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9-Aminoacridine Inhibits Ribosome Biogenesis by Targeting Both Transcription and Processing of Ribosomal RNA. Int J Mol Sci 2022; 23:ijms23031260. [PMID: 35163183 PMCID: PMC8836032 DOI: 10.3390/ijms23031260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 12/13/2022] Open
Abstract
Aminoacridines, used for decades as antiseptic and antiparasitic agents, are prospective candidates for therapeutic repurposing and new drug development. Although the mechanisms behind their biological effects are not fully elucidated, they are most often attributed to the acridines’ ability to intercalate into DNA. Here, we characterized the effects of 9-aminoacridine (9AA) on pre-rRNA metabolism in cultured mammalian cells. Our results demonstrate that 9AA inhibits both transcription of the ribosomal RNA precursors (pre-rRNA) and processing of the already synthesized pre-rRNAs, thereby rapidly abolishing ribosome biogenesis. Using a fluorescent intercalator displacement assay, we further show that 9AA can bind to RNA in vitro, which likely contributes to its ability to inhibit post-transcriptional steps in pre-rRNA maturation. These findings extend the arsenal of small-molecule compounds that can be used to block ribosome biogenesis in mammalian cells and have implications for the pharmacological development of new ribosome biogenesis inhibitors.
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Kostjukova LO, Leontieva SV, Kostjukov VV. The vibronic absorption spectra and electronic states of proflavine in aqueous solution. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Li S, Hwang XY, Stav S, Breaker RR. The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds. RNA (NEW YORK, N.Y.) 2016; 22:530-41. [PMID: 26843526 PMCID: PMC4793209 DOI: 10.1261/rna.054890.115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/10/2015] [Indexed: 05/21/2023]
Abstract
The yjdF motif RNA is an orphan riboswitch candidate that almost exclusively associates with the yjdF protein-coding gene in many bacteria. The function of the YjdF protein is unknown, which has made speculation regarding the natural ligand for this putative riboswitch unusually challenging. By using a structure-probing assay for ligand binding, we found that a surprisingly broad diversity of nitrogen-containing aromatic heterocycles, or "azaaromatics," trigger near-identical changes in the structures adopted by representative yjdF motif RNAs. Regions of the RNA that undergo ligand-induced structural modulation reside primarily in portions of the putative aptamer region that are highly conserved in nucleotide sequence, as is typical for riboswitches. Some azaaromatic molecules are bound by the RNA with nanomolar dissociation constants, and a subset of these ligands activate riboswitch-mediated gene expression in cells. Furthermore, genetic elements most commonly adjacent to the yjdF motif RNA or to the yjdF protein-coding region are homologous to protein regulators implicated in mitigating the toxic effects of diverse phenolic acids or polycyclic compounds. Although the precise type of natural ligand sensed by yjdF motif RNAs remains unknown, our findings suggest that this riboswitch class might serve as part of a genetic response system to toxic or signaling compounds with chemical structures similar to azaaromatics.
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Affiliation(s)
- Sanshu Li
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Xue Ying Hwang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Shira Stav
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Ronald R Breaker
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
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Shestopalova AV, Pesina DA, Kashpur VA, Khorunzhaya OV. Hydration of DNA-binding biological active compounds: EHF dielectrometry and molecular modeling results. Struct Chem 2015. [DOI: 10.1007/s11224-015-0695-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kemp S, Wheate NJ, Stootman FH, Aldrich-Wright JR. The Host-Guest Chemistry of Proflavine with Cucurbit[6,7,8]urils. Supramol Chem 2007. [DOI: 10.1080/10610270601124019] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Sharon Kemp
- a School of Biomedical and Health Sciences, University of Western Sydney , Locked Bag 1797, Penrith South DC, NSW, 1797, Australia
| | - Nial J. Wheate
- a School of Biomedical and Health Sciences, University of Western Sydney , Locked Bag 1797, Penrith South DC, NSW, 1797, Australia
| | - Frank H. Stootman
- a School of Biomedical and Health Sciences, University of Western Sydney , Locked Bag 1797, Penrith South DC, NSW, 1797, Australia
| | - Janice R. Aldrich-Wright
- a School of Biomedical and Health Sciences, University of Western Sydney , Locked Bag 1797, Penrith South DC, NSW, 1797, Australia
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Westhof E, Sundaralingam M. Proflavine binding to poly(rC-rA) inverts the CD spectrum but not the helix handedness. J Biomol Struct Dyn 1984; 2:159-64. [PMID: 6400929 DOI: 10.1080/07391102.1984.10507554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The interaction of proflavine hemisulfate with the sodium salt of poly(rC-rA) in solution (unbuffered) yields an inverted (mirror-like) circular dichroism (CD) spectrum to that of the free poly(rC-rA). Simultaneously, an induced negative Cotton effect appears in the proflavine band region with a maximum at 467 nm and a slight shoulder at 420 nm. This observation may be explained as resulting from the formation of a poly(rC-rA).proflavine complex with the polynucleotide existing as a right-handed parallel chain duplex with the proflavine intercalated between the CpA sequence and not the ApC sequence. The intercalation geometry here is expected to be analogous to that found in the crystal structure of the dinucleotide CpA.proflavine complex (Westhof et al. J. Mol. Biol., 1981) which forms a miniature right-handed helix. Although normally an inverted spectra could be attributed to a reversal in the helix handedness, the similarity in the 31P nuclear magnetic resonance spectra between the free and proflavine bound poly(rC-rA) indicates that their handedness is the same. The inverted CD spectrum may be a result of the different stacking orientation between the intercalated proflavine and the A-A base-pair on one hand and the triply hydrogen bonded protonated C-C base-pair on the other.
