Regulation of gene expression with pyrrole–imidazole polyamides. J Biotechnol 2004; 112:195-220. [PMID: 15288953 DOI: 10.1016/j.jbiotec.2004.03.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Revised: 02/23/2004] [Accepted: 03/19/2004] [Indexed: 10/26/2022]
Abstract
The pyrrole-imidazole (Py-Im) polyamides represent the only available class of small molecules that can be designed to recognize virtually any predetermined DNA sequence. These molecules have affinities and specificities that equal or exceed natural eukaryotic transcriptional regulatory proteins. Studies with model gene systems, and a variety of eukaryotic and viral transcription factors, have shown that these molecules are potent inhibitors of protein-DNA interactions. Polyamides have been shown to regulate gene expression in simple in vitro systems using defined DNA templates and nuclear extracts as a source of the transcriptional machinery. Activation of gene expression has also been achieved in vitro with polyamide-activator peptide conjugates. Most importantly, polyamides are cell permeable and localize in the nucleus in various cultured cell lines and are capable of down regulating target genes in these cells. Polyamides have been shown to bind to their target sites in chromosomal DNA and both gain- and loss-of-function have been observed by targeting repeated DNA sequences in developing Drosophila embryos.
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Affiliation(s)
- Christian Melander
- Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
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38
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Dudouet B, Burnett R, Dickinson LA, Wood MR, Melander C, Belitsky JM, Edelson B, Wurtz N, Briehn C, Dervan PB, Gottesfeld JM. Accessibility of nuclear chromatin by DNA binding polyamides. ACTA ACUST UNITED AC 2004; 10:859-67. [PMID: 14522056 DOI: 10.1016/j.chembiol.2003.09.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Pyrrole-imidazole polyamides bind DNA with affinities comparable to those of transcriptional regulatory proteins and inhibit the DNA binding activities of components of the transcription apparatus. If polyamides are to be useful for the regulation of gene expression in cell culture experiments, one pivotal issue is accessibility of specific sites in nuclear chromatin. We first determined the kinetics of uptake and subcellular distribution of polyamides in lymphoid and myeloid cells using fluorescent polyamide-bodipy conjugates and deconvolution microscopy. Then cells were incubated with a polyamide-chlorambucil conjugate, and the sites of specific DNA cleavage in the nuclear chromatin were assayed by ligation-mediated PCR. In addition, DNA microarray analysis revealed that two different polyamides generated distinct transcription profiles. Remarkably, the polyamides affected only a limited number of genes.
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Affiliation(s)
- Brigitte Dudouet
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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39
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Anthony NG, Fox KR, Johnston BF, Khalaf AI, Mackay SP, McGroarty IS, Parkinson JA, Skellern GG, Suckling CJ, Waigh RD. DNA binding of a short lexitropsin. Bioorg Med Chem Lett 2004; 14:1353-6. [PMID: 14980697 DOI: 10.1016/j.bmcl.2003.11.068] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2003] [Revised: 11/12/2003] [Accepted: 11/18/2003] [Indexed: 11/24/2022]
Abstract
Footprinting, capillary electrophoresis, molecular modelling and NMR studies have been used to examine the binding of a short polyamide to DNA. This molecule, which contains an isopropyl-substituted thiazole in place of one of the N-methylpyrroles, is selective for the sequence 5'-ACTAGT-3' to which it binds with high affinity. Two molecules bind side-by-side in the minor groove, but their binding is staggered so that the molecule reads six base pairs, unlike the related natural products, which tend to bind to four-base-pair sequences. The result suggests that high affinity and selectivity may be gained without resort to very large molecules, which may be difficult to deliver to the site of action.
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Affiliation(s)
- Nahoum G Anthony
- Department of Physiology and Pharmacology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO9 3TU, UK
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40
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Abstract
Chemical substances that can recognize and bind DNA in a sequence-specific manner have enormous importance in modern biology and medicine. When covalently linked, hairpin polyamides made up of N-methylpyrrole (Py) and N-methylimidazole (Im) can bind to DNA in a sequence-specific manner. An Im opposite a Py recognizes and binds G:C from C:G, whereas a Py opposite an Im recognizes and binds to C:G. A Py-Py pair degenerately binds to T:A or A:T, whereas a hydroxypyrrole opposite a Py recognizes and binds to T:A from A:T, and vice versa. A variant in this recognition is the beta-alanine (beta-ala-beta-ala) pair, which also degenerately binds to A:T or T:A. The hairpin polyamides are cell permeable and bind to DNA at nanomolar concentrations, with binding coefficients similar to those of transcription factors. This review comprehensively discusses the current literature on using the sequence-specific recognition ability of the polyamides to study various DNA-protein interactions.
