1
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Price AK, Paegel BM. Considerations for Achieving Maximized DNA Recovery in Solid-Phase DNA-Encoded Library Synthesis. ACS COMBINATORIAL SCIENCE 2020; 22:649-655. [PMID: 32786319 DOI: 10.1021/acscombsci.0c00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-encoded library (DEL) technology enables rapid, economical synthesis, and exploration of novel chemical space. Reaction development for DEL synthesis has recently accelerated in pace with a specific emphasis on ensuring that the reaction does not compromise the integrity of the encoding DNA. However, the factors that contribute to a reaction's "DNA compatibility" remain relatively unknown. We investigated several solid-phase reactions and encoding conditions and determined their impact on DNA compatibility. Conditions that minimized the accessibility of reactive groups on the DNA encoding tag (switching solvent, low temperature, double-stranded encoding tag) significantly improved compatibility. We showcased this approach in the multistep synthesis of an acyldepsipeptide (ADEP1) fragment, which preserved 73% of DNA for a >100-fold improvement over canonical conditions. These results are particularly encouraging in the context of multistep reaction sequences to access natural product-like scaffolds and more broadly underscore the importance of reconciling the biophysical properties and reactivity of DNA with chemistry development to yield high-quality libraries of those scaffolds.
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Affiliation(s)
- Alexander K. Price
- Department of Chemistry Scripps Research 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department of Chemistry Scripps Research 130 Scripps Way, Jupiter, Florida 33458, United States
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2
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Ratnayake AS, Flanagan ME, Foley TL, Smith JD, Johnson JG, Bellenger J, Montgomery JI, Paegel BM. A Solution Phase Platform to Characterize Chemical Reaction Compatibility with DNA-Encoded Chemical Library Synthesis. ACS COMBINATORIAL SCIENCE 2019; 21:650-655. [PMID: 31425646 PMCID: PMC6938256 DOI: 10.1021/acscombsci.9b00113] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA-encoded chemical library (DECL) synthesis must occur in aqueous media under conditions that preserve the integrity of the DNA encoding tag. While the identification of "DNA-compatible" reaction conditions is critical for the development of DECL designs that explore previously inaccessible chemical space, reports measuring such compatibility have been largely restricted to methods that do not faithfully capture the impact of reaction conditions on DNA fidelity in solution phase. Here we report a comprehensive methodology that uses soluble DNA substrates that exactly recapitulate DNA's exposure to the chemically reactive species of DECL synthesis. This approach includes the assessment of chemical fidelity (reaction yield and purity), encoding fidelity (ligation efficiency), and readability (DNA compatibility), revealing the fate of the DNA tag during DECL chemistry from a single platform.
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Affiliation(s)
- Anokha S. Ratnayake
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Mark E. Flanagan
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Timothy L. Foley
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Justin D. Smith
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Jillian G. Johnson
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Justin Bellenger
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Justin I. Montgomery
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Brian M. Paegel
- Department of Chemistry, The Scripps Research Institute 130 Scripps Way Jupiter, Florida 33458, United States
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3
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Thomas EM, Testa SM. The colorimetric determination of selectively cleaved adenosines and guanosines in DNA oligomers using bicinchoninic acid and copper. J Biol Inorg Chem 2016; 22:31-46. [PMID: 27807667 DOI: 10.1007/s00775-016-1405-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/14/2016] [Indexed: 10/20/2022]
Abstract
Colorimetric methods combined with color-changing chemical probes are widely used as simple yet effective tools for identifying and quantifying a wide variety of molecules in solution. For nucleic acids (DNA and RNA), perhaps the most commonly used colorimetric probe is potassium permanganate, which can be used to identify single-stranded pyrimidines (thymine and cytosine) in polymers. Unfortunately, permanganate is not an effective probe for identifying purines (adenine and guanine), especially in the presence of the more reactive pyrimidines. Therefore, robust methods for discriminating between the purines remain elusive, thereby creating a barrier toward developing more complex colorimetric applications. In this proof-of-principle study, we demonstrate that bicinchoninic acid (BCA) and copper, when combined with purine-specific chemical cleavage reactions, can be a colorimetric probe for the identification and quantification of adenosines and/or guanosines in single-stranded DNA oligomers, even in the presence of pyrimidines. Furthermore, the reactions are stoichiometric, which allows for the quantification of the number of adenosines and/or guanosines in these oligomers. Because the BCA/copper reagent detects the reducing sugar, 2-deoxyribose, that results from the chemical cleavage of a given nucleotide's N-glycosidic bond, these colorimetric assays are effectively detecting apurinic sites in DNA oligomers, which are known to occur via DNA damage in biological systems. We demonstrate that simple digital analysis of the color-changing chromophore (BCA/copper) is all that is necessary to obtain quantifiable and reproducible data, which indicates that these assays should be broadly accessible.
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Affiliation(s)
- Elizabeth M Thomas
- Department of Chemistry, University of Kentucky, 550 Rose Street, Lexington, KY, 40506, USA
| | - Stephen M Testa
- Department of Chemistry, University of Kentucky, 550 Rose Street, Lexington, KY, 40506, USA.
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4
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Drouin R, Bastien N, Millau JF, Vigneault F, Paradis I. In Cellulo DNA Analysis: LMPCR Footprinting. Methods Mol Biol 2016; 1334:41-84. [PMID: 26404143 DOI: 10.1007/978-1-4939-2877-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The in cellulo analysis of protein-DNA interactions and chromatin structure is very important to better understand the mechanisms involved in the regulation of gene expression. The nuclease-hypersensitive sites and sequences bound by transcription factors often correspond to genetic regulatory elements. Using the ligation-mediated polymerase chain reaction (LMPCR) technology, it is possible to precisely analyze these DNA sequences to demonstrate the existence of DNA-protein interactions or unusual DNA structures directly in living cells. Indeed, the ideal chromatin substrate is, of course, found inside intact cells. LMPCR, a genomic sequencing technique that map DNA single-strand breaks at the sequence level of resolution, is the method of choice for in cellulo footprinting and DNA structure studies because it can be used to investigate complex animal genomes, including human. The detailed conventional and automated LMPCR protocols are presented in this chapter.
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Affiliation(s)
- Régen Drouin
- Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada. .,Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001 12th Avenue North, Sherbrooke, QC, Canada, J1H 5N4.
| | - Nathalie Bastien
- Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-François Millau
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | - Isabelle Paradis
- Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
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5
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Abstract
DNA-encoded synthesis can generate vastly diverse screening libraries of arbitrarily complex molecules as long as chemical reaction conditions do not compromise DNA's informational integrity, a fundamental constraint that "DNA-compatible" reaction development does not presently address. We devised DNA-encoded reaction rehearsal, an integrated analysis of reaction yield and impact on DNA, to acquire these key missing data. Magnetic DNA-functionalized sensor beads quantitatively report the % DNA template molecules remaining viable for PCR amplification after exposure to test reaction conditions. Analysis of solid-phase bond forming (e.g., Suzuki-Miyaura cross-coupling, reductive amination) and deprotection reactions (e.g., allyl esters, silyl ethers) guided the definition and optimization of DNA-compatible reaction conditions (>90% yield, >30% viable DNA molecules), most notably in cases that involved known (H(+), Pd) and more obscure (Δ, DMF) hazards to DNA integrity. The data provide an empirical yet mechanistically consistent and predictive framework for designing successful DNA-encoded reaction sequences for combinatorial library synthesis.
