1
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Sarkar P, Gopi P, Pandya P, Paria S, Hossain M, Siddiqui MH, Alamri S, Bhadra K. Insights on the comparative affinity of ribonucleic acids with plant-based beta carboline alkaloid, harmine: Spectroscopic, calorimetric and computational evaluation. Heliyon 2024; 10:e34183. [PMID: 39100473 PMCID: PMC11295990 DOI: 10.1016/j.heliyon.2024.e34183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 08/06/2024] Open
Abstract
Small molecules as ligands target multifunctional ribonucleic acids (RNA) for therapeutic engagement. This study explores how the anticancer DNA intercalator harmine interacts various motifs of RNAs, including the single-stranded A-form poly (rA), the clover leaf tRNAphe, and the double-stranded A-form poly (rC)-poly (rG). Harmine showed the affinity to the polynucleotides in the order, poly (rA) > tRNAphe > poly (rC)·poly (rG). While no induced circular dichroism change was detected with poly (rC)poly (rG), significant structural alterations of poly (rA) followed by tRNAphe and occurrence of concurrent initiation of optical activity in the attached achiral molecule of alkaloid was reported. At 25 °C, the affinity further showed exothermic and entropy-driven binding. The interaction also highlighted heat capacity (ΔC o p ) and Gibbs energy contribution from the hydrophobic transfer (ΔG hyd) of binding with harmine. Molecular docking calculations indicated that harmine exhibits higher affinity for poly (rA) compared to tRNAphe and poly (rC)·poly (rG). Subsequent molecular dynamics simulations were conducted to investigate the binding mode and stability of harmine with poly(A), tRNAphe, and poly (rC)·poly (rG). The results revealed that harmine adopts a partial intercalative binding with poly (rA) and tRNAphe, characterized by pronounced stacking forces and stronger binding free energy observed with poly (rA), while a comparatively weaker binding free energy was observed with tRNAphe. In contrast, the stacking forces with poly (rC)·poly (rG) were comparatively less pronounced and adopts a groove binding mode. It was also supported by ferrocyanide quenching analysis. All these findings univocally provide detailed insight into the binding specificity of harmine, to single stranded poly (rA) over other RNA motifs, probably suggesting a self-structure formation in poly (rA) with harmine and its potential as a lead compound for RNA based drug targeting.
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Affiliation(s)
- Paromita Sarkar
- University of Kalyani, Department of Zoology, Nadia, W. Bengal, 741235, India
| | - Priyanka Gopi
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
| | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
| | - Samaresh Paria
- Vidyasagar University, Department of Chemistry, Midnapore 721 102, West Bengal, India
| | - Maidul Hossain
- Vidyasagar University, Department of Chemistry, Midnapore 721 102, West Bengal, India
| | - Manzer H. Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saud Alamri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Kakali Bhadra
- University of Kalyani, Department of Zoology, Nadia, W. Bengal, 741235, India
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2
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Cruz-Pulido YE, Mounce BC. Good cop, bad cop: Polyamines play both sides in host immunity and viral replication. Semin Cell Dev Biol 2023; 146:70-79. [PMID: 36604249 PMCID: PMC10101871 DOI: 10.1016/j.semcdb.2022.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 01/05/2023]
Abstract
Viruses rely on host cells for energy and synthesis machinery required for genome replication and particle assembly. Due to the dependence of viruses on host cells, viruses have evolved multiple mechanisms by which they can induce metabolic changes in the host cell to suit their specific requirements. The host immune response also involves metabolic changes to be able to react to viral insult. Polyamines are small ubiquitously expressed polycations, and their metabolism is critical for viral replication and an adequate host immune response. This is due to the variety of functions that polyamines have, ranging from condensing DNA to enhancing the translation of polyproline-containing proteins through the hypusination of eIF5A. Here, we review the diverse mechanisms by which viruses exploit polyamines, as well as the mechanisms by which immune cells utilize polyamines for their functions. Furthermore, we highlight potential avenues for further study of the host-virus interface.
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Affiliation(s)
- Yazmin E Cruz-Pulido
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Bryan C Mounce
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA; Infectious Disease and Immunology Research Institute, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA.
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3
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Azfar M, van Veen S, Houdou M, Hamouda NN, Eggermont J, Vangheluwe P. P5B-ATPases in the mammalian polyamine transport system and their role in disease. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119354. [PMID: 36064065 DOI: 10.1016/j.bbamcr.2022.119354] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
Polyamines (PAs) are physiologically relevant molecules that are ubiquitous in all organisms. The vitality of PAs to the healthy functioning of a cell is due to their polycationic nature causing them to interact with a vast plethora of cellular players and partake in numerous cellular pathways. Naturally, the homeostasis of such essential molecules is tightly regulated in a strictly controlled interplay between intracellular synthesis and degradation, uptake from and secretion to the extracellular compartment, as well as intracellular trafficking. Not surprisingly, dysregulated PA homeostasis and signaling are implicated in multiple disorders, ranging from cancer to neurodegeneration; leading many to propose rectifying the PA balance as a potential therapeutic strategy. Despite being well characterized in bacteria, fungi and plants, the molecular identity and properties of the PA transporters in animals are poorly understood. This review brings together the current knowledge of the cellular function of the mammalian PA transport system (PTS). We will focus on the role of P5B-ATPases ATP13A2-5 which are PA transporters in the endosomal system that have emerged as key players in cellular PA uptake and organelle homeostasis. We will discuss recent breakthroughs on their biochemical and structural properties as well as their implications for disease and therapy.
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Affiliation(s)
- Mujahid Azfar
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, KU Leuven, B-3000 Leuven, Belgium
| | - Sarah van Veen
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, KU Leuven, B-3000 Leuven, Belgium
| | - Marine Houdou
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, KU Leuven, B-3000 Leuven, Belgium
| | - Norin Nabil Hamouda
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Jan Eggermont
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Peter Vangheluwe
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, KU Leuven, B-3000 Leuven, Belgium.
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4
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Williams AM, Poudyal RR, Bevilacqua PC. Long Tracts of Guanines Drive Aggregation of RNA G-Quadruplexes in the Presence of Spermine. Biochemistry 2021; 60:2715-2726. [PMID: 34448586 DOI: 10.1021/acs.biochem.1c00467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
G-Quadruplexes (GQs) are compact, stable structures in DNA and RNA comprised of two or more tiers of quartets whose G-rich motif of tracts of two or more G's occurs commonly within genomes and transcriptomes. While thermodynamically stable in vitro, these structures remain difficult to study in vivo. One approach to understanding GQ in vivo behavior is to test whether conditions and molecules found in cells facilitate their folding. Polyamines are biogenic polycations that interact with RNA. Among common polyamines, spermine contains the highest charge and is found in eukaryotes, making it a good candidate for association with high-charge density nucleic acid structures like GQs. Using a variety of techniques, including ultraviolet-detected thermal denaturation, circular dichroism, size exclusion chromatography, and confocal microscopy, on an array of quadruplex sequence variants, we find that eukaryotic biological concentrations of spermine induce microaggregation of three-tiered G-rich sequences, but not of purely two-tiered structures, although higher spermine concentrations induce aggregation of even these. The formation of microaggregates can also be induced by addition of as little as a single G to a two-tiered structure; moreover, they form at biological temperatures, are sensitive to salt, and can form in the presence of at least some flanking sequence. Notably, GQ aggregation is not observed under prokaryotic-like conditions of no spermine and higher NaCl concentrations. The sequence, polyamine, and salt specificity of microaggregation reported herein have implications for the formation and stability of G-rich nucleic acid aggregates in vivo and for functional roles for understudied GQ sequences with only two quadruplex tiers.
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Affiliation(s)
- Allison M Williams
- Department of Biochemistry, Microbiology, and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Raghav R Poudyal
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Philip C Bevilacqua
- Department of Biochemistry, Microbiology, and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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5
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Winther KS, Sørensen MA, Svenningsen SL. Polyamines are Required for tRNA Anticodon Modification in Escherichia coli. J Mol Biol 2021; 433:167073. [PMID: 34058151 DOI: 10.1016/j.jmb.2021.167073] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/19/2021] [Accepted: 05/23/2021] [Indexed: 11/25/2022]
Abstract
Biogenic polyamines are natural aliphatic polycations formed from amino acids by biochemical pathways that are highly conserved from bacteria to humans. Their cellular concentrations are carefully regulated and dysregulation causes severe cell growth defects. Polyamines have high affinity for nucleic acids and are known to interact with mRNA, tRNA and rRNA to stimulate the translational machinery, but the exact molecular mechanism(s) for this stimulus is still unknown. Here we exploit that Escherichia coli is viable in the absence of polyamines, including the universally conserved putrescine and spermidine. Using global macromolecule labelling approaches we find that ribosome efficiency is reduced by 50-70% in the absence of polyamines and this reduction is caused by slow translation elongation speed. The low efficiency causes rRNA and multiple tRNA species to be overproduced in the absence of polyamines, suggesting an impact on the feedback regulation of stable RNA transcription. Importantly, we find that polyamine deficiency affects both tRNA levels and tRNA modification patterns. Specifically, a large fraction of tRNAhis, tRNAtyr and tRNAasn lack the queuosine modification in the anticodon "wobble" base, which can be reversed by addition of polyamines to the growth medium. In conclusion, we demonstrate that polyamines are needed for modification of specific tRNA, possibly by facilitating the interaction with modification enzymes.