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Affiliation(s)
- Musti Sree Rama Chandra Murty
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Surugadai, Kanda, Chiyoda-ku, Tokyo 101-0062, Japan
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41
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Best TP, Edelson BS, Nickols NG, Dervan PB. Nuclear localization of pyrrole-imidazole polyamide-fluorescein conjugates in cell culture. Proc Natl Acad Sci U S A 2003; 100:12063-8. [PMID: 14519850 PMCID: PMC218713 DOI: 10.1073/pnas.2035074100] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A series of hairpin pyrrole-imidazole polyamide-fluorescein conjugates were synthesized and assayed for cellular localization. Thirteen cell lines, representing 11 human cancers, one human transformed kidney cell line, and one murine leukemia cell line, were treated with 5 microM polyamide-fluorescein conjugates for 10-14 h, then imaged by confocal laser scanning microscopy. A conjugate containing a beta-alanine residue at the C terminus of the polyamide moiety showed no nuclear localization, whereas an analogous compound lacking the beta-alanine residue was strongly localized in the nuclei of all cell lines tested. The localization profiles of several other conjugates suggest that pyrrole-imidazole sequence and content, dye choice and position, linker composition, and molecular weight are determinants of nuclear localization. The attachment of fluorescein to the C terminus of a hairpin polyamide results in an approximately 10-fold reduction in DNA-binding affinity, with no loss of binding specificity with reference to mismatch binding sites.
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Affiliation(s)
- Timothy P Best
- Division of Chemistry and Chemical Engineering and The Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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42
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Briehn CA, Weyermann P, Dervan PB. Alternative heterocycles for DNA recognition: the benzimidazole/imidazole pair. Chemistry 2003; 9:2110-22. [PMID: 12740860 DOI: 10.1002/chem.200204689] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Boc-protected benzimidazole-pyrrole, benzimidazole-imidazole, and benzimidazole-methoxypyrrole amino acids were synthesized and incorporated into DNA binding polyamides, comprised of N-methyl pyrrole and N-methyl imidazole amino acids, by means of solid-phase synthesis on an oxime resin. These hairpin polyamides were designed to determine the DNA recognition profile of a side-by-side benzimidazole/imidazole pair for the designated six base pair recognition sequence. Equilibrium association constants of the polyamide-DNA complexes were determined at two of the six base pair positions of the recognition sequence by quantitative DNase I footprinting titrations on DNA fragments each containing matched and single base pair mismatched binding sites. The results indicate that the benzimidazole-heterocycle building blocks can replace pyrrole-pyrrole, pyrrole-imidazole, and pyrrole-hydroxypyrrole constructs while retaining relative site specifities and subnanomolar match site affinities. The benzimidazole-containing hairpin polyamides represent a novel class of DNA binding ligands featuring tunable target recognition sequences combined with the favorable properties of the benzimidazole type DNA minor groove binders.
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Affiliation(s)
- Christoph A Briehn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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43
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Crowley KS, Phillion DP, Woodard SS, Schweitzer BA, Singh M, Shabany H, Burnette B, Hippenmeyer P, Heitmeier M, Bashkin JK. Controlling the intracellular localization of fluorescent polyamide analogues in cultured cells. Bioorg Med Chem Lett 2003; 13:1565-70. [PMID: 12699756 DOI: 10.1016/s0960-894x(03)00152-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The intracellular distribution of fluorescent-labeled polyamides was examined in live cells. We showed that BODIPY-labeled polyamides accumulate in acidic vesicles, mainly lysosomes, in the cytoplasm of HCT116 colon cancer cells and human rheumatoid synovial fibroblasts (RSF). Verapamil blocked vesicular accumulation and led to nuclear accumulation of the BODIPY-labeled polyamide in RSFs. We infer that the basic amine group commonly found at the end of synthetic polyamide chains is responsible for their accumulation in cytoplasmic vesicles in mammalian cells. Modifying the charge on a polyamide by replacing the BODIPY moiety with a fluorescein moiety on the amine tail allowed the polyamide to localize in the nucleus of the cell and bypass the cytoplasmic vesicles in HCT116 cells.
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Affiliation(s)
- Kathleen S Crowley
- Pharmacia Corporation, 700 Chesterfield Parkway North, Chesterfield, MO 63198, USA.