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Affiliation(s)
- Marie L. Malone
- Department of Chemistry and ‡Doctoral Program
in Chemical and Biological
Sciences, The Scripps Research Institute 130 Scripps Way Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department of Chemistry and ‡Doctoral Program
in Chemical and Biological
Sciences, The Scripps Research Institute 130 Scripps Way Jupiter, Florida 33458, United States
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6
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Rhoden Smith A, Iverson BL. Threading polyintercalators with extremely slow dissociation rates and extended DNA binding sites. J Am Chem Soc 2013; 135:12783-9. [PMID: 23919778 DOI: 10.1021/ja4057344] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The development of small molecules that bind DNA sequence specifically has the potential to modulate gene expression in a general way. One mode of DNA binding is intercalation, or the insertion of molecules between DNA base pairs. We have developed a modular polyintercalation system in which intercalating naphthalene diimide (NDI) units are connected by flexible linkers that alternate between the minor and major grooves of DNA when bound. We recently reported a threading tetraintercalator with a dissociation half-life of 16 days, the longest reported to date, from its preferred 14 bp binding site. Herein, three new tetraintercalator derivatives were synthesized with one, two, and three additional methylene units in the central major groove-binding linker. These molecules displayed dissociation half-lives of 57, 27, and 18 days, respectively, from the 14 bp site. The optimal major groove-binding linker was used in the design of an NDI hexaintercalator that was analyzed by gel-shift assays, DNase I footprinting, and UV-vis spectroscopy. The hexaintercalator bound its entire 22 bp binding site, the longest reported specific binding site for a synthetic, non-nucleic acid-based DNA binding molecule, but with a significantly faster dissociation rate compared to the tetraintercalators.
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Affiliation(s)
- Amy Rhoden Smith
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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7
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Cianfrocco MA, Kassavetis GA, Grob P, Fang J, Juven-Gershon T, Kadonaga JT, Nogales E. Human TFIID binds to core promoter DNA in a reorganized structural state. Cell 2013; 152:120-31. [PMID: 23332750 DOI: 10.1016/j.cell.2012.12.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 09/20/2012] [Accepted: 11/28/2012] [Indexed: 12/23/2022]
Abstract
A mechanistic description of metazoan transcription is essential for understanding the molecular processes that govern cellular decisions. To provide structural insights into the DNA recognition step of transcription initiation, we used single-particle electron microscopy (EM) to visualize human TFIID with promoter DNA. This analysis revealed that TFIID coexists in two predominant and distinct structural states that differ by a 100 Å translocation of TFIID's lobe A. The transition between these structural states is modulated by TFIIA, as the presence of TFIIA and promoter DNA facilitates the formation of a rearranged state of TFIID that enables promoter recognition and binding. DNA labeling and footprinting, together with cryo-EM studies, were used to map the locations of TATA, Initiator (Inr), motif ten element (MTE), and downstream core promoter element (DPE) promoter motifs within the TFIID-TFIIA-DNA structure. The existence of two structurally and functionally distinct forms of TFIID suggests that the different conformers may serve as specific targets for the action of regulatory factors.
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Affiliation(s)
- Michael A Cianfrocco
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
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8
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Smith AR, Ikkanda BA, Holman GG, Iverson BL. Subtle recognition of 14-base pair DNA sequences via threading polyintercalation. Biochemistry 2012; 51:4445-52. [PMID: 22554127 PMCID: PMC3369501 DOI: 10.1021/bi300317n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small molecules that bind DNA in a sequence-specific manner could act as antibiotic, antiviral, or anticancer agents because of their potential ability to manipulate gene expression. Our laboratory has developed threading polyintercalators based on 1,4,5,8-naphthalene diimide (NDI) units connected in a head-to-tail fashion by flexible peptide linkers. Previously, a threading tetraintercalator composed of alternating minor-major-minor groove-binding modules was shown to bind specifically to a 14 bp DNA sequence with a dissociation half-life of 16 days [Holman, G. G., et al. (2011) Nat. Chem. 3, 875-881]. Herein are described new NDI-based tetraintercalators with a different major groove-binding module and a reversed N to C directionality of one of the minor groove-binding modules. DNase I footprinting and kinetic analyses revealed that these new tetraintercalators are able to discriminate, by as much as 30-fold, 14 bp DNA binding sites that differ by 1 or 2 bp. Relative affinities were found to correlate strongly with dissociation rates, while overall C(2) symmetry in the DNA-binding molecule appeared to contribute to enhanced association rates.
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Affiliation(s)
- Amy Rhoden Smith
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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9
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Wang RE, Pandita RK, Cai J, Hunt CR, Taylor JS. Inhibition of heat shock transcription factor binding by a linear polyamide binding in an unusual 1:1 mode. Chembiochem 2012; 13:97-104. [PMID: 22134972 PMCID: PMC3516905 DOI: 10.1002/cbic.201100524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Indexed: 11/05/2022]
Abstract
Heat shock proteins (HSPs) are known to protect cells from heat, oxidative stress, and the cytotoxic effects of drugs, and thus can enhance cancer cell survival. As a result, HSPs are a newly emerging class of protein targets for chemotherapy. Among the various HSPs, the HSP70 family is the most highly conserved and prevalent. Herein we describe the development of a β-alanine rich linear polyamide that binds the GGA heat shock elements (HSEs) 3 and 4 in the HSP70 promoter in an unusual 1:1 mode and inhibits heat shock transcription factor 1 (HSF1) binding in vitro.
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Affiliation(s)
- Rongsheng E. Wang
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Raj K. Pandita
- Radiation Oncology Department, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jianfeng Cai
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Clayton R. Hunt
- Radiation Oncology Department, Washington University School of Medicine, St. Louis, MO 63108, USA
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10
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Zhang Y, Sicot G, Cui X, Vogel M, Wuertzer CA, Lezon-Geyda K, Wheeler J, Harki DA, Muzikar KA, Stolper DA, Dervan PB, Perkins AS. Targeting a DNA binding motif of the EVI1 protein by a pyrrole-imidazole polyamide. Biochemistry 2011; 50:10431-41. [PMID: 22039883 PMCID: PMC3619939 DOI: 10.1021/bi200962u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The zinc finger protein EVI1 is causally associated with acute myeloid leukemogenesis, and inhibition of its function with a small molecule therapeutic may provide effective therapy for EVI1-expressing leukemias. In this paper we describe the development of a pyrrole-imidazole polyamide to specifically block EVI1 binding to DNA. We first identify essential domains for leukemogenesis through structure-function studies on both EVI1 and the t(3;21)(q26;q22)-derived RUNX1-MDS1-EVI1 (RME) protein, which revealed that DNA binding to the cognate motif GACAAGATA via the first of two zinc finger domains (ZF1, encompassing fingers 1-7) is essential transforming activity. To inhibit DNA binding via ZF1, we synthesized a pyrrole-imidazole polyamide 1, designed to bind to a subsite within the GACAAGATA motif and thereby block EVI1 binding. DNase I footprinting and electromobility shift assays revealed a specific and high affinity interaction between polyamide 1 and the GACAAGATA motif. In an in vivo CAT reporter assay using NIH-3T3-derived cell line with a chromosome-embedded tet-inducible EVI1-VP16 as well as an EVI1-responsive reporter, polyamide 1 completely blocked EVI1-responsive reporter activity. Growth of a leukemic cell line bearing overexpressed EVI1 was also inhibited by treatment with polyamide 1, while a control cell line lacking EVI1 was not. Finally, colony formation by RME was attenuated by polyamide 1 in a serial replating assay. These studies provide evidence that a cell permeable small molecule may effectively block the activity of a leukemogenic transcription factor and provide a valuable tool to dissect critical functions of EVI1 in leukemogenesis.
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Affiliation(s)
- Yi Zhang
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Géraldine Sicot
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Xiaohui Cui
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Marion Vogel
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Charles A. Wuertzer
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Kimberly Lezon-Geyda
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06510, United States
| | - John Wheeler
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06510, United States
| | - Daniel A. Harki
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Katy A. Muzikar
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | - Peter B. Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Archibald S. Perkins
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
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11
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Holman GG, Zewail-Foote M, Smith AR, Johnson KA, Iverson BL. A sequence-specific threading tetra-intercalator with an extremely slow dissociation rate constant. Nat Chem 2011; 3:875-81. [PMID: 22024884 PMCID: PMC3209807 DOI: 10.1038/nchem.1151] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 08/17/2011] [Indexed: 12/02/2022]
Abstract
A long-lived and sequence specific ligand-DNA complex would make possible the modulation of biological processes for extended periods. We have been investigating the threading polyintercalation approach to DNA recognition in which chains of aromatic units thread back and forth repeatedly through the double helix. Here we report the preliminary sequence specificity and detailed kinetic analysis of a structurally characterized threading tetraintercalator. Specific binding on a relatively long DNA strand was observed, strongly favoring a predicted 14-base pair sequence. Kinetic studies revealed a multi-step association process and specificity was found to derive primarily from large differences in dissociation rates. Importantly, the rate-limiting dissociation rate constant of the tetraintercalator complex dissociating from its preferred binding site was extremely slow, corresponding to a 16 day half-life, making it one of the longer non-covalent complex half-lives yet measured, and, to the best of our knowledge, the longest for a DNA binding molecule.