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Affiliation(s)
| | - Michael Askvad Sørensen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Sine Lo Svenningsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
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6
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Mastrodomenico V, Esin JJ, Qazi S, Khomutov MA, Ivanov AV, Mukhopadhyay S, Mounce BC. Virion-Associated Polyamines Transmit with Bunyaviruses to Maintain Infectivity and Promote Entry. ACS Infect Dis 2020; 6:2490-2501. [PMID: 32687697 DOI: 10.1021/acsinfecdis.0c00402] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Viruses require host cell metabolites to productively infect, and the mechanisms by which viruses usurp these molecules are diverse. One group of cellular metabolites important in virus infection is the polyamines, small positively charged molecules involved in cell cycle, translation, and nucleic acid metabolism, among other cellular functions. Polyamines support replication of diverse viruses, and they are important for processes such as transcription, translation, and viral protein enzymatic activity. Rift Valley fever virus (RVFV) is a negative and ambisense RNA virus that requires polyamines to produce infectious particles. In polyamine depleted conditions, noninfectious particles are produced that interfere with virus replication and stimulate immune signaling. Here, we find that RVFV relies on virion-associated polyamines to maintain infectivity and enhance viral entry. We show that RVFV replication is facilitated by a limited set of polyamines and that spermidine and closely related molecules associate with purified virions and transmit from cell to cell during infection. Virion-associated spermidine maintains virion infectivity, as virions devoid of polyamines rapidly lose infectivity and are temperature sensitive. Further, virions without polyamines bind to cells but exhibit a defect in entry, requiring more acidic conditions than virions containing spermidine. These data highlight a unique role for polyamines, and spermidine particularly, to maintain virus infectivity. Further, these studies are the first to identify polyamines associated with RVFV virions. Targeting polyamines represents a promising antiviral strategy, and this work highlights a new mechanism by which we can inhibit virus replication through FDA-approved polyamine depleting pharmaceuticals.
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Affiliation(s)
- Vincent Mastrodomenico
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois 60153, United States
| | - Jeremy J. Esin
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois 60153, United States
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois 60153, United States
| | - Shefah Qazi
- Department of Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - Maxim A. Khomutov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexander V. Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | | | - Bryan C. Mounce
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois 60153, United States
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois 60153, United States
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7
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Chanphai P, Cloutier F, Reyes-Moreno C, Bérubé G, Tajmir-Riahi HA. Locating the binding sites of two aminobenzoic acid derivatives on tRNA: drug binding efficacy and RNA structure. J Biomol Struct Dyn 2020; 40:130-135. [PMID: 32811341 DOI: 10.1080/07391102.2020.1808076] [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: 10/23/2022]
Abstract
The binding of tRNA to aminobenzoic acid derivatives DAB-0 (N'-[4-(2,5-dioxo-pyrrolidin-1-yl)-benzoyl]-hydrazine carboxylic acid tert-butyl ester) and DAB-1 (N'-[4-(2,5-dioxo-2,5-dihydro-pyrrol-1-yl)-benzoyl]-hydrazine carboxylic acid tert-butyl ester) was investigated in aqueous solution at physiological pH. Thermodynamic parameters ΔH0 -4.8 to -4.30 (kJ mol-1), ΔS0 24.20 to 22 (J mol-1K-1) and ΔG0 -12 to -11.40 (kJ mol-1) showed that DAB-0 and DAB-1 readily bind tRNA via ionic interactions with DAB-1 forming stronger tRNA adducts. Similar binding sites to A-T and G-C bases were located with DAB-0 and DAB-1. The binding efficacy ranged from 40% to 50%. No alteration of tRNA conformation was detected upon drug complexation. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Penparapa Chanphai
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Francis Cloutier
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada.,Groupe de Recherche en Signalisation Cellulaire, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Carlos Reyes-Moreno
- Groupe de Recherche en Signalisation Cellulaire, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada.,Department of Medical Biology, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Gervais Bérubé
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada.,Groupe de Recherche en Signalisation Cellulaire, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Heidar-Ali Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
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8
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Chanphai P, Tajmir-Riahi H. Vitamin C binding efficacy with DNA and RNA. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.110925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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9
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Hori H. Regulatory Factors for tRNA Modifications in Extreme- Thermophilic Bacterium Thermus thermophilus. Front Genet 2019; 10:204. [PMID: 30906314 PMCID: PMC6418473 DOI: 10.3389/fgene.2019.00204] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/26/2019] [Indexed: 01/02/2023] Open
Abstract
Thermus thermophilus is an extreme-thermophilic bacterium that can grow at a wide range of temperatures (50-83°C). To enable T. thermophilus to grow at high temperatures, several biomolecules including tRNA and tRNA modification enzymes show extreme heat-resistance. Therefore, the modified nucleosides in tRNA from T. thermophilus have been studied mainly from the view point of tRNA stabilization at high temperatures. Such studies have shown that several modifications stabilize the structure of tRNA and are essential for survival of the organism at high temperatures. Together with tRNA modification enzymes, the modified nucleosides form a network that regulates the extent of different tRNA modifications at various temperatures. In this review, I describe this network, as well as the tRNA recognition mechanism of individual tRNA modification enzymes. Furthermore, I summarize the roles of other tRNA stabilization factors such as polyamines and metal ions.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Sciences and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
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10
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Chanphai P, Tajmir-Riahi HA. Effect of tea catechins on tRNA structure and dynamics. J Biomol Struct Dyn 2019; 38:302-306. [PMID: 30739592 DOI: 10.1080/07391102.2019.1570869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
AbbreviationsCcatechinECGepicatechin gallateEGCGEpigallocatechin gallateAAdenineCcytosineGGuanineUuracilFTIRFourier transform infraredCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- P Chanphai
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, QC, Canada
| | - H A Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, QC, Canada
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11
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Chanphai P, Ouellette V, Mandal S, Mandal SK, Bérubé G, Tajmir-Riahi HA. Location of multiple binding sites for testo and testo-Pt(II) with tRNA. J Biomol Struct Dyn 2018; 37:4133-4139. [PMID: 30417741 DOI: 10.1080/07391102.2018.1541142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report the binding of testo and testo-Pt(II) complexes (testosterone derivatives) with tRNA in aqueous solution at physiological pH. Thermodynamic parameter ΔH0 -8 to -3 (kJ mol-1), ΔS0 35 to 18 (J mol-1K-1) and ΔG0 -14 to -13 (kJ mol-1) and other spectroscopic results showed drug-tRNA binding occurs via ionic contacts with testo-Pt(II) forming more stable tRNA complexes in comparison to testo: Ktesto-Pt(II)-tRNA= 3.2 (± 0.9) × 105 M-1 > Ktesto-tRNA= 2.1 (± 0.7) × 105 M-1. Molecular modeling showed multiple binding sites for testo and testo-Pt(II) on tRNA molecule. Some of the useful molecular descriptors are calculated. Major structural changes were observed for biopolymers upon drug complexation, while tRNA remains in the A-family structures.