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Affiliation(s)
- E Westhof
- Institut de Biologie Moleculaire et Cellulaire, Centre National de la Recherche Scientifique, Strasbourg, France
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Egly JM, Plassat JL, Boschetti E. Separation of single-stranded from double-stranded nucleic acids using acriflavin-agarose chromatography. J Chromatogr A 1982; 243:301-6. [PMID: 7119072 DOI: 10.1016/s0021-9673(00)82421-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Westhof E, Rao ST, Sundaralingam M. Crystallographic studies of drug-nucleic acid interactions: proflavine intercalation between the non-complementary base-pairs of cytidilyl-3',5'-adenosine. J Mol Biol 1980; 142:331-61. [PMID: 7463478 DOI: 10.1016/0022-2836(80)90276-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Abstract
Acridines and a very large number of acridine derivatives are used in enormous quantities both in medicine and industry. The mutagenic action of these compounds has been demonstrated in a wide variety of organisms and is known to occur both in the dark as well as in the presence of light (photodynamic action). At the molecular level, acridines have been shown to cause frameshift mutations of both the addition and deletion types, a characteristic which has been of tremendous help in elucidating the nature of the genetic code. These and various other biological effects of acridines, such as inhibition of DNA repair, curing of plasmids and cell-growth inhibition, are examined in this review.
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Roth D, London M. Acridine probe study into synergistic DNA-denaturing action of heat and ultraviolet light in squamous cells. J Invest Dermatol 1977; 69:368-72. [PMID: 903664 DOI: 10.1111/1523-1747.ep12510247] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Roth D. Effect of ultraviolet irradiation of DNA on the dissociation transition of the strong DNA-acriflavine complex. Photochem Photobiol 1973; 18:437-9. [PMID: 4796460 DOI: 10.1111/j.1751-1097.1973.tb06446.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Brinker JM, Madore HP, Bello LJ. Stabilization of heterogeneous nuclear RNA by intercalating drugs. Biochem Biophys Res Commun 1973; 52:928-34. [PMID: 4710572 DOI: 10.1016/0006-291x(73)91026-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Tal M, Rotem H, Alfasi M, Berg RA. The effect of acridine orange on the structure of ribosomes. Biopolymers 1973; 12:173-9. [PMID: 4568932 DOI: 10.1002/bip.1973.360120116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Balda BR, Birkmayer GD. Zur Hemmwirkung von Proflavin auf den Einbau von DNS-, RNS- und Proteinvorstufen im Hamstermelanom. Arch Dermatol Res 1972. [DOI: 10.1007/bf00595223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Gray PN, Saunders GF. Binding of ethidium bromide to 5-S ribosomal RNA. BIOCHIMICA ET BIOPHYSICA ACTA 1971; 254:60-77. [PMID: 4332416 DOI: 10.1016/0005-2787(71)90114-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Dourlent M, Hélène C. A quantitative analysis of proflavine binding to polyadenylic acid, polyuridylic acid, and transfer RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1971; 23:86-95. [PMID: 5127390 DOI: 10.1111/j.1432-1033.1971.tb01595.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Robison B, Zimmerman TP. A Conformational Study of Yeast Phenylalanine Transfer Ribonucleic Acid. J Biol Chem 1971. [DOI: 10.1016/s0021-9258(18)62539-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Madsen NP, Christie GS, Hegarty MP. Effect of indospicine on incorporation of L-arginine-14C into protein and transfer ribonucleic acid by cell-free systems from rat liver. Biochem Pharmacol 1970; 19:853-7. [PMID: 5507690 DOI: 10.1016/0006-2952(70)90247-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Bittman R. Studies of the binding of ethidium bromide to transfer ribonucleic acid: absorption, fluorescence, ultracentrifugation and kinetic investigations. J Mol Biol 1969; 46:251-68. [PMID: 4902518 DOI: 10.1016/0022-2836(69)90420-3] [Citation(s) in RCA: 89] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Krémers P, Fredericq E. Interactions of ribosomal RNA with synthetic and naural polybases. EUROPEAN JOURNAL OF BIOCHEMISTRY 1969; 9:275-9. [PMID: 5817027 DOI: 10.1111/j.1432-1033.1969.tb00605.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Roth D, Manjon ML. Studies of a specific association between acriflavine and DNA in intact cells. Biopolymers 1969; 7:695-705. [PMID: 5797713 DOI: 10.1002/bip.1969.360070507] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Grosjean H, Wérenne J, Chantrenne H. The binding of proflavine to transfer ribonucleic acid: dependence on secondary structure. BIOCHIMICA ET BIOPHYSICA ACTA 1968; 166:616-27. [PMID: 4881743 DOI: 10.1016/0005-2787(68)90368-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Abstract
X-ray structural analysis of a crystalline complex between acridine C(13)H(9)N, cytosine C(4)H(5)N(3)O, and water (1:1:1) has been completed. The cytosine and water molecules form a sheet-like structure through a series of hydrogen bonds. The acridine molecules are bound to this layer through a hydrogen bridge from the water to the ring nitrogen. The acridine molecules stack in a parallel fashion normal to the cytosine-water sheets, with an average interplanar spacing of 3.5 angstroms.
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