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Affiliation(s)
- Garen G Holman
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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12
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Drouin R, Bastien N, Millau JF, Vigneault F, Paradis I. In cellulo DNA analysis (LMPCR footprinting). Methods Mol Biol 2009; 543:293-336. [PMID: 19378174 DOI: 10.1007/978-1-60327-015-1_20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The in cellulo analysis of DNA protein interactions and chromatin structure is very important to better understand the mechanisms involved in the regulation of gene expression. The nuclease-hypersensitive sites and sequences bound by transcription factors often correspond to genetic regulatory elements. Using the Ligation-mediated polymerase chain reaction (LMPCR) technology, it is possible to precisely analyze these DNA sequences to demonstrate the existence of DNA-protein interactions or unusual DNA structures directly in living cells. Indeed, the ideal chromatin substrate is, of course, found inside intact cells. LMPCR, a genomic-sequencing, technique that map DNA single-strand breaks at the sequence level of resolution, is the method of choice for in cellulo footprinting and DNA structure studies because it can be used to investigate any complex genomes, including human. The detailed conventional and automated LMPCR protocols are presented in this chapter.
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Affiliation(s)
- Régen Drouin
- Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, QC, Canada J1H 5N4
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13
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Lippert B. Coordinative Bond Formation Between Metal Ions and Nucleic Acid Bases. NUCLEIC ACID–METAL ION INTERACTIONS 2008. [DOI: 10.1039/9781847558763-00039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Bernhard Lippert
- Fakultät für Chemie, Technische Universität Dortmund Otto-Hahn-Strasse 6 D-44227 Dortmund Germany
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14
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Hsu CF, Phillips JW, Trauger JW, Farkas ME, Belitsky JM, Heckel A, Olenyuk BZ, Puckett JW, Wang CCC, Dervan PB. Completion of a Programmable DNA-Binding Small Molecule Library. Tetrahedron 2007; 63:6146-6151. [PMID: 18596841 DOI: 10.1016/j.tet.2007.03.041] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Hairpin pyrrole-imidazole (Py-Im) polyamides are programmable oligomers that bind the DNA minor groove in a sequence-specific manner with affinities comparable to those of natural DNA-binding proteins. These cell-permeable small molecules have been shown to enter the nuclei of live cells and downregulate endogenous gene expression. We complete here a library of 27 hairpin Py-Im polyamides which bind 7-base-pair sequences of the general form 5'-WWGNNNW-3' (where W = A or T, N = W, G, or C). Their equilibrium association constants (K(a)) range from K(a) = 1×10(8) M(-1) to 4×10(10) M(-1) with good sequence specificity. A table of binding affinities and sequence contexts for this completed 27-member library has been assembled for the benefit of the chemical biology community interested in molecular control of transcription.
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Affiliation(s)
- Carey F Hsu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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15
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González-Jasso E, Arredondo-Vázquez G, Martínez P, Pless RC. Comparison of different amines for the one-lane sequence determination of 5'-end-labeled oligodeoxyribonucleotides by chemical cleavage. Anal Biochem 2007; 369:112-9. [PMID: 17631853 DOI: 10.1016/j.ab.2007.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 06/06/2007] [Accepted: 06/07/2007] [Indexed: 10/23/2022]
Abstract
Hot aqueous solutions of a wide variety of aliphatic amines bring about efficient cleavage of 5'-(32)P-labeled oligodeoxyribonucleotides. Electrophoretic resolution of the product mixtures produces a radioactivity pattern that can be analyzed in terms of relative band intensities and band separations to deduce the base sequence of the original oligonucleotide. Amines differ in their overall reactivity with respect to the oligonucleotide as well as in their preference for reaction with the various heterocyclic bases. Guanine sites, in particular, vary markedly in their cleavage susceptibility when reacted with the different amines, being more vulnerable to scission when reacted with less basic amines. Guanine cleavage propensity can also be affected markedly by the ionic strength of the aminolysis solution. Both effects are interpreted in terms of variable extents of deprotonation of the guanine sites in the basic medium. Some of the amines produce fragment patterns that are marred by the presence of minor extraneous bands; these probably are due to an incomplete extent of the second beta-elimination involved in backbone cleavage. The methodology is applicable to confirmatory sequencing of synthetic oligonucleotides and can also be used to prepare standard ladders for use in footprinting experiments or chemical reactivity studies.
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Affiliation(s)
- Eva González-Jasso
- Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada Querétaro, Instituto Politécnico Nacional, Querétaro, 76090 Querétaro, Mexico
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16
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Rochette PJ, Bastien N, Todo T, Drouin R. Pyrimidine (6-4) pyrimidone photoproduct mapping after sublethal UVC doses: nucleotide resolution using terminal transferase-dependent PCR. Photochem Photobiol 2007; 82:1370-6. [PMID: 16776547 DOI: 10.1562/2004-12-01-ra-390] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
UVC irradiation of genomic DNA induces two main types of potentially mutagenic base modifications: cyclobutane pyrimidine dimers (CPDs) and the less frequent (15-30% of CPD levels) pyrimidine (6-4) pyrimidone photoproducts (6-4PP). Ligation-mediated PCR (LMPCR), a genomic sequencing technique, allows CPD mapping at nucleotide resolution following irradiation with sublethal doses of UVB or UVC for most cell types. In contrast, a dose of 80 J/m(2) of UVC that is lethal for the majority of cell types is necessary to map 6-4PP by the LMPCR technique. This compromises the use of LMPCR to study the repair of 6-4PP. To date, no other techniques have been developed to study 6-4PP repair at nucleotide resolution. We have therefore adapted a recently developed technique for the mapping of 6-4PP: terminal transferase-dependent PCR (TDPCR). TDPCR is in many ways similar to LMPCR. This technique is more sensitive and allows the mapping of 6-4PP at UVC doses as low as 10 J/m(2) in genomic DNA and in living cells.
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Affiliation(s)
- Patrick J Rochette
- Division of Pathology, Department of Medical Biology, Université Laval, Quebec, PQ, Canada
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17
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Viger A, Dervan PB. Exploring the limits of benzimidazole DNA-binding oligomers for the hypoxia inducible factor (HIF) site. Bioorg Med Chem 2006; 14:8539-49. [PMID: 16971129 DOI: 10.1016/j.bmc.2006.08.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Revised: 08/19/2006] [Accepted: 08/22/2006] [Indexed: 11/16/2022]
Abstract
The vascular endothelial growth factor (VEGF) and its receptors have been implicated as key-factors in tumor angiogenesis and are major targets in cancer therapy. New oligomers which mimic the architecture of DNA-binding polyamides have been designed to target the hypoxia inducible factor (HIF-1alpha) binding site on the promoter of VEGF gene. These oligomers incorporate an increasing number of six-five fused rings such as hydroxybenzimidazole-imidazole, benzimidazole-pyrrole, benzimidazole-chlorothiophene, and imidazopyridine-pyrrole, and bind the VEGF hypoxia response element (HRE) 5'-TACGT-3' with high affinity and selectivity.