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Affiliation(s)
- P Chanphai
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières C. P. 500 , Trois-Rivières , QC , Canada
| | - V Ouellette
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières C. P. 500 , Trois-Rivières , QC , Canada
| | - S Mandal
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Department of Physiology and Pathophysiology, College of Medicine, Rady Faculty of Health Sciences, University of Manitoba , Winnipeg , MB , Canada
| | - S K Mandal
- St. John's, Newfoundland, Canada and College of the North Atlantic, Faculty of Medicine, Memorial University of Newfoundland , Newfoundland , Canada
| | - G Bérubé
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières C. P. 500 , Trois-Rivières , QC , Canada
| | - H A Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières C. P. 500 , Trois-Rivières , QC , Canada
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12
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Hori H, Kawamura T, Awai T, Ochi A, Yamagami R, Tomikawa C, Hirata A. Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA. Microorganisms 2018; 6:E110. [PMID: 30347855 PMCID: PMC6313347 DOI: 10.3390/microorganisms6040110] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/11/2022] Open
Abstract
To date, numerous modified nucleosides in tRNA as well as tRNA modification enzymes have been identified not only in thermophiles but also in mesophiles. Because most modified nucleosides in tRNA from thermophiles are common to those in tRNA from mesophiles, they are considered to work essentially in steps of protein synthesis at high temperatures. At high temperatures, the structure of unmodified tRNA will be disrupted. Therefore, thermophiles must possess strategies to stabilize tRNA structures. To this end, several thermophile-specific modified nucleosides in tRNA have been identified. Other factors such as RNA-binding proteins and polyamines contribute to the stability of tRNA at high temperatures. Thermus thermophilus, which is an extreme-thermophilic eubacterium, can adapt its protein synthesis system in response to temperature changes via the network of modified nucleosides in tRNA and tRNA modification enzymes. Notably, tRNA modification enzymes from thermophiles are very stable. Therefore, they have been utilized for biochemical and structural studies. In the future, thermostable tRNA modification enzymes may be useful as biotechnology tools and may be utilized for medical science.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takuya Kawamura
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takako Awai
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Anna Ochi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
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13
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Lomozik L, Bregier-Jarzebowska R, Gasowska A, Hoffmann S, Zalewska A. Biocoordination reactions in copper(II) ions and l-glutamic acid systems including tetramines: 1,11-diamino-4,8-diazaundecane or 1,12-diamino-4,9-diazadodecane. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.07.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Chanphai P, Tajmir-Riahi H. Binding efficacy of tRNA with folic acid-PAMAM nanoparticles. Int J Biol Macromol 2018; 114:851-854. [DOI: 10.1016/j.ijbiomac.2018.03.181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 03/29/2018] [Accepted: 03/30/2018] [Indexed: 11/26/2022]
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15
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Whitham JM, Moon JW, Rodriguez M, Engle NL, Klingeman DM, Rydzak T, Abel MM, Tschaplinski TJ, Guss AM, Brown SD. Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:98. [PMID: 29632556 PMCID: PMC5887222 DOI: 10.1186/s13068-018-1095-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 03/24/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Clostridium (Ruminiclostridium) thermocellum is a model fermentative anaerobic thermophile being studied and engineered for consolidated bioprocessing of lignocellulosic feedstocks into fuels and chemicals. Engineering efforts have resulted in significant improvements in ethanol yields and titers although further advances are required to make the bacterium industry-ready. For instance, fermentations at lower pH could enable co-culturing with microbes that have lower pH optima, augment productivity, and reduce buffering cost. C. thermocellum is typically grown at neutral pH, and little is known about its pH limits or pH homeostasis mechanisms. To better understand C. thermocellum pH homeostasis we grew strain LL1210 (C. thermocellum DSM1313 Δhpt ΔhydG Δldh Δpfl Δpta-ack), currently the highest ethanol producing strain of C. thermocellum, at different pH values in chemostat culture and applied systems biology tools. RESULTS Clostridium thermocellum LL1210 was found to be growth-limited below pH 6.24 at a dilution rate of 0.1 h-1. F1F0-ATPase gene expression was upregulated while many ATP-utilizing enzymes and pathways were downregulated at pH 6.24. These included most flagella biosynthesis genes, genes for chemotaxis, and other motility-related genes (> 50) as well as sulfate transport and reduction, nitrate transport and nitrogen fixation, and fatty acid biosynthesis genes. Clustering and enrichment of differentially expressed genes at pH values 6.48, pH 6.24 and pH 6.12 (washout conditions) compared to pH 6.98 showed inverse differential expression patterns between the F1F0-ATPase and genes for other ATP-utilizing enzymes. At and below pH 6.24, amino acids including glutamate and valine; long-chain fatty acids, their iso-counterparts and glycerol conjugates; glycolysis intermediates 3-phosphoglycerate, glucose 6-phosphate, and glucose accumulated intracellularly. Glutamate was 267 times more abundant in cells at pH 6.24 compared to pH 6.98, and intercellular concentration reached 1.8 μmol/g pellet at pH 5.80 (stopped flow). CONCLUSIONS Clostridium thermocellum LL1210 can grow under slightly acidic conditions, similar to limits reported for other strains. This foundational study provides a detailed characterization of a relatively acid-intolerant bacterium and provides genetic targets for strain improvement. Future studies should examine adding gene functions used by more acid-tolerant bacteria for improved pH homeostasis at acidic pH values.
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Affiliation(s)
- Jason M. Whitham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Ji-Won Moon
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Thomas Rydzak
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
- Present Address: Department of Biological Science, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Malaney M. Abel
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Adam M. Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
- BioEnergy Science Center, National Laboratory, Oak Ridge, TN USA
- Present Address: LanzaTech, Inc., Skokie, IL USA
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Bignon E, Chan CH, Morell C, Monari A, Ravanat JL, Dumont E. Molecular Dynamics Insights into Polyamine-DNA Binding Modes: Implications for Cross-Link Selectivity. Chemistry 2017; 23:12845-12852. [DOI: 10.1002/chem.201702065] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Emmanuelle Bignon
- Institut des Sciences Analytiques, UMR 5280; Université de Lyon 1 (UCBL) CNRS, ENS Lyon; Lyon France
- Laboratoire de Chimie; Univ Lyon; Ecole Normale Supérieure de Lyon, CNRS UMR 5182; Université Lyon 1; Laboratoire de Chimie; 46 allée d'Italie 69364 Lyon France
| | - Chen-Hui Chan
- Laboratoire de Chimie; Univ Lyon; Ecole Normale Supérieure de Lyon, CNRS UMR 5182; Université Lyon 1; Laboratoire de Chimie; 46 allée d'Italie 69364 Lyon France
| | - Christophe Morell
- Institut des Sciences Analytiques, UMR 5280; Université de Lyon 1 (UCBL) CNRS, ENS Lyon; Lyon France
| | - Antonio Monari
- Université de Lorraine Nancy; Theory-Modeling-Simulation, SRSMC; 54506 Vandoeuvre-lès-Nancy France
- CNRS; UMR 7565, SRSMC; 54506 Vandoeuvre-lès- Nancy France
| | - Jean-Luc Ravanat
- CEA and Université Grenoble Alpes, INAC-SyMMES; 38000 Grenoble France
| | - Elise Dumont
- Laboratoire de Chimie; Univ Lyon; Ecole Normale Supérieure de Lyon, CNRS UMR 5182; Université Lyon 1; Laboratoire de Chimie; 46 allée d'Italie 69364 Lyon France
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17
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Chanphai P, Tajmir-Riahi HA. tRNA conjugation with folic acid-chitosan conjugates. Int J Biol Macromol 2017; 105:810-815. [PMID: 28735004 DOI: 10.1016/j.ijbiomac.2017.07.113] [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: 06/27/2017] [Revised: 07/15/2017] [Accepted: 07/17/2017] [Indexed: 01/06/2023]
Abstract
The conjugation of tRNA with folic acid-chitosan conjugates was studied, using multiple spectroscopic methods and transmission electron microscopy (TEM). Thermodynamic analysis ΔH -14 to -10 (KJMol-1) and ΔS 14 to -1 (JMol-1, K-1) showed tRNA-folic acid-chitosan bindings occur via H-bonding, hydrophobic and van der Waals contacts. The loading efficacy and the stability of tRNA conjugates were enhanced as folic acid-chitosan size increased. TEM analysis showed major tRNA morphological changes, upon folic acid-chitosan conjugation. No alteration of tRNA conformation was observed on conjugate formation. Folic acid-chitosan conjugates can deliver tRNA in vitro.
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Affiliation(s)
- P Chanphai
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, G9A 5H7, Canada
| | - H A Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, G9A 5H7, Canada.