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44
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Schaal TD, Holmes MC, Rebar EJ, Case CC. Novel approaches to controlling transcription. GENETIC ENGINEERING 2003; 24:137-78. [PMID: 12416304 DOI: 10.1007/978-1-4615-0721-5_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Thomas D Schaal
- Sangamo Biosciences, Inc., 501 Canal Boulevard, Richmond, CA 94804, USA
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45
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Schaal TD, Mallet WG, McMinn DL, Nguyen NV, Sopko MM, John S, Parekh BS. Inhibition of human papilloma virus E2 DNA binding protein by covalently linked polyamides. Nucleic Acids Res 2003; 31:1282-91. [PMID: 12582248 PMCID: PMC150225 DOI: 10.1093/nar/gkg206] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2002] [Revised: 12/03/2002] [Accepted: 12/03/2002] [Indexed: 11/13/2022] Open
Abstract
Polyamides are a class of heterocyclic small molecules with the potential of controlling gene expression by binding to the minor groove of DNA in a sequence-specific manner. To evaluate the feasibility of this class of compounds as antiviral therapeutics, molecules were designed to essential sequence elements occurring numerous times in the HPV genome. This sequence element is bound by a virus-encoded transcription and replication factor E2, which binds to a 12 bp recognition site as a homodimeric protein. Here, we take advantage of polyamide:DNA and E2:DNA co-crystal structural information and advances in polyamide synthetic chemistry to design tandem hairpin polyamides that are capable of displacing the major groove-binding E2 homodimer from its DNA binding site. The binding of tandem hairpin polyamides and the E2 DNA binding protein to the DNA site is mutually exclusive even though the two ligands occupy opposite faces of the DNA double helix. We show with circular permutation studies that the tandem hairpin polyamide prevents the intrinsic bending of the E2 DNA site important for binding of the protein. Taken together, these results illustrate the feasibility of inhibiting the binding of homodimeric, major groove-binding transcription factors by altering the local DNA geometry using minor groove-binding tandem hairpin polyamides.
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Affiliation(s)
- Thomas D Schaal
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, Building 41, Room B307, NCI, NIH, Bethesda, MD 20892-5055, USA
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46
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Shaffer CD, Stephens GE, Thompson BA, Funches L, Bernat JA, Craig CA, Elgin SCR. Heterochromatin protein 2 (HP2), a partner of HP1 in Drosophila heterochromatin. Proc Natl Acad Sci U S A 2002; 99:14332-7. [PMID: 12376620 PMCID: PMC137884 DOI: 10.1073/pnas.212458899] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2002] [Indexed: 11/18/2022] Open
Abstract
Heterochromatin protein 1 (HP1), first discovered in Drosophila melanogaster, is a highly conserved chromosomal protein implicated in both heterochromatin formation and gene silencing. We report here characterization of an HP1-interacting protein, heterochromatin protein 2 (HP2), which codistributes with HP1 in the pericentric heterochromatin. HP2 is a large protein with two major isoforms of approximately 356 and 176 kDa. The smaller isoform is produced from an alternative splicing pattern in which two exons are skipped. Both isoforms contain the domain that interacts with HP1; the larger isoform contains two AT-hook motifs. Mutations recovered in HP2 act as dominant suppressors of position effect variegation, confirming a role in heterochromatin spreading and gene silencing.
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47
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Krutzik PO, Chamberlin AR. Rapid solid-phase synthesis of DNA-binding pyrrole-imidazole polyamides. Bioorg Med Chem Lett 2002; 12:2129-32. [PMID: 12127520 DOI: 10.1016/s0960-894x(02)00359-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Pyrrole-imidazole polyamides can be synthesized to target predetermined sequences of DNA with nanomolar affinity and high specificity, and have been shown to modulate gene transcription both in vitro and in vivo. To make polyamides more readily available to biological laboratories, we have developed a rapid solid-phase synthesis based on azabenzotriazole (OAt) activation that decreases synthesis time 60% compared to standard benzotriazole (OBt) techniques, without loss of yield or purity.