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Affiliation(s)
- Anne Viger
- The Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Angers M, Drouin R, Bachvarova M, Paradis I, Bissell B, Hiromura M, Usheva A, Bachvarov D. In vivo DNase I-mediated footprinting analysis along the human bradykinin B1 receptor (BDKRB1) gene promoter: evidence for cell-specific regulation. Biochem J 2005; 389:37-46. [PMID: 15705059 PMCID: PMC1184537 DOI: 10.1042/bj20042104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
By applying in vivo dimethyl sulphate and UV light type C-footprinting analysis, we previously showed that specific DNA sequences in the -1349/+42 core promoter region of the inducible human BDKRB1 (bradykinin B1 receptor) gene correlated with its transcriptional activity. In the present study we used the highly sensitive DNase I in vivo footprinting approach to delineate more precisely the functional domains of the BDKRB1 gene promoter in human SMCs (smooth muscle cells). Human lymphocytes that do not express a functional BDKRB1 were also studied as a reference using dimethyl sulphate, UV light type C and DNase I treatments. An obvious difference was found in the DNase I-footprinting patterns between cellular systems that express a functional BDKRB1 (SMCs) in comparison with human lymphocytes, where randomly distributed nucleosome-like footprinting patterns were found in the bulk of the core promoter region studied. Gel-shift assays and expression studies pointed to the implication of the YY1 and a TBP/TFIIB (TATA-box-binding protein/transcription factor IIB) transcription factor in the regulation of BDKRB1 gene expression in SMCs and possible YY1 involvement in the mechanisms of nuclear factor kappaB-mediated regulation of the receptor expression. No significant changes in the promoter foot-printing pattern were found after treatment with interleukin-1beta or serum (known BDKRB1 gene inducers), indicating that definite regulatory motifs could exist outside the BDKRB1 gene core promoter region studied.
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Affiliation(s)
- Martin Angers
- *Unité de Recherche en Génétique Humaine et Moléculaire, Research Centre, Hôpital St-François d'Assise, Centre Hospitalier Universitaire de Québec, 10 de l'Espinay Street, QC, Canada G1L 3L5
- †Division of Pathology, Department of Medical Biology, Faculty of Medicine, Laval University, QC, Canada
| | - Régen Drouin
- *Unité de Recherche en Génétique Humaine et Moléculaire, Research Centre, Hôpital St-François d'Assise, Centre Hospitalier Universitaire de Québec, 10 de l'Espinay Street, QC, Canada G1L 3L5
- †Division of Pathology, Department of Medical Biology, Faculty of Medicine, Laval University, QC, Canada
| | - Magdalena Bachvarova
- ‡Cancer Research Centre, Hôpital l'Hôtel-Dieu de Québec, Centre Hospitalier Universitaire de Québec, 9 rue McMahon, QC, Canada G1R 2J6
| | - Isabelle Paradis
- *Unité de Recherche en Génétique Humaine et Moléculaire, Research Centre, Hôpital St-François d'Assise, Centre Hospitalier Universitaire de Québec, 10 de l'Espinay Street, QC, Canada G1L 3L5
- †Division of Pathology, Department of Medical Biology, Faculty of Medicine, Laval University, QC, Canada
| | - Brad Bissell
- §Division of Endocrinology, Department of Medicine, Beth Israel Deaconess Medical Center Harvard Medical School, 99 Brookline Ave., RN313, Boston, MA 02215, U.S.A
| | - Makoto Hiromura
- §Division of Endocrinology, Department of Medicine, Beth Israel Deaconess Medical Center Harvard Medical School, 99 Brookline Ave., RN313, Boston, MA 02215, U.S.A
| | - Anny Usheva
- §Division of Endocrinology, Department of Medicine, Beth Israel Deaconess Medical Center Harvard Medical School, 99 Brookline Ave., RN313, Boston, MA 02215, U.S.A
| | - Dimcho Bachvarov
- ‡Cancer Research Centre, Hôpital l'Hôtel-Dieu de Québec, Centre Hospitalier Universitaire de Québec, 9 rue McMahon, QC, Canada G1R 2J6
- ∥Department of Medicine, Faculty of Medicine, Laval University, QC, Canada
- To whom correspondence should be addressed, at Cancer Research Centre, Hôpital l'Hôtel-Dieu de Québec (email )
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Vigneault F, Drouin R. Optimal conditions and specific characteristics of Vent exo- DNA polymerase in ligation-mediated polymerase chain reaction protocols. Biochem Cell Biol 2005; 83:147-65. [PMID: 15864324 DOI: 10.1139/o04-134] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
An optimized procedure for the ligation-mediated polymerase chain reaction (PCR) technique using Thermococcus litoralis exo- DNA polymerase (Vent exo-) was developed. The optimal dosage of Vent exo- at the primer extension and PCR amplification steps as well as the optimal DNA quantity to use were established. We showed that Vent exo- can efficiently create the blunt-ended termini required for subsequent linker ligation. Vent exo- proves to be more efficient than Pyrococcus furiosus exo- (Pfu exo-) for this task. Vent exo- resolves highly GC-rich sequence substantially better than Thermus aquaticus DNA polymerase (Taq) and with a similar efficiency as Pfu exo-. The DNA/DNA polymerase activity ratio is significantly higher for Vent exo- than for Pfu exo-, which is reflected by the sensibility of Vent exo- in efficiently amplifying genomic DNA. Furthermore, the range of efficiency of Vent exo- demonstrates the importance of conducting evaluative testing to identify the optimal dosage of use of this polymerase to obtain successful PCR amplification. Optimal MgSO4 concentrations to use with Vent exo- were established. Our results show that Vent exo- DNA polymerase produces bands of uniform and strong intensity and can efficiently be used for the analysis of DNA in living cells by ligation-mediated PCR.
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Affiliation(s)
- François Vigneault
- Unité de Recherche en Génétique Humaine et Moléculaire, Research Center, Hôpital St-François d'Assise, Centre Hospitalier Universitaire de Québec, QC, Canada
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20
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Bales BC, Kodama T, Weledji YN, Pitié M, Meunier B, Greenberg MM. Mechanistic studies on DNA damage by minor groove binding copper-phenanthroline conjugates. Nucleic Acids Res 2005; 33:5371-9. [PMID: 16186134 PMCID: PMC1235636 DOI: 10.1093/nar/gki856] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Copper-phenanthroline complexes oxidatively damage and cleave nucleic acids. Copper bis-phenanthroline and copper complexes of mono- and bis-phenanthroline conjugates are used as research tools for studying nucleic acid structure and binding interactions. The mechanism of DNA oxidation and cleavage by these complexes was examined using two copper-phenanthroline conjugates of the sequence-specific binding molecule, distamycin. The complexes contained either one or two phenanthroline units that were bonded to the DNA-binding domain through a linker via the 3-position of the copper ligand. A duplex containing independently generated 2-deoxyribonolactone facilitated kinetic analysis of DNA cleavage. Oxidation rate constants were highly dependent upon the ligand environment but rate constants describing elimination of the alkali-labile 2-deoxyribonolactone intermediate were not. Rate constants describing DNA cleavage induced by each molecule were 11-54 times larger than the respective oxidation rate constants. The experiments indicate that DNA cleavage resulting from beta-elimination of 2-deoxyribonolactone by copper-phenanthroline complexes is a general mechanism utilized by this family of molecules. In addition, the experiments confirm that DNA damage mediated by mono- and bis-phenanthroline copper complexes proceeds through distinct species, albeit with similar outcomes.