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18
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Nakashima M, Yamagami R, Tomikawa C, Ochi Y, Moriya T, Asahara H, Fourmy D, Yoshizawa S, Oshima T, Hori H. Long and branched polyamines are required for maintenance of the ribosome, tRNAHisand tRNATyrinThermus thermophiluscells at high temperatures. Genes Cells 2017; 22:628-645. [DOI: 10.1111/gtc.12502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 04/19/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Misa Nakashima
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Yuki Ochi
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Toshiyuki Moriya
- Institute of Environmental Microbiology; Kyowa Kako Co. Ltd.; Tadao 2-15-5 Machida 194-0035 Japan
| | - Haruichi Asahara
- New England Biolabs, Inc; 240 County Road Ipswich Massachusetts 01938 USA
| | - Dominique Fourmy
- Institute for Integrative Biology of the Cell (I2BC); CEA, CNRS; Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Satoko Yoshizawa
- Institute for Integrative Biology of the Cell (I2BC); CEA, CNRS; Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Tairo Oshima
- Institute of Environmental Microbiology; Kyowa Kako Co. Ltd.; Tadao 2-15-5 Machida 194-0035 Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
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19
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Oguro A, Yanagida A, Fujieda Y, Amano R, Otsu M, Sakamoto T, Kawai G, Matsufuji S. Two stems with different characteristics and an internal loop in an RNA aptamer contribute to spermine-binding. J Biochem 2017; 161:197-206. [PMID: 28173167 DOI: 10.1093/jb/mvw062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 08/30/2016] [Indexed: 11/14/2022] Open
Abstract
Though polyamines (putrescine, spermidine, and spermine) bind to the specific position in RNA molecules, interaction mechanisms are poorly understood. SELEX procedure has been used to isolate high-affinity oligoribonucleotides (aptamers) from randomized RNA libraries. Selected aptamers are useful in exploring sequences and/or structures in RNAs for binding molecules. In this study, to analyze the interaction mechanism of polyamine to RNA, we selected RNA aptamers targeted for spermine. Two spermine-binding aptamers (#5 and #24) were obtained and both of them had two stem-loop structures. The 3′ stem-loop of #5 (SL_2) bound to spermine more effectively than the 5′ stem-loop of #5 did. A thermodynamic analysis by an isothermal titration calorimetry revealed that the dissociation constant of SL_2 for spermine was 27.2 μM and binding ratio was nearly 1:1. Binding assay with base-pair replaced variants showed that two stem regions and an internal loop in SL_2 were important for their spermine-binding activities. NMR analyses proposed that a terminal-side and a loop-side stem in SL_2 take a loose and a stable structure, respectively and a conformational change of SL_2 is induced by spermine. It is conclusive that two stems with different characteristics and an internal loop in SL_2 contribute to the specific spermine-binding.
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Affiliation(s)
- Akihiro Oguro
- Department of Molecular Biology, The Jikei University School of Medicine, 3-25-8 Nishi-Shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Asumi Yanagida
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Yuta Fujieda
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Ryo Amano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Maina Otsu
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Senya Matsufuji
- Department of Molecular Biology, The Jikei University School of Medicine, 3-25-8 Nishi-Shinbashi, Minato-ku, Tokyo 105-8461, Japan
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20
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Ouimet CM, D’Amico CI, Kennedy RT. Advances in capillary electrophoresis and the implications for drug discovery. Expert Opin Drug Discov 2017; 12:213-224. [PMID: 27911223 PMCID: PMC5521262 DOI: 10.1080/17460441.2017.1268121] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Many screening platforms are prone to assay interferences that can be avoided by directly measuring the target or enzymatic product. Capillary electrophoresis (CE) and microchip electrophoresis (MCE) have been applied in a variety of formats to drug discovery. CE provides direct detection of the product allowing for the identification of some forms of assay interference. The high efficiency, rapid separations, and low volume requirements make CE amenable to drug discovery. Areas covered: This article describes advances in capillary electrophoresis throughput, sample introduction, and target assays as they pertain to drug discovery and screening. Instrumental advances discussed include integrated droplet microfluidics platforms and multiplexed arrays. Applications of CE to assays of diverse drug discovery targets, including enzymes and affinity interactions are also described. Expert opinion: Current screening with CE does not fully take advantage of the throughputs or low sample volumes possible with CE and is most suitable as a secondary screening method or for screens that are inaccessible with more common platforms. With further development, droplet microfluidics coupled to MCE could take advantage of the low sample requirements by performing assays on the nanoliter scale at high throughput.
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Affiliation(s)
- Claire M. Ouimet
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI, 48109, United States
| | - Cara I. D’Amico
- Department of Pharmacology, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109, United States
| | - Robert T. Kennedy
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI, 48109, United States
- Department of Pharmacology, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109, United States
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21
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Chanphai P, Agudelo D, Vesper AR, Bérubé G, Tajmir-Riahi HA. Testosterone and its dimers alter tRNA morphology. J Pharm Biomed Anal 2016; 134:269-274. [PMID: 27930994 DOI: 10.1016/j.jpba.2016.11.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 11/28/2016] [Indexed: 12/28/2022]
Abstract
The morphology of tRNA was studied upon conjugation with testosterone and its aliphatic and aromatic dimers, using multiple spectroscopic methods, transmission electron microscopy (TEM) and molecular modeling. Structural analysis showed that testosterone binds tRNA through A62, A64, C60, C61, C63, G51, U50 and U59 bases. The binding affinity was testosterone dimer-aromatic>testosterone dimer-aliphatic>testosterone. The steroid loading efficacy was 35-45%. Transmission electron microscopy showed major changes in tRNA morphology upon testosterone interaction with an increase in the diameter of the tRNA aggregate, indicating encapsulation of testosterone by tRNA.
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Affiliation(s)
- P Chanphai
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec G9A 5H7, Canada
| | - D Agudelo
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec G9A 5H7, Canada
| | - A R Vesper
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec G9A 5H7, Canada
| | - G Bérubé
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec G9A 5H7, Canada
| | - H A Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec G9A 5H7, Canada.
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22
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Agarwal S, Tyagi G, Chadha D, Mehrotra R. Structural-conformational aspects of tRNA complexation with chloroethyl nitrosourea derivatives: A molecular modeling and spectroscopic investigation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 166:1-11. [PMID: 27838504 DOI: 10.1016/j.jphotobiol.2016.09.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 09/18/2016] [Accepted: 09/20/2016] [Indexed: 11/19/2022]
Abstract
Chloroethyl nitrosourea derivatives (CENUs) represent an important family of anticancer chemotherapeutic agents, which are used in the treatment of different types of cancer such as brain tumors, resistant or relapsed Hodgkin's disease, small cell lung cancer and malignant melanoma. This work focuses towards understanding the interaction of chloroethyl nitrosourea derivatives; lomustine, nimustine and semustine with tRNA using spectroscopic approach in order to elucidate their auxiliary anticancer action mechanism inside the cell. Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR), Fourier transform infrared difference spectroscopy, circular dichroism spectroscopy and UV-visible spectroscopy were employed to investigate the binding parameters of tRNA-CENUs complexation. Results of present study demonstrate that all CENUs, studied here, interact with tRNA through guanine nitrogenous base residues and possibly further crosslink cytosine residues in paired region of tRNA. Moreover, spectral data collected for nimustine-tRNA and semustine-tRNA complex formation indicates towards the groove-directed-alkylation as their anti-malignant action, which involves the participation of uracil moiety located in major groove of tRNA. Besides this, tRNA-CENUs adduct formation did not alter the native conformation of biopolymer and tRNA remains in A-form after its interaction with all three nitrosourea derivatives studied. The binding constants (Ka) estimated for tRNA complexation with lomustine, nimustine and semustine are 2.55×102M-1, 4.923×102M-1 and 4.223×102M-1 respectively, which specify weak type of CENU's binding with tRNA. Moreover, molecular modeling simulations were also performed to predict preferential binding orientation of CENUs with tRNA that corroborates well with spectral outcomes. The findings, presented here, recognize tRNA binding properties of CENUs that can further help in rational designing of more specific and efficient RNA targeted chemotherapeutic agents.
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Affiliation(s)
- Shweta Agarwal
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India; Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Gunjan Tyagi
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Deepti Chadha
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India; Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Ranjana Mehrotra
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India; Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India.
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23
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Ray B, Agarwal S, Kadian H, Gambhir K, Sharma P, Mehrotra R. Deciphering molecular aspects of interaction between anticancer drug mitoxantrone and tRNA. J Biomol Struct Dyn 2016; 35:2090-2102. [DOI: 10.1080/07391102.2016.1213185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Bhumika Ray
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Shweta Agarwal
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Heena Kadian
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Kaweri Gambhir
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Parag Sharma
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Ranjana Mehrotra
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
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Bhattacharjee P, Sarkar S, Pandya P, Bhadra K. Targeting different RNA motifs by beta carboline alkaloid, harmalol: a comparative photophysical, calorimetric, and molecular docking approach. J Biomol Struct Dyn 2016; 34:2722-2740. [DOI: 10.1080/07391102.2015.1126694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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25
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Review on the binding of anticancer drug doxorubicin with DNA and tRNA: Structural models and antitumor activity. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 158:274-9. [PMID: 26971631 DOI: 10.1016/j.jphotobiol.2016.02.032] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/13/2016] [Indexed: 01/08/2023]
Abstract
In this review, we have compared the results of multiple spectroscopic studies and molecular modeling of anticancer drug doxorubicin (DOX) bindings to DNA and tRNA. DOX was intercalated into DNA duplex, while tRNA binding is via major and minor grooves. DOX-DNA intercalation is close to A-7, C-5, *C-19 (H-bonding with DOX NH2 group), G-6, T-8 and T-18 with the free binding energy of -4.99kcal/mol. DOX-tRNA groove bindings are near A-29, A-31, A-38, C-25, C-27, C-28, *G-30 (H-bonding) and U-41 with the free binding energy of -4.44kcal/mol. Drug intercalation induced a partial B to A-DNA transition, while tRNA remained in A-family structure. The structural differences observed between DOX bindings to DNA and tRNA can be the main reasons for drug antitumor activity. The results of in vitro MTT assay on SKC01 colon carcinoma are consistent with the observed DNA structural changes. Future research should be focused on finding suitable nanocarriers for delivery of DOX in vivo in order to exploit the full capacity of this very important anticancer drug.