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Affiliation(s)
- Peter O Krutzik
- Department of Chemistry, University of California-Irvine, CA 92697, Irvine, USA
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48
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Monod C, Aulner N, Cuvier O, Käs E. Modification of position-effect variegation by competition for binding to Drosophila satellites. EMBO Rep 2002; 3:747-52. [PMID: 12151333 PMCID: PMC1084209 DOI: 10.1093/embo-reports/kvf155] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2002] [Revised: 06/11/2002] [Accepted: 06/17/2002] [Indexed: 11/14/2022] Open
Abstract
White-mottled (w(m4)) position-effect variegation (PEV) arises by translocation of the white gene near the pericentric AT-rich 1.688 g/cm3 satellite III (SATIII) repeats of the X chromosome of Drosophila. The natural and artificial A*T-hook proteins D1 and MATH20 modify w(m4) PEV in opposite ways. D1 binds SATIII repeats and enhances PEV, presumably via a recruitment of protein partners, whereas MATH20 suppresses it. We show that D1 and MATH20 compete for binding to identical sites of SATIII repeats in vitro and that conditional MATH20 expression results in a displacement of D1 from pericentric heterochromatin in vivo. In the presence of intermediate levels of MATH20, we show that this displacement becomes selective for SATIII repeats. These results strongly suggest that the suppression of w(m4) PEV by MATH20 is due to a displacement of D1 from its preferred binding sites and provide additional support for a direct role of D1 in the assembly of AT-rich heterochromatin.
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Affiliation(s)
- Caroline Monod
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS UMR 5099, Toulouse, France
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49
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Urbach AR, Love JJ, Ross SA, Dervan PB. Structure of a beta-alanine-linked polyamide bound to a full helical turn of purine tract DNA in the 1:1 motif. J Mol Biol 2002; 320:55-71. [PMID: 12079334 DOI: 10.1016/s0022-2836(02)00430-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Polyamides composed of N-methylpyrrole (Py), N-methylimidazole (Im) and N-methylhydroxypyrrole (Hp) amino acids linked by beta-alanine (beta) bind the minor groove of DNA in 1:1 and 2:1 ligand to DNA stoichiometries. Although the energetics and structure of the 2:1 complex has been explored extensively, there is remarkably less understood about 1:1 recognition beyond the initial studies on netropsin and distamycin. We present here the 1:1 solution structure of ImPy-beta-Im-beta-ImPy-beta-Dp bound in a single orientation to its match site within the DNA duplex 5'-CCAAAGAGAAGCG-3'.5'-CGCTTCTCTTTGG-3' (match site in bold), as determined by 2D (1)H NMR methods. The representative ensemble of 12 conformers has no distance constraint violations greater than 0.13 A and a pairwise RMSD over the binding site of 0.80 A. Intermolecular NOEs place the polyamide deep inside the minor groove, and oriented N-C with the 3'-5' direction of the purine-rich strand. Analysis of the high-resolution structure reveals the ligand bound 1:1 completely within the minor groove for a full turn of the DNA helix. The DNA is B-form (average rise=3.3 A, twist=38 degrees ) with a narrow minor groove closing down to 3.0-4.5 A in the binding site. The ligand and DNA are aligned in register, with each polyamide NH group forming bifurcated hydrogen bonds of similar length to purine N3 and pyrimidine O2 atoms on the floor of the minor groove. Each imidazole group is hydrogen bonded via its N3 atom to its proximal guanine's exocyclic amino group. The important roles of beta-alanine and imidazole for 1:1 binding are discussed.
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Affiliation(s)
- Adam R Urbach
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Ehley JA, Melander C, Herman D, Baird EE, Ferguson HA, Goodrich JA, Dervan PB, Gottesfeld JM. Promoter scanning for transcription inhibition with DNA-binding polyamides. Mol Cell Biol 2002; 22:1723-33. [PMID: 11865052 PMCID: PMC135605 DOI: 10.1128/mcb.22.6.1723-1733.2002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
When targeted to sequences adjacent to a TATA element, pyrrole-imidazole (Py-Im) polyamides inhibit the DNA binding activity of TATA box binding protein (TBP) and basal transcription by RNA polymerase II. In the present study, we scanned the human immunodeficiency virus type 1 promoter for polyamide inhibition of TBP binding and transcription using a series of DNA constructs in which a polyamide binding site was placed at various distances from the TATA box. Polyamide interference with either TBP-DNA or TFIID-TFIIA-DNA contacts both upstream and downstream of the TATA element resulted in inhibition of transcription. Our results define important protein-DNA interactions outside of the TATA element and suggest that transcription inhibition of selected gene promoters can be achieved with polyamides that target unique sequences within these promoters at a distance from the TATA element. Our studies also demonstrate the utility of the Py-Im polyamides for discovery of functionally important protein-DNA contacts involved in transcription.
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Affiliation(s)
- Jennifer A Ehley
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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