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Affiliation(s)
| | - Tetsuya Kodama
- Department of Chemistry, Johns Hopkins University3400 North Charles Street, Baltimore, MD 21218, USA
| | - Yvonne N. Weledji
- Department of Chemistry, Johns Hopkins University3400 North Charles Street, Baltimore, MD 21218, USA
| | - Marguerite Pitié
- Laboratoire de Chimie de Coordination du CNRS205 route de Narbonne, 31 077 Toulouse Cedex 4, France
| | - Bernard Meunier
- Laboratoire de Chimie de Coordination du CNRS205 route de Narbonne, 31 077 Toulouse Cedex 4, France
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University3400 North Charles Street, Baltimore, MD 21218, USA
- To whom correspondence should be addressed. Tel: +33 410 516 8095; Fax: +33 410 616 7044;
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Barry CG, Day CS, Bierbach U. Duplex-promoted platination of adenine-N3 in the minor groove of DNA: challenging a longstanding bioinorganic paradigm. J Am Chem Soc 2005; 127:1160-9. [PMID: 15669855 DOI: 10.1021/ja0451620] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interactions of [Pt(en)Cl(ACRAMTU-S)](NO3)2 (PT-ACRAMTU, en = ethane-1,2-diamine, ACRAMTU = 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea) with adenine in DNA have been studied using a combination of analytical and high-resolution structural methods. For the first time, a cytotoxic platinum(II) complex has been demonstrated to form adducts in the minor groove of DNA through platination of the adenine-N3 endocyclic nitrogen. An acidic depurination assay was developed that allowed the controlled and selective (pH 2, 60 degrees C, 12 h) release of platinum-modified adenine from drug-treated nucleic acid samples. From the digested mixtures, three adducts were isolated by semipreparative reverse phase high-performance liquid chromatography and studied by electrospray ionization mass spectrometry (in-line LC-MS), variable-pH 1H NMR spectroscopy, and, where applicable, X-ray crystallography. The three species were identified as the N7 (A-I), N3 (A-II), and N1 (A-III) linkage isomers of [Pt(en)(ACRAMTU-S)(adenine)]3+ (A). Incubations carried out with the single- and double-stranded model sequences, d(TA)5 and d(TA)15, as well as native DNA indicate that the adduct profiles (A-I:A-II:A-IIIratios) are sensitive to the nature of the nucleic acid template. A-II was found to be a double-strand specific adduct. The crystal structure of this adduct has been determined, providing ultimate evidence for the N3 connectivity of platinum. A-II crystallizes in the triclinic space group P in the form of centrosymmetric dimers, {[Pt(en)(ACRAMTU-S)(adenine-N3)]2}6+. The cations are stabilized by a combination of adenine-adenine base pairing (N6...N1 2.945(5) A) and mutual acridine-adenine base stacking. Tandem mass spectra and 1H chemical shift anomalies indicate that this type of self-association is not merely a crystal packing effect but persists in solution. The monofunctional platination of adenine at its N7, N3, and N1 positions in a significant fraction of adducts breaks a longstanding paradigm in platinum-DNA chemistry, the requirement for nucleophilic attack of guanine-N7 as the principal step in cross-link formation. The biological consequences and potential therapeutic applications of the unique base and groove recognition of PT-ACRAMTU are discussed.
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Affiliation(s)
- Colin G Barry
- Department of Chemistry, Wake Forest University, PO Box 7486, Reynolda Station, Winston-Salem, North Carolina 27109, USA
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22
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Urbach AR, Waring MJ. Visualising DNA: Footprinting and 1-2D Gels. MOLECULAR BIOSYSTEMS 2005; 1:287-93. [PMID: 16880993 DOI: 10.1039/b509471m] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The study of molecular recognition of DNA by natural and synthetic ligands has made enormous progress due in large part to the discovery and development of methods for separating DNA fragments by gel electrophoresis in one and two dimensions, and for characterizing DNA-ligand complexes by footprinting techniques.
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Affiliation(s)
- Adam R Urbach
- Department of Chemistry, Trinity University, One Trinity Place, San Antonio, TX 78212, USA.
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23
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Arpalahti J, Jokilammi A, Hakala H, Lönnberg H. Depurination of (dien)Pt(II) complexes of purine deoxyribonucleosides. Comparison with the effects of (dien)Pd(II) ion complexing. J PHYS ORG CHEM 2004. [DOI: 10.1002/poc.610040507] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Renneberg D, Dervan PB. Imidazopyridine/Pyrrole and hydroxybenzimidazole/pyrrole pairs for DNA minor groove recognition. J Am Chem Soc 2003; 125:5707-16. [PMID: 12733909 DOI: 10.1021/ja0300158] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DNA binding properties of fused heterocycles imidazo[4,5-b]pyridine (Ip) and hydroxybenzimidazole (Hz) paired with pyrrole (Py) in eight-ring hairpin polyamides are reported. The recognition profile of Ip/Py and Hz/Py pairs were compared to the five-membered ring pairs Im/Py and Hp/Py on a DNA restriction fragment at four 6-base pair recognition sites which vary at a single position 5'-TGTNTA-3', where N = G, C, T, A. The Ip/Py pair distinguishes G.C from C.G, T.A, and A.T, and the Hz/Py pair distinguishes T.A from A.T, G.C, and C.G, affording a new set of heterocycle pairs to target the four Watson-Crick base pairs in the minor groove of DNA.
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Affiliation(s)
- Dorte Renneberg
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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26
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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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27
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Olenyuk B, Jitianu C, Dervan PB. Parallel synthesis of H-pin polyamides by alkene metathesis on solid phase. J Am Chem Soc 2003; 125:4741-51. [PMID: 12696892 DOI: 10.1021/ja0213221] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A small library of H-pin polyamides with variable aliphatic bridge lengths (CH(2))(n)(), where n = 4-8, connecting a central Py/Py pair was prepared via parallel synthesis with Ru-catalyzed alkene metathesis on solid phase as a complexity-generating cross-linking reaction. DNA binding affinities and sequence specificities were analyzed for each member of the library to determine the optimum linker length. An H-pin polyamide with a six-methylene bridge was found to have the highest affinity to its match site with high selectivity over a 1-bp mismatch site. The relationship between the number of methylenes in the linker (CH(2))(n)() and affinity is n = 6 > 4 > 7 > 5 > 8. These results indicate that 6 followed by 4 methylene-bridged polyamides represent the optimum spacer length for the H-pin motif in the DNA minor groove. Importantly, the H-pin is competitive with hairpin polyamides with respect to affinity and specificity. The metathesis-based convergent synthetic route to H-pin polyamides expands the scope of readily available DNA recognition motifs for small molecule-based gene regulation studies.
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Affiliation(s)
- Bogdan Olenyuk
- Division of Chemistry and Chemical Engineering, The Beckman Institute, California Institute of Technology, Pasadena, California 91125, USA
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28
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Weyermann P, Dervan PB. Recognition of ten base pairs of DNA by head-to-head hairpin dimers. J Am Chem Soc 2002; 124:6872-8. [PMID: 12059208 DOI: 10.1021/ja020258k] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hairpin polyamides coupled head-to head with alkyl linkers of varying lengths were synthesized, and their DNA binding properties were determined. The DNA binding affinities of six-ring hairpin dimers Im-Im-Py-(R)[Im-Im-Py-(R)(HNCO(CH))(n)(CO)gamma-Py-Py-Py-beta-Dp](NH)gamma-Im-Py-Py-beta-Dp (1-4) (where n = 1-4) for their 10-bp, 11-bp, and 12-bp match sites 5'-TGGCATACCA-3', 5'-TGGCATTACCA-3', and 5'-TGGCATATACCA-3' were determined by quantitative DNase I footprint titrations. The most selective dimer Im-Im-Py-(R)[Im-Im-Py-(R)(HNCO(CH)(2))(2)(CO)gamma-Py-Py-Py-beta-Dp](NH)gamma-Im-Py-Py-beta-Dp (2) binds the 10-bp site match site with an equilibrium association constant of K(a) = 7.5 x 10(10) M(-1) and displays 25- and 140-fold selectivity over the 11-bp and 12-bp match sites, respectively. The affinity toward single base pair mismatched sequences is 4- to 8-fold lower if one hairpin module of the dimer is affected, but close to 200-fold lower if both hairpin modules face a single mismatch base pair. The head-to-head hairpin dimer motif expands the binding site size of DNA sequences targetable with polyamides.