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26
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Tian Z, Huang Y, Zhang Y, Song L, Qiao Y, Xu X, Wang C. Spectroscopic and molecular modeling methods to study the interaction between naphthalimide-polyamine conjugates and DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 158:1-15. [PMID: 26926663 DOI: 10.1016/j.jphotobiol.2016.01.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/29/2016] [Indexed: 11/28/2022]
Abstract
The effect of polyamine side chains on the interaction between naphthalimide-polyamine conjugates (1-7) and herring sperm DNA was studied by UV/vis absorption and fluorescent spectra under physiological conditions (pH=7.4). The diverse spectral data and further molecular docking simulation in silico indicated that the aromatic moiety of these compounds could intercalate into the DNA base pairs while the polyamine motif might simultaneously locate in the minor groove. The triamine compound 7 can interact more potently with DNA than the corresponding diamine compounds (1-6). The presence of the bulky terminal group in the diamine side chain reduced the binding strength of compound 1 with DNA, compared to other diamine compounds (2-6). In addition, the increasing methylene number in the diamine backbone generally results in the elevated binding constant of compounds-DNA complex. The fluorescent tests at different temperature revealed that the quenching mechanism was a static type. The binding constant and thermodynamic parameter showed that the binding strength and the type of interaction force, associated with the side chains, were mainly hydrogen bonding and hydrophobic force. And the calculated free binding energies of molecular docking are generally consistent with the stability of polyamine-DNA complexes. The circular dichroism assay about the impact of compounds 1-7 on DNA conformation testified the B to A-like conformational change.
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Affiliation(s)
- Zhiyong Tian
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Yingying Huang
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Yan Zhang
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Lina Song
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Yan Qiao
- Basic Medical College, Zhengzhou University, Zhengzhou, 475008, China; State Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xuejun Xu
- Basic Medical College, Zhengzhou University, Zhengzhou, 475008, China; The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, china.
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, china.
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27
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Hori H, Terui Y, Nakamoto C, Iwashita C, Ochi A, Watanabe K, Oshima T. Effects of polyamines from Thermus thermophilus, an extreme-thermophilic eubacterium, on tRNA methylation by tRNA (Gm18) methyltransferase (TrmH). J Biochem 2015; 159:509-17. [PMID: 26721905 DOI: 10.1093/jb/mvv130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/05/2015] [Indexed: 12/13/2022] Open
Abstract
Thermus thermophilus is an extreme-thermophilic eubacterium, which grows at a wide range of temperatures (50-83°C). This thermophile produces various polyamines including long and branched polyamines. In tRNAs from T. thermophilus, three distinct modifications, 2'-O-methylguanosine at position 18 (Gm18), 5-methyl-2-thiouridine at position 54 and N(1)-methyladenosine at position 58, are assembled at the elbow region to stabilize the L-shaped tRNA structure. However, the structures of unmodified tRNA precursors are disrupted at high temperatures. We hypothesize that polyamine(s) might have a positive effect on the modification process of unmodified tRNA transcript. We investigated the effects of eight polyamines on Gm18 formation in the yeast tRNA(Phe) transcript by tRNA (Gm18) methyltransferase (TrmH). Higher concentrations of linear polyamines inhibited TrmH activity at 55°C, while optimum concentration increased TrmH activity at 45-75°C. Exceptionally, caldohexamine, a long polyamine, did not show any positive effect on the TrmH activity at 55°C. However, temperature-dependent experiments revealed that 1 mM caldohexamine increased TrmH activity at 60-80°C. Furthermore, 0.25 mM tetrakis(3-aminopropy)ammonium, a branched polyamine, increased TrmH activity at a broad range of temperatures (40-85°C). Thus, caldohexamine and tetrakis(3-aminopropy)ammonium were found to enhance the TrmH activity at high temperatures.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577;
| | - Yusuke Terui
- Faculty of Pharmacy, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba; and
| | - Chisato Nakamoto
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577
| | - Chikako Iwashita
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577
| | - Anna Ochi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577
| | - Kazunori Watanabe
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577
| | - Tairo Oshima
- Institute of Environmental Microbiology, Kyowa Kako Co. Ltd., Tadao 2-15-5, Machida 194-0035, Japan
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Agudelo D, Kreplak L, Tajmir-Riahi HA. tRNA conjugation with chitosan nanoparticles: An AFM imaging study. Int J Biol Macromol 2015; 85:150-6. [PMID: 26723249 DOI: 10.1016/j.ijbiomac.2015.12.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 02/06/2023]
Abstract
The conjugation of tRNA with chitosan nanoparticles of different sizes 15,100 and 200 kDa was investigated in aqueous solution using multiple spectroscopic methods and atomic force microscopy (AFM). Structural analysis showed that chitosan binds tRNA via G-C and A-U base pairs as well as backbone PO2 group, through electrostatic, hydrophilic and H-bonding contacts with overall binding constants of KCh-15-tRNA=4.1 (±0.60)×10(3)M(-1), KCh-100-tRNA=5.7 (±0.8)×10(3)M(-1) and KCh-200-tRNA=1.2 (±0.3)×10(4)M(-1). As chitosan size increases more stable polymer-tRNA conjugate is formed. AFM images showed major tRNA aggregation and particle formation occurred as chitosan concentration increased. Even though chitosan induced major biopolymer structural changes, tRNA remains in A-family structure.
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Affiliation(s)
- D Agudelo
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada
| | - L Kreplak
- Department of Physics and Atmospheric Science, Sir James Dunn Building Dalhousie University, Lord Dalhousie Drive, Halifax, NS B3H4R2, Canada
| | - H A Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada.
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Liu J, Zeng C, Hogan V, Zhou S, Monwar MM, Hines JV. Identification of Spermidine Binding Site in T-box Riboswitch Antiterminator RNA. Chem Biol Drug Des 2015; 87:182-9. [PMID: 26348362 DOI: 10.1111/cbdd.12660] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 07/24/2015] [Accepted: 08/14/2015] [Indexed: 01/08/2023]
Abstract
The T-box transcription antitermination riboswitch controls bacterial gene expression by structurally responding to uncharged, cognate tRNA. Previous studies indicated that cofactors, such as the polyamine spermidine, might serve a specific functional role in enhancing riboswitch efficacy. As riboswitch function depends on key RNA structural changes involving the antiterminator element, the interaction of spermidine with the T-box riboswitch antiterminator element was investigated. Spermidine binds antiterminator model RNA with high affinity (micromolar Kd ) based on isothermal titration calorimetry and fluorescence-monitored binding assays. NMR titration studies, molecular modeling, and inline and enzymatic probing studies indicate that spermidine binds at the 3' portion of the highly conserved seven-nucleotide bulge in the antiterminator. Together, these results support the conclusion that spermidine binds the T-box antiterminator RNA preferentially in a location important for antiterminator function. The implications of these findings are significant both for better understanding of the T-box riboswitch mechanism and for antiterminator-targeted drug discovery efforts.
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Affiliation(s)
- Jia Liu
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Chunxi Zeng
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Vivian Hogan
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Shu Zhou
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Md Masud Monwar
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Jennifer V Hines
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
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Abstract
The T box riboswitch is an intriguing potential target for antibacterial drug discovery. Found primarily in Gram-positive bacteria, the riboswitch regulates gene expression by selectively responding to uncharged tRNA to control transcription readthrough. Polyamines and molecular crowding are known to specifically affect RNA function, but their effect on T box riboswitch efficacy and tRNA affinity have not been fully characterized. A fluorescence-monitored in vitro transcription assay was developed to readily quantify these molecular interactions and to provide a moderate-throughput functional assay for a comprehensive drug discovery screening cascade. The polyamine spermidine specifically enhanced T box riboswitch readthrough efficacy with an EC50 = 0.58 mM independent of tRNA binding. Molecular crowding, simulated by the addition of polyethylene glycol, had no effect on tRNA affinity for the riboswitch, but did reduce the efficacy of tRNA-induced readthrough. These results indicate that the T box riboswitch tRNA affinity and readthrough efficacy are intricately modulated by environmental factors.