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Affiliation(s)
- Philipp Weyermann
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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Trauger JW, Dervan PB. Footprinting methods for analysis of pyrrole-imidazole polyamide/DNA complexes. Methods Enzymol 2001; 340:450-66. [PMID: 11494863 DOI: 10.1016/s0076-6879(01)40436-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- J W Trauger
- Department of Chemistry, California Institute of Technology, Pasadena, California 91125, USA
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30
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Angers M, Cloutier JF, Castonguay A, Drouin R. Optimal conditions to use Pfu exo(-) DNA polymerase for highly efficient ligation-mediated polymerase chain reaction protocols. Nucleic Acids Res 2001; 29:E83. [PMID: 11504891 PMCID: PMC55867 DOI: 10.1093/nar/29.16.e83] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ligation-Mediated Polymerase Chain Reaction (LMPCR) is the most sensitive sequencing technique available to map single-stranded DNA breaks at the nucleotide level of resolution using genomic DNA. LMPCR has been adapted to map DNA damage and reveal DNA-protein interactions inside living cells. However, the sequence context (GC content), the global break frequency and the current combination of DNA polymerases used in LMPCR affect the quality of the results. In this study, we developed and optimized an LMPCR protocol adapted for Pyrococcus furiosus exo(-) DNA polymerase (Pfu exo(-)). The relative efficiency of Pfu exo(-) was compared to T7-modified DNA polymerase (Sequenase 2.0) at the primer extension step and to Thermus aquaticus DNA polymerase (Taq) at the PCR amplification step of LMPCR. At all break frequencies tested, Pfu exo(-) proved to be more efficient than Sequenase 2.0. During both primer extension and PCR amplification steps, the ratio of DNA molecules per unit of DNA polymerase was the main determinant of the efficiency of Pfu exo(-), while the efficiency of Taq was less affected by this ratio. Substitution of NaCl for KCl in the PCR reaction buffer of Taq strikingly improved the efficiency of the DNA polymerase. Pfu exo(-) was clearly more efficient than Taq to specifically amplify extremely GC-rich genomic DNA sequences. Our results show that a combination of Pfu exo(-) at the primer extension step and Taq at the PCR amplification step is ideal for in vivo DNA analysis and DNA damage mapping using LMPCR.
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Affiliation(s)
- M Angers
- Unite de Recherche en Genetique Humaine et Moleculaire, Centre de Recherche, Hopital Saint-Francois d'Assise, Centre Hospitalier Universitaire de Quebec, 10 rue de l'Espinay, Quebec, QC G1L 3L5, Canada
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31
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Bremer RE, Wurtz NR, Szewczyk JW, Dervan PB. Inhibition of major groove DNA binding bZIP proteins by positive patch polyamides. Bioorg Med Chem 2001; 9:2093-103. [PMID: 11504645 DOI: 10.1016/s0968-0896(01)00122-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cell permeable synthetic ligands that bind to predetermined DNA sequences offer a chemical approach to gene regulation, provided inhibition of a broad range of DNA transcription factors can be achieved. DNA minor groove binding polyamides containing aminoalkyl substituents at the N-1 of a single pyrrole residue display inhibitory effects for a bZIP protein which binds exclusively in the DNA major groove. For major groove protein inhibition, specific protein-DNA contacts along the phosphate backbone were targeted with the positively charged dimethylamino substituent on the backbone of a minor groove binding polyamide hairpin. Remarkably, these polyamides bind DNA with enhanced affinity and uncompromised specificity when compared to polyamides with the aminoalkyl moiety at the C-terminus. By adding bZIP transcription factors to the class of protein-DNA complexes that can be disrupted by minor groove binding ligands, these results may increase the functional utility of polyamides as regulators of gene expression.
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Affiliation(s)
- R E Bremer
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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32
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Abstract
Polyamides composed of four amino acids, imidazole (Im), pyrrole (Py), hydroxypyrrole (Hp), and beta-alanine (beta), are synthetic ligands that form highly stable complexes in the minor groove of DNA. Although specific pairing rules within the 2:1 motif can be used to distinguish the four Watson. Crick base pairs, a comparable recognition code for 1:1 polyamide:DNA complexes had not been described. To set a quantitative baseline for the field, the sequence specificities of Im, Py, Hp, and beta for the four Watson. Crick base pairs were determined for two polyamides, Im-beta-ImPy-beta-Im-beta-ImPy-beta-Dp (1, for Im, Py, and beta) and Im-beta-ImHp-beta-Im-beta-ImPy-beta-Dp (2, for Hp), in a 1:1 complex within the DNA sequence context 5'-AAAGAGAAGAG-3'. Im residues do not distinguish G,C from A,T but bind all four base pairs with high affinity. Py and beta residues exhibit > or = 10-fold preference for A,T over G,C base pairs. The Hp residue displays a unique preference for a single A.T base pair with an energetic penalty.
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Affiliation(s)
- A R Urbach
- Division of Chemistry and Chemical Engineering, 164-30, California Institute of Technology, Pasadena, CA 91125, USA
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33
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Wang CC, Ellervik U, Dervan PB. Expanding the recognition of the minor groove of DNA by incorporation of beta-alanine in hairpin polyamides. Bioorg Med Chem 2001; 9:653-7. [PMID: 11310600 DOI: 10.1016/s0968-0896(00)00282-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In order to expand the recognition code by hairpin polyamides to include DNA sequences of the type 5'-CWWC-3' two polyamides, PyPyPyPy-(R)(H2N)gamma-ImPyPyIm-beta-Dp (1) and PyPyPyPy-(R)(H2N)gamma-ImPy-beta-Im-beta-Dp (2) were synthesized which have in common an Py/Im pair in the terminal position for targeting C x G but differ with respect to internal placement of a beta-alanine residue. The equilibrium association constants (Ka) were determined at four DNA sites which differ at a single common position, 5'-TNTACA-3' (N = T, A, G, C). Quantitative DNase I footprint titration experiments reveal that the eight-ring hairpin PyPyPyPy-(R)(H2N)gamma-ImPyPyIm-beta-Dp (1) binds the four binding sites with similar affinities, Ka = 1.3-1.9 x 10(10) M(-1) indicating that there is no preference for the position N. In contrast, a redesigned polyamide PyPyPyPy-(R)(H2N)gamma-ImPy-beta-Im-beta-Dp (2) that places an internal flexible aliphatic beta-alanine to the 5'-side of a key imidazole group bound the match site 5'-TCTACA-3' with high affinity and good sequence discrimination (Ka(match) = 4.9 x 10(10) M(-1) and the single base pair mismatch sites with 5- to 25-fold lower affinity). These results expand the repertoire of sequences targetable by hairpins and emphasize the importance of beta-alanine as a key element for minor groove recognition.
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Affiliation(s)
- C C Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA
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Abstract
Eight-ring cyclic polyamides containing pyrrole (Py), imidazole (Im), and hydroxypyrrole (Hp) aromatic amino acids recognize predetermined six base pair sites in the minor groove of DNA. Two four-ring polyamide subunits linked by (R)-2,4-diaminobutyric acid [(R)H2Ngamma] residue form hairpin polyamide structures with enhanced DNA binding properties. In hairpin polyamides, substitution of Hp/Py for Py/Py pairs enhances selectivity for T. A base pairs but compromises binding affinity for specific sequences. In an effort to enhance the binding properties of polyamides containing Hp/Py pairings, four eight ring cyclic polyamides were synthesized and analyzed on a DNA restriction fragment containing three 6-bp sites 5'-tAGNNCTt-3', where NN = AA, TA, or AT. Quantitative footprint titration experiments demonstrate that contiguous placement of Hp/Py pairs in cyclo-(gamma-ImPyPyPy-(R)H2Ngamma-ImHpHpPy-) (1) provides a 20-fold increase in affinity for the 5'-tAGAACTt-3' site (Ka = 7.5 x 10(7)M(-1)) relative to ImPyPyPy-(R)H2Ngamma-ImHpHpPy-C3-OH (2). A cyclic polyamide of sequence composition cyclo-(gamma-ImHpPyPy-(R)H2Ngamma-ImHpPyPy-) (3) binds a 5'-tAGTACTt-3' site with an equilibrium association constant KA= 3.2 x 10(9)M(-1), representing a fivefold increase relative to the hairpin analogue ImHpPyPy-(R)H2Ngamma-ImHpPyPy-C3-OH (4). Arrangement of Hp/Py pairs in a 3'-stagger regulates specificity of cyclo-(gamma-ImPyHpPy-(R)H2Ngamma-ImPyHpPy-) (5) for the 5'-tAGATCTt-3' site (Ka = 7.5 x 10(7)M(-1)) threefold increase in affinity relative to the hairpin analogue ImPyHpPy-(R)H2Ngamma-ImPyHpPy-C3-OH (6), respectively. This study identifies cyclic polyamides as a viable motif for restoring recognition properties of polyamides containing Hp/Py pairs.
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Affiliation(s)
- C Melander
- Arnold and Mabel Beckman Laboratories of Chemical Synthesis, California Institute of Technology, Pasadena 91125, USA
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35
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Ellervik U, Wang CCC, Dervan PB. Hydroxybenzamide/Pyrrole Pair Distinguishes T·A from A·T Base Pairs in the Minor Groove of DNA. J Am Chem Soc 2000. [DOI: 10.1021/ja001692u] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ulf Ellervik
- Contribution from the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Clay C. C. Wang
- Contribution from the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Peter B. Dervan
- Contribution from the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
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36
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Bremer RE, Szewczyk JW, Baird EE, Dervan PB. Recognition of the DNA minor groove by pyrrole-imidazole polyamides: comparison of desmethyl- and N-methylpyrrole. Bioorg Med Chem 2000; 8:1947-55. [PMID: 11003140 DOI: 10.1016/s0968-0896(00)00145-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Polyamides consisting of N-methylpyrrole (Py), N-methylimidazole (Im), and N-methyl-3-hydroxypyrrole (Hp) are synthetic ligands that recognize predetermined DNA sequences with affinities and specificities comparable to many DNA-binding proteins. As derivatives of the natural products distamycin and netropsin, Py/Im/Hp polyamides have retained the N-methyl substituent, although structural studies of polyamide:DNA complexes have not revealed an obvious function for the N-methyl. In order to assess the role of the N-methyl moiety in polyamide:DNA recognition, a new monomer, desmethylpyrrole (Ds), where the N-methyl moiety has been replaced with hydrogen, was incorporated into an eight-ring hairpin polyamide by solid-phase synthesis. MPE footprinting, affinity cleavage, and quantitative DNase I footprinting revealed that replacement of each Py residue with Ds resulted in identical binding site size and orientation and similar binding affinity for the six-base-pair (bp) target DNA sequence. Remarkably, the Ds-containing polyamide exhibited an 8-fold loss in specificity for the match site versus a mismatched DNA site, relative to the all-Py parent. Polyamides with Ds exhibit increased water solubility, which may alter the cell membrane permeability properties of the polyamide. The addition of Ds to the repertoire of available monomers may prove useful as polyamides are applied to gene regulation in vivo. However, the benefits of Ds incorporation must be balanced with a potential loss in specificity.
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Affiliation(s)
- R E Bremer
- Arnold and Mabel Beckman Laboratories of Chemical Synthesis, California Institute of Technology, Pasadena 91125, USA
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37
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Hollenbeck JJ, Oakley MG. GCN4 binds with high affinity to DNA sequences containing a single consensus half-site. Biochemistry 2000; 39:6380-9. [PMID: 10828952 DOI: 10.1021/bi992705n] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
bZip proteins contain a bipartite DNA-binding motif consisting of a "leucine zipper" dimerization domain and a highly charged "basic region" that directly contacts DNA. These transcription factors form dimeric complexes with each monomer recognizing half of a symmetric or nearly symmetric DNA site. We have found that the bZip protein GCN4 can also bind with high affinity to DNA sites containing only a single GCN4 consensus half-site. Because several recent lines of evidence have suggested a role for monomeric DNA binding by bZip proteins, we investigated the structure of the GCN4.half-site complex. Quantitative DNA binding and affinity cleaving studies support a model in which GCN4 binds as a dimer, with one monomer making specific contacts to the consensus half-site and the other monomer forming nonspecific contacts that are nonetheless important for binding affinity. We also examined the folding transition induced in the basic regions of this complex upon binding DNA. Circular dichroism (CD) studies demonstrate that the basic regions of both monomers are helical, suggesting that a protein folding transition may be required for both specific and nonspecific DNA binding by GCN4.
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Affiliation(s)
- J J Hollenbeck
- Department of Chemistry, Indiana University, Bloomington 47405, USA
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38
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Angers M, Drouin R, Bachvarova M, Paradis I, Marceau F, Bachvarov DR. In vivo protein-DNA interactions at the kinin B(1) receptor gene promoter: no modification on interleukin-1 beta or lipopolysaccharide induction. J Cell Biochem 2000; 78:278-96. [PMID: 10842322 DOI: 10.1002/(sici)1097-4644(20000801)78:2<278::aid-jcb10>3.0.co;2-f] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The kinin B(1) receptor (B(1)R) gene is strongly upregulated following tissue injury and inflammation. In an attempt to define the regulatory elements that account for the control of B(1)R gene expression, we have conducted in vivo footprinting analysis of the B(1)R gene promoter region in three human cell types: embryonic lung fibroblast cells (IMR-90), embryonic kidney cells (HEK-293), and primary cultures of vascular umbilical smooth muscle cells. Initial in vitro delineation of the B(1)R gene promoter by transient transfection experiments with a reporter gene indicated that a 1.4-kb region, located just upstream of the transcription initiation site, bears all the characteristics of a core promoter with a functional TATA box and additional positive and negative control elements, as some of them could be tissue-specific. In vivo ultraviolet and dimethylsulfate footprinting analyses of the 1.4-kb region revealed no difference between the footprint patterns in the three cell types studied. We found that even in the noninduced state, the B(1)R gene promoter is possibly bound by several sequence-specific DNA binding proteins (GATA-1, PEA3, AP-1, CAAT, Sp1, Pit-1a, Oct-1, CREB). Some other footprints were detected on sequences that do not correspond to any known transcription factor binding site. No additional changes in protein-DNA complexes were observed upon treatment with interleukin-1 beta (IL-1beta) or bacterial lipopolysaccharide, shown previously to induce B(1)R gene expression. These results indicate that complex protein-DNA interactions exist at the B(1)R gene promoter prior to induction by external stimuli even in cells (HEK-293) that do not express a functional B(1)R.
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Affiliation(s)
- M Angers
- Division of Pathology, Department of Medical Biology, Faculty of Medicine, Laval University and Unité de recherche en génetique humaine et moléculaire, Research Centre, Hôpital St-François d'Assise, Centre Hospitalier Universitaire de Québec, CanadaI
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Chen T, Cook GP, Koppisch AT, Greenberg MM. Investigation of the Origin of the Sequence Selectivity for the 5-Halo-2‘-deoxyuridine Sensitization of DNA to Damage by UV-Irradiation. J Am Chem Soc 2000. [DOI: 10.1021/ja994357i] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tongqian Chen
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Gary P. Cook
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Andrew T. Koppisch
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Marc M. Greenberg
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
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Wurtz NR, Dervan PB. Sequence specific alkylation of DNA by hairpin pyrrole-imidazole polyamide conjugates. CHEMISTRY & BIOLOGY 2000; 7:153-61. [PMID: 10712931 DOI: 10.1016/s1074-5521(00)00085-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Pyrrole-imidazole polyamides are synthetic ligands that recognize predetermined sequences in the minor groove of DNA with affinities and specificities comparable to those of DNA-binding proteins. As a result of their DNA-binding properties, polyamides could deliver reactive moieties for covalent reaction at specific DNA sequences and thereby inhibit DNA-protein interactions. Site-specific alkylation of DNA could be a useful tool for regulating gene expression. As a minimal first step, we set out to design and synthesize a class of hairpin polyamides equipped with DNA alkylating agents and characterize the specificity and yield of covalent modification. RESULTS Bis(dichloroethylamino)benzene derivatives of the well-characterized chlorambucil (CHL) were attached to the gamma turn of an eight-ring hairpin polyamide targeted to the HIV-1 promoter. We found that a hairpin polyamide-CHL conjugate binds and selectively alkylates predetermined sites in the HIV promoter at subnanomolar concentrations. Cleavage sites were determined on both strands of a restriction fragment containing the HIV-1 promoter, revealing good specificity and a high yield of alkylation. CONCLUSIONS The ability of polyamide-CHL conjugates to sequence specifically alkylate double-stranded DNA in high yield and at low concentrations sets the stage for testing their use as regulators of gene expression in cell culture and ultimately in complex organisms.