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N'soukpoé-Kossi CN, Bourassa P, Mandeville JS, Bekale L, Bariyanga J, Tajmir-Riahi HA. Locating the binding sites of antioxidants resveratrol, genistein and curcumin with tRNA. Int J Biol Macromol 2015; 80:41-7. [PMID: 26093317 DOI: 10.1016/j.ijbiomac.2015.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/03/2015] [Accepted: 06/06/2015] [Indexed: 12/26/2022]
Abstract
We located the binding sites of antioxidants resveratrol, genistein and curcumin on tRNA in aqueous solution at physiological conditions using constant tRNA concentration and various polyphenol contents. FTIR, UV-visible, CD spectroscopic methods and molecular modeling were used to determine polyphenol binding sites, the binding constant and the effects of polyphenol complexation on tRNA conformation and particle formation. Structural analysis showed that polyphenols bind tRNA via G-C and A-U base pairs through hydrophilic, hydrophobic and H-bonding contacts with overall binding constants of K(res-tRNA)=8.95(±0.80)×10(3) M(-1), K(gen-tRNA)=3.07(±0.5)×10(3) M(-1) and K(cur-tRNA)=1.55(±0.3)×10(4) M(-1). Molecular modeling showed the participation of several nucleobases in polyphenol-tRNA adduct formation with free binding energy of -4.43 for resveratrol, -4.26 kcal/mol for genistein and -4.84 kcal/mol for curcumin, indicating that the interaction process is spontaneous at room temperature. While tRNA remains in A-family structure, major biopolymer aggregation and particle formation occurred at high polyphenol contents.
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Affiliation(s)
- C N N'soukpoé-Kossi
- Department of Chemistry-Physics, Université du Québec à Trois-Riviéres, C. P. 500v, Trois-Riviéres, Québec, Canada G9A 5H7
| | - P Bourassa
- Department of Chemistry-Physics, Université du Québec à Trois-Riviéres, C. P. 500v, Trois-Riviéres, Québec, Canada G9A 5H7
| | - J S Mandeville
- Department of Chemistry-Physics, Université du Québec à Trois-Riviéres, C. P. 500v, Trois-Riviéres, Québec, Canada G9A 5H7
| | - L Bekale
- Department of Chemistry-Physics, Université du Québec à Trois-Riviéres, C. P. 500v, Trois-Riviéres, Québec, Canada G9A 5H7
| | - J Bariyanga
- Department of Chemistry, University of Hawaii-West O'ahu, 96-129 Ala Ike, Pearl City, HI 96782, USA
| | - H A Tajmir-Riahi
- Department of Chemistry-Physics, Université du Québec à Trois-Riviéres, C. P. 500v, Trois-Riviéres, Québec, Canada G9A 5H7.
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Bourassa P, Tajmir-Riahi H. Folic acid binds DNA and RNA at different locations. Int J Biol Macromol 2015; 74:337-42. [DOI: 10.1016/j.ijbiomac.2014.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/14/2014] [Accepted: 12/15/2014] [Indexed: 12/19/2022]
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Bregier-Jarzebowska R. Stability and Solution Structure of Binary and Ternary Cu(II) Complexes with l-Glutamic Acid and Diamines as Well as Adducts in Metal-Free Systems in Aqueous Solution. J SOLUTION CHEM 2014; 43:2144-2162. [PMID: 25484474 PMCID: PMC4255084 DOI: 10.1007/s10953-014-0269-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 08/31/2014] [Indexed: 11/29/2022]
Abstract
Binary and ternary complexes of copper(II) with l-glutamic acid (Glu) and diamines 1,3-diaminopropane and 1,4-diaminobutane, putrescine (tn, Put), as well as adducts formed in the metal-free systems, have been investigated in aqueous solutions. The types of complexes formed and their overall stability constants were established on the basis of computer analysis of potentiometric results. The reaction centers and the modes of interaction were identified on the basis of spectroscopic studies (NMR, Vis and EPR). In the ligands studied the interaction centers are the oxygen atoms from carboxyl groups, nitrogen atom from the amine group of glutamic acid and the nitrogen atoms from amine groups of the diamines. The centers of noncovalent interaction in the adducts that formed in the metal-free systems are also potential sites of metal ion coordination, which is important in biological systems. In the Glu–diamine systems, molecular complexes of the (Glu)Hx(diamine) type are formed. In the (Glu)H2(tn) adduct, in contrast to the corresponding complex with Put, an inversion effect was observed in which the first deprotonated amine group of tn became a negative reaction center and interacted with the protonated amine groups from Glu. Depending on the pH, the amine groups from the diamine can be either a positive or a negative center of interaction. In the Cu(Glu)2 species the first molecule of Glu takes part in metallation through all functional groups, whereas the second molecule makes a “glycine-like” coordination with the Cu(II) ions that is only through two functional groups. According to the results, introduction of Cu(II) ions into metal-free systems (Glu–diamine) changes the character of interactions between the bioligands in the complexes that form in Cu(II)–Glu–diamine systems and no ML…L′ type complexes are formed. However, in the ternary systems only the heteroligand complexes Cu(Glu)(diamine) and Cu(Glu)(diamine)(OH) are observed.
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Kabir A, Kumar GS. Probing the interaction of spermine and 1-naphthyl acetyl spermine with DNA polynucleotides: a comparative biophysical and thermodynamic investigation. MOLECULAR BIOSYSTEMS 2014; 10:1172-83. [PMID: 24643290 DOI: 10.1039/c3mb70616h] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The interaction of spermine and its analogue, 1-naphthyl acetyl spermine with four double stranded DNA polynucleotides has been studied to understand the structural and thermodynamic basis of the binding. The efficacy and specificity of DNA binding of this analogue has not yet been revealed. The energetics of the interaction was studied by isothermal titration calorimetry and differential scanning calorimetry. Circular dichroism spectroscopy, UV-thermal melting and ethidium bromide displacement assay have been employed to characterize the association. Circular dichroism studies showed that 1-naphthyl acetyl spermine caused a stronger structural perturbation in the polynucleotides. Among the adenine-thymine polynucleotides the alternating polynucleotide was more preferred by naphthyl acetyl spermine compared to the preference of spermine for the homo sequence. The higher melting stabilization revealed by the optical melting and differential scanning calorimetry results suggested that the binding of 1-naphthyl acetyl spermine increased the melting temperature and the total standard molar enthalpy of the transition of adenine-thymine polynucleotides. Microcalorimetry results revealed that unlike spermine the binding of 1-naphthyl acetyl spermine was endothermic. The interaction was characterized by total enthalpy-entropy compensation and high standard molar heat capacity values. There are differences in the mode of association of 1-naphthyl acetyl spermine and spermine. 1-naphthyl acetyl spermine binds with an enhanced affinity with the adenine-thymine hetero polynucleotide. Thus, the result suggests the importance of polyamine analogues and their ability to interfere with normal polyamine interactions.
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Affiliation(s)
- Ayesha Kabir
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India.
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N'soukpoé-Kossi C, Bourassa P, Mandeville J, Tajmir-Riahi H. Modelling of vitamin A binding to tRNA. J Pharm Biomed Anal 2014; 99:28-34. [DOI: 10.1016/j.jpba.2014.06.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/25/2014] [Accepted: 06/13/2014] [Indexed: 10/25/2022]
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Bourassa P, Thomas TJ, Bariyanga J, Tajmir-Riahi HA. Breast anticancer drug tamoxifen and its metabolites bind tRNA at multiple sites. Int J Biol Macromol 2014; 72:692-8. [PMID: 25263468 DOI: 10.1016/j.ijbiomac.2014.09.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/07/2014] [Accepted: 09/08/2014] [Indexed: 12/17/2022]
Abstract
The binding sites of breast anticancer drug tamoxifen and its metabolites with tRNA were located by FTIR, CD, UV-visible, and fluorescence spectroscopic methods and molecular modeling. Structural analysis showed that tamoxifen and its metabolites bind tRNA at several binding sites with overall binding constants of K(tam-tRNA) = 5.2 (± 0.6) × 10(4) M(-1), K(4-hydroxytam-tRNA) = 6.5 ( ± 0.5) × 10(4) M(-1) and K(endox-tRNA) = 1.3 (± 0.2) × 10(4) M(-1). The number of binding sites occupied by drug molecules on tRNA were 1 (tamoxifen), 0.8 (4-hydroxitamoxifen) and 1.2 (endoxifen). Docking showed the participation of several nucleobases in drug-tRNA complexes with the free binding energy of -4.31 (tamoxifen), -4.45 (4-hydroxtamoxifen) and -4.38 kcal/mol (endoxifen). The order of binding is 4-hydroxy-tamoxifen > tamoxifen > endoxifen. Drug binding did not alter tRNA conformation from A-family structure, while biopolymer aggregation occurred at high drug concentration.