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Affiliation(s)
- N R Wurtz
- Arnold and Mabel Beckman Laboratories of Chemical Synthesis, California Institute of Technology, Pasadena, CA 91125, USA
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41
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Urbach AR, Szewczyk JW, White S, Turner JM, Baird EE, Dervan PB. Sequence Selectivity of 3-Hydroxypyrrole/Pyrrole Ring Pairings in the DNA Minor Groove. J Am Chem Soc 1999. [DOI: 10.1021/ja9930667] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Adam R. Urbach
- Contribution from the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Jason W. Szewczyk
- Contribution from the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Sarah White
- Contribution from the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - James M. Turner
- Contribution from the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Eldon E. Baird
- Contribution from the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Peter B. Dervan
- Contribution from the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
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Hwang JT, Greenberg MM, Fuchs T, Gates KS. Reaction of the hypoxia-selective antitumor agent tirapazamine with a C1'-radical in single-stranded and double-stranded DNA: the drug and its metabolites can serve as surrogates for molecular oxygen in radical-mediated DNA damage reactions. Biochemistry 1999; 38:14248-55. [PMID: 10571998 DOI: 10.1021/bi991488n] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The compound 3-amino-1,2,4-benzotriazine 1,4-dioxide (1, tirapazamine; also known as SR4233, WIN 59075, and tirazone) is a clinically promising anticancer agent that selectively kills the oxygen-poor (hypoxic) cells found in tumors. When activated by one-electron enzymatic reduction, tirapazamine induces radical-mediated oxidative DNA strand cleavage. Using the ability to generate a single deoxyribose radical at a defined site in an oligonucleotide, we recently provided direct evidence that, in addition to initiating the formation of DNA radicals, tirapazamine can react with these radicals and convert them into base-labile lesions [Daniels et al. (1998) Chem. Res. Toxicol. 11, 1254-1257]. The rate constant for trapping of a C1'-radical in single-stranded DNA by tirapazamine was shown to be approximately 2 x 10(8) M(-1) s(-1), demonstrating that tirapazamine can substitute for molecular oxygen in radical-mediated DNA strand damage reactions. Because reactions of tirapazamine with DNA radicals may play an important role in its ability to damage DNA, we have further characterized the ability of the drug and its metabolites to convert a C1'-DNA radical into a base-labile lesion. We find that tirapazamine reacts with a C1'-radical in double-stranded DNA with a rate constant of 4.6 x 10(6) M(-1) s(-1). The mono-N-oxide (3) stemming from bioreductive metabolism of tirapazamine converts the C1'-radical to an alkaline-labile lesion more effectively than the parent drug. Compound 3 traps a C1'-radical in single-stranded DNA with a rate constant of 4.6 x 10(8) M(-1) s(-1) and in double-stranded DNA with a rate constant of 1.4 x 10(7) M(-)(1) s(-)(1). We have also examined the rate and mechanism of reactions between the C1'-radical and representatives from two known classes of "oxygen mimetic" agents: the nitroxyl radical 2,2,6, 6-tetramethylpiperidin-N-oxyl (4, TEMPO) and the nitroimidazole misonidazole (5). TEMPO traps the C1'-radical in single-stranded DNA (7.2 x 10(7) M(-1) s(-1)) approximately 3 times less effectively than tirapazamine, but 2 times as fast in double-stranded DNA (9.1 x 10(6) M(-1) s(-1)). Misonidazole traps the radical in single- (6. 9 x 10(8) M(-1) s(-1)) and double-stranded DNA (2.9 x 10(7) M(-1) s(-1)) with rate constants that are roughly comparable to those measured for the mono-N-oxide metabolite of tirapazamine. Finally, information regarding the chemical mechanism by which these compounds oxidize a monomeric C1'-nucleoside radical has been provided by product analysis and isotopic labeling studies.
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Affiliation(s)
- J T Hwang
- Departments of Chemistry and Biochemistry, University of Missouri-Columbia 65211, USA
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Cook GP, Chen T, Koppisch AT, Greenberg MM. The effects of secondary structure and O2 on the formation of direct strand breaks upon UV irradiation of 5-bromodeoxyuridine-containing oligonucleotides. CHEMISTRY & BIOLOGY 1999; 6:451-9. [PMID: 10381405 DOI: 10.1016/s1074-5521(99)80063-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND 5-Bromodeoxyuridine is a radiosensitizing agent that is currently being evaluated in clinical trials as an adjuvant in the treatment of a variety of cancers. gamma-Radiolysis and UV irradiation of oligonucleotides containing 5-bromodeoxyuridine result in the formation of direct strand breaks at the 5'-adjacent nucleotide by oxidation of the respective deoxyribose. We investigated the effects of DNA secondary structure and O2 on the induction of direct strand breaks in 5-bromodeoxyuridine-containing oligonucleotides. RESULTS The efficiency of direct strand break formation in duplex DNA is dependent upon O2 and results in fragments containing 3'-phosphate and the labile 3'-ketodeoxyadenosine termini. The ratio of the 3'-termini is also dependent upon O2 and structure. Deuterium product isotope effects and tritium-transfer studies indicate that hydrogen-atom abstraction from the C1'- and C2'-positions occurs in an O2- and structure-dependent manner. CONCLUSIONS The reaction mechanisms by which DNA containing 5-bromodeoxyuridine is sensitized to damage by UV irradiation are dependent upon whether the substrate is hybridized and upon the presence or absence of O2. Oxygen reduces the efficiency of direct strand break formation in duplex DNA, but does not affect the overall strand damage. It is proposed that the sigma radical abstracts hydrogen atoms from the C1'- and C2'-positions of the 5'-adjacent deoxyribose moiety, whereas the nucleobase peroxyl radical selectively abstracts the C1'-hydrogen atom from this site. This is the second example of DNA damage amplification by a nucleobase peroxyl radical, and might be indicative of a general reaction pattern for this family of reactive intermediates.
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Affiliation(s)
- G P Cook
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
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44
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Hwang JT, Greenberg MM. Kinetics and Stereoselectivity of Thiol Trapping of Deoxyuridin-1‘-yl in Biopolymers and Their Relationship to the Formation of Premutagenic α-Deoxynucleotides. J Am Chem Soc 1999. [DOI: 10.1021/ja990152y] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jae-Taeg Hwang
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Marc M. Greenberg
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
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Swalley SE, Baird EE, Dervan PB. Effects of γ-Turn and β-Tail Amino Acids on Sequence-Specific Recognition of DNA by Hairpin Polyamides. J Am Chem Soc 1999. [DOI: 10.1021/ja9830905] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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White S, Turner JM, Szewczyk JW, Baird EE, Dervan PB. Affinity and Specificity of Multiple Hydroxypyrrole/Pyrrole Ring Pairings for Coded Recognition of DNA. J Am Chem Soc 1998. [DOI: 10.1021/ja9830593] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sarah White
- Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California, 91125
| | - James M. Turner
- Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California, 91125
| | - Jason W. Szewczyk
- Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California, 91125
| | - Eldon E. Baird
- Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California, 91125
| | - Peter B. Dervan
- Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena, California, 91125
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Turner JM, Swalley SE, Baird EE, Dervan PB. Aliphatic/Aromatic Amino Acid Pairings for Polyamide Recognition in the Minor Groove of DNA. J Am Chem Soc 1998. [DOI: 10.1021/ja980147e] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Burrows CJ, Muller JG. Oxidative Nucleobase Modifications Leading to Strand Scission. Chem Rev 1998; 98:1109-1152. [PMID: 11848927 DOI: 10.1021/cr960421s] [Citation(s) in RCA: 1395] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112-0850
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DNA damage induced via independent generation of the radical resulting from formal hydrogen atom abstraction from the C1′-position of a nucleotide. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s1074-5521(98)90619-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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