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Affiliation(s)
- P Bourassa
- Department of Chemistry-Physics, University of Québec in Trois-Rivières, C. P. 500, Trois-Rivières, Québec G9A 5H7, Canada
| | - T J Thomas
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, and Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - J Bariyanga
- Division of Humanities: Math/Sciences, University of Hawaii-West O'ahu, 91-1001 Farrington Highway, Kapolei, HI 96707, USA
| | - H A Tajmir-Riahi
- Department of Chemistry-Physics, University of Québec in Trois-Rivières, C. P. 500, Trois-Rivières, Québec G9A 5H7, Canada.
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Abstract
Recent progress with techniques for monitoring RNA structure in cells such as ‘DMS-Seq’ and ‘Structure-Seq’ suggests that a new era of RNA structure-function exploration is on the horizon. This will also include systematic investigation of the factors required for the structural integrity of RNA. In this context, much evidence accumulated over 50 years suggests that polyamines play important roles as modulators of RNA structure. Here, we summarize and discuss recent literature relating to the roles of these small endogenous molecules in RNA function. We have included studies directed at understanding the binding interactions of polyamines with polynucleotides, tRNA, rRNA, mRNA and ribozymes using chemical, biochemical and spectroscopic tools. In brief, polyamines bind RNA in a sequence-selective fashion and induce changes in RNA structure in context-dependent manners. In some cases the functional consequences of these interactions have been observed in cells. Most notably, polyamine-mediated effects on RNA are frequently distinct from those of divalent cations (i.e. Mg2+) confirming their roles as independent molecular entities which help drive RNA-mediated processes.
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Affiliation(s)
- Helen L Lightfoot
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, CH-8093, Zürich, Switzerland
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Kabir A, Suresh Kumar G. Targeting double-stranded RNA with spermine, 1-naphthylacetyl spermine and spermidine: a comparative biophysical investigation. J Phys Chem B 2014; 118:11050-64. [PMID: 25184857 DOI: 10.1021/jp5035294] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RNA targeting is an evolving new approach to anticancer therapeutics that requires identification of small molecules to selectively target specific RNA structures. In this report, the interaction of biogenic polyamines spermine, spermidine and the synthetic analogue 1-naphthylacetyl spermine with three double-stranded RNA polynucleotides--poly(I)·poly(C), poly(C)·poly(G), and poly(A)·poly(U)--has been described to understand the structural and thermodynamic basis of the binding and the comparative efficacy of the analogue over the natural polyamines. Circular dichroism spectroscopy, thermal melting experiments, and ethidium bromide displacement assay were used to characterize the interaction. Microcalorimetry studies were performed to deduce the energetics of the interaction and atomic force microscopy experiments done to gain insight into the interaction at the molecular level. The experiments demonstrated structural perturbations in the polynucleotides on binding of the polyamines. Thermal melting studies showed enhanced stabilization of RNA-polyamine complexes with increase in the total standard molar enthalpy of transition. The binding affinity was strongest for poly(I)·poly(C) as revealed by microcalorimetry results and varied as poly(I)·poly(C) > poly(C)·poly(G) > poly(A)·poly(U). The order of affinity for the polyamines was spermine >1-naphthylacetyl spermine > spermidine. Total enthalpy-entropy compensation and high standard molar heat capacity values characterized the interactions. The results of the study on the binding of polyamines to dsRNAs presented here have been compared to those reported earlier with dsDNAs. The present findings advance our knowledge on the mechanism of interaction of polyamines with RNA and may help in the search for analogues that can interfere with biogenic polyamine metabolism and function.
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Affiliation(s)
- Ayesha Kabir
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR - Indian Institute of Chemical Biology , Kolkata 700 032, India
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39
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Encapsulation of biogenic and synthetic polyamines by nanoparticles PEG and mPEG-anthracene. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 130:30-9. [DOI: 10.1016/j.jphotobiol.2013.10.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/20/2013] [Accepted: 10/22/2013] [Indexed: 11/19/2022]
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40
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Tyagi G, Pradhan S, Srivastava T, Mehrotra R. Nucleic acid binding properties of allicin: Spectroscopic analysis and estimation of anti-tumor potential. Biochim Biophys Acta Gen Subj 2014; 1840:350-6. [DOI: 10.1016/j.bbagen.2013.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 08/03/2013] [Accepted: 09/06/2013] [Indexed: 12/14/2022]
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Hayashi Y, Sugiyama H, Suganami A, Higashi K, Kashiwagi K, Igarashi K, Kawauchi S, Tamura Y. Prediction of the interaction between spermidine and the G-G mismatch containing acceptor stem in tRNA(Ile): molecular modeling, density functional theory, and molecular dynamics study. Biochem Biophys Res Commun 2013; 441:999-1004. [PMID: 24239547 DOI: 10.1016/j.bbrc.2013.11.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 11/03/2013] [Indexed: 11/26/2022]
Abstract
Polyamines, putrescine, spermidine (SPD), and spermine are closely linked to cell growth, and highly regulate the levels of transcription, translation and protein turnover. We propose that SPD stimulates the formation of Ile-tRNA(Ile) by inducing a selective structural change of the G-G mismatch containing acceptor stem in tRNA(Ile). Here, we provide insight into how SPD recognizes and stabilizes the G-G mismatch containing acceptor stem in tRNA(Ile) with molecular modeling (MM), density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. The results of the MM and DFT calculations indicate that the negatively charged region of the G-G mismatch containing acceptor stem in tRNA(Ile) is preferentially recognized by positively charged SPD. In addition, MD simulations indicate that all of the positively charged amino groups of SPD under physiological conditions (N1(NH3(+)), N5(NH2(+)), and N10(NH3(+)) could form hydrogen bonds with tRNA(Ile) and trigger the SPD-induced stabilization and structural change of the G-G mismatch containing acceptor stem in tRNA(Ile). Thus, this approach should be useful for determining the preferential binding site and appropriate binding mode of polyamines on tRNA(Ile).
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Affiliation(s)
- Yoshihiro Hayashi
- Department of Organic and Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8522, Japan
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Ramani D, De Bandt JP, Cynober L. Aliphatic polyamines in physiology and diseases. Clin Nutr 2013; 33:14-22. [PMID: 24144912 DOI: 10.1016/j.clnu.2013.09.019] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/26/2013] [Accepted: 09/30/2013] [Indexed: 01/01/2023]
Abstract
Aliphatic polyamines are a family of polycationic molecules derived from decarboxylation of the amino acid ornithine that classically comprise three molecules: putrescine, spermidine and spermine. In-cell polyamine homeostasis is tightly controlled at key steps of cell metabolism. Polyamines are involved in an array of cellular functions from DNA stabilization, and regulation of gene expression to ion channel function and, particularly, cell proliferation. As such, aliphatic polyamines play an essential role in rapidly dividing cells such as in the immune system and digestive tract. Because of their role in cell proliferation, polyamines are also involved in carcinogenesis, prompting intensive research into polyamine metabolism as a target in cancer therapy. More recently, another aliphatic polyamine, agmatine, the decarboxylated derivative of arginine, has been identified as a neurotransmitter in mammals, and investigations have focused on its effects in the CNS, notably as a neuroprotector in brain injury.
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Affiliation(s)
- D Ramani
- EA 4466, Faculté des Sciences Pharmaceutiques et Biologiques, Paris Descartes University, Sorbonne Paris Cité, and Clinical Chemistry Department, Hopitaux Universitaires Paris Centre, APHP, Paris, France
| | - J P De Bandt
- EA 4466, Faculté des Sciences Pharmaceutiques et Biologiques, Paris Descartes University, Sorbonne Paris Cité, and Clinical Chemistry Department, Hopitaux Universitaires Paris Centre, APHP, Paris, France.
| | - L Cynober
- EA 4466, Faculté des Sciences Pharmaceutiques et Biologiques, Paris Descartes University, Sorbonne Paris Cité, and Clinical Chemistry Department, Hopitaux Universitaires Paris Centre, APHP, Paris, France
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Agudelo D, Bourassa P, Beauregard M, Bérubé G, Tajmir-Riahi HA. tRNA binding to antitumor drug doxorubicin and its analogue. PLoS One 2013; 8:e69248. [PMID: 23922696 PMCID: PMC3726733 DOI: 10.1371/journal.pone.0069248] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/06/2013] [Indexed: 12/16/2022] Open
Abstract
The binding sites of antitumor drug doxorubicin (DOX) and its analogue N-(trifluoroacetyl) doxorubicin (FDOX) with tRNA were located, using FTIR, CD, fluorescence spectroscopic methods and molecular modeling. Different binding sites are involved in drug-tRNA adducts with DOX located in the vicinity of A-29, A-31, A-38, C-25, C-27, C-28, G-30 and U-41, while FDOX bindings involved A-23, A-44, C-25, C-27, G-24, G-42, G-53, G-45 and U-41 with similar free binding energy (-4.44 for DOX and -4.41 kcal/mol for FDOX adducts). Spectroscopic results showed that both hydrophilic and hydrophobic contacts are involved in drug-tRNA complexation and FDOX forms more stable complexes than DOX with K DOX-tRNA=4.7 (± 0.5)× 10(4) M(-1) and K FDOX-tRNA=6.3 (± 0.7)× 10(4) M(-1). The number of drug molecules bound per tRNA (n) was 0.6 for DOX and 0.4 for FDOX. No major alterations of tRNA structure were observed and tRNA remained in A-family conformation, while biopolymer aggregation and particle formation occurred at high drug concentrations.
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Affiliation(s)
- Daniel Agudelo
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Philippe Bourassa
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Marc Beauregard
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Gervais Bérubé
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Heidar-Ali Tajmir-Riahi
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
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Kabir A, Suresh Kumar G. Binding of the biogenic polyamines to deoxyribonucleic acids of varying base composition: base specificity and the associated energetics of the interaction. PLoS One 2013; 8:e70510. [PMID: 23894663 PMCID: PMC3722294 DOI: 10.1371/journal.pone.0070510] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 06/24/2013] [Indexed: 11/18/2022] Open
Abstract
Background The thermodynamics of the base pair specificity of the binding of the polyamines spermine, spermidine, putrescine, and cadaverine with three genomic DNAs Clostridium perfringens, 27% GC, Escherichia coli, 50% GC and Micrococcus lysodeikticus, 72% GC have been studied using titration calorimetry and the data supplemented with melting studies, ethidium displacement and circular dichroism spectroscopy results. Methodology/Principal Findings Isothermal titration calorimetry, differential scanning calorimetry, optical melting studies, ethidium displacement, circular dichroism spectroscopy are the various techniques employed to characterize the interaction of four polyamines, spermine, spermidine, putersine and cadaverine with the DNAs. Polyamines bound stronger with AT rich DNA compared to the GC rich DNA and the binding varied depending on the charge on the polyamine as spermine>spermidine >putrescine>cadaverine. Thermodynamics of the interaction revealed that the binding was entropy driven with small enthalpy contribution. The binding was influenced by salt concentration suggesting the contribution from electrostatic forces to the Gibbs energy of binding to be the dominant contributor. Each system studied exhibited enthalpy-entropy compensation. The negative heat capacity changes suggested a role for hydrophobic interactions which may arise due to the non polar interactions between DNA and polyamines. Conclusion/Significance From a thermodynamic analysis, the AT base specificity of polyamines to DNAs has been elucidated for the first time and supplemented by structural studies.
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Affiliation(s)
- Ayesha Kabir
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- * E-mail:
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Vijayanathan V, Agostinelli E, Thomas T, Thomas TJ. Innovative approaches to the use of polyamines for DNA nanoparticle preparation for gene therapy. Amino Acids 2013; 46:499-509. [DOI: 10.1007/s00726-013-1549-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 06/26/2013] [Indexed: 12/19/2022]
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Minarini A, Milelli A, Tumiatti V, Rosini M, Lenzi M, Ferruzzi L, Turrini E, Hrelia P, Sestili P, Calcabrini C, Fimognari C. Exploiting RNA as a new biomolecular target for synthetic polyamines. Gene 2013; 524:232-40. [DOI: 10.1016/j.gene.2013.04.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 03/28/2013] [Accepted: 04/01/2013] [Indexed: 01/07/2023]
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Wen LN, Xie MX. Evidence of different G-quadruplex DNA binding with biogenic polyamines probed by electrospray ionization-quadrupole time of flight mass spectrometry, circular dichroism and atomic force microscopy. Biochimie 2013; 95:1185-95. [PMID: 23352964 DOI: 10.1016/j.biochi.2013.01.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/14/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Li-Na Wen
- Analytical & Testing Center of Beijing Normal University, Xinjiekouwaidajie No. 19, Beijing 100875, People's Republic of China
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Basu A, Jaisankar P, Suresh Kumar G. Binding of the 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs to tRNA(phe.). PLoS One 2013; 8:e58279. [PMID: 23526972 PMCID: PMC3602459 DOI: 10.1371/journal.pone.0058279] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 02/01/2013] [Indexed: 12/19/2022] Open
Abstract
Background Three new analogs of berberine with aryl/arylalkyl amino carbonyl methyl substituent at the 9-position of the isoquinoline chromophore along with berberrubine were studied for their binding to tRNAphe by wide variety of biophysical techniques like spectrophotometry, spectrofluorimetry, circular dichroism, thermal melting, viscosity and isothermal titration calorimetry. Methodology/Principal Findings Scatchard binding isotherms revealed that the cooperative binding mode of berberine was propagated in the analogs also. Thermal melting studies showed that all the 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs stabilized the tRNAphe more in comparison to berberine. Circular dichroism studies showed that these analogs perturbed the structure of tRNAphe more in comparison to berberine. Ferrocyanide quenching studies and viscosity results proved the intercalative binding mode of these analogs into the helical organization of tRNAphe. The binding was entropy driven for the analogs in sharp contrast to the enthalpy driven binding of berberine. The introduction of the aryl/arylalkyl amino carbonyl methyl substituent at the 9-position thus switched the enthalpy driven binding of berberine to entropy dominated binding. Salt and temperature dependent calorimetric studies established the involvement of multiple weak noncovalent interactions in the binding process. Conclusions/Significance The results showed that 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs exhibited almost ten folds higher binding affinity to tRNAphe compared to berberine whereas the binding of berberrubine was dramatically reduced by about twenty fold in comparison to berberine. The spacer length of the substitution at the 9-position of the isoquinoline chromophore appears to be critical in modulating the binding affinities towards tRNAphe.
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Affiliation(s)
- Anirban Basu
- Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | | | - Gopinatha Suresh Kumar
- Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- * E-mail:
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Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing. Proc Natl Acad Sci U S A 2012; 109:16149-54. [PMID: 22991464 DOI: 10.1073/pnas.1209062109] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Ribonuclease P (RNase P) catalyzes the maturation of the 5' end of tRNA precursors. Typically these enzymes are ribonucleoproteins with a conserved RNA component responsible for catalysis. However, protein-only RNase P (PRORP) enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana. PRORP enzymes are nuclear encoded and conserved among many eukaryotes, having evolved recently as yeast mitochondrial genomes encode an RNase P RNA. Here we report the crystal structure of PRORP1 from A. thaliana at 1.75 Å resolution, revealing a prototypical metallonuclease domain tethered to a pentatricopeptide repeat (PPR) domain by a structural zinc-binding domain. The metallonuclease domain is a unique high-resolution structure of a Nedd4-BP1, YacP Nucleases (NYN) domain that is a member of the PIN domain-like fold superfamily, including the FLAP nuclease family. The structural similarity between PRORP1 and the FLAP nuclease family suggests that they evolved from a common ancestor. Biochemical data reveal that conserved aspartate residues in PRORP1 are important for catalytic activity and metal binding and that the PPR domain also enhances activity, likely through an interaction with pre-tRNA. These results provide a foundation for understanding tRNA maturation in organelles. Furthermore, these studies allow for a molecular-level comparison of the catalytic strategies used by the only known naturally evolved protein and RNA-based catalysts that perform the same biological function, pre-tRNA maturation, thereby providing insight into the differences between the prebiotic RNA world and the present protein-dominated world.
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Mandeville JS, Bourassa P, Thomas TJ, Tajmir-Riahi HA. Biogenic and synthetic polyamines bind cationic dendrimers. PLoS One 2012; 7:e36087. [PMID: 22558341 PMCID: PMC3338638 DOI: 10.1371/journal.pone.0036087] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 03/26/2012] [Indexed: 11/19/2022] Open
Abstract
Biogenic polyamines are essential for cell growth and differentiation, while polyamine analogues exert antitumor activity in multiple experimental model systems, including breast and lung cancer. Dendrimers are widely used for drug delivery in vitro and in vivo. We report the bindings of biogenic polyamines, spermine (spm), and spermidine (spmd), and their synthetic analogues, 3,7,11,15-tetrazaheptadecane.4HCl (BE-333) and 3,7,11,15,19-pentazahenicosane.5HCl (BE-3333) to dendrimers of different compositions, mPEG-PAMAM (G3), mPEG-PAMAM (G4) and PAMAM (G4). FTIR and UV-visible spectroscopic methods as well as molecular modeling were used to analyze polyamine binding mode, the binding constant and the effects of polyamine complexation on dendrimer stability and conformation. Structural analysis showed that polyamines bound dendrimers through both hydrophobic and hydrophilic contacts with overall binding constants of K(spm-mPEG-G3) = 7.6 × 10(4) M(-1), K(spm-mPEG-PAMAM-G4) = 4.6 × 10(4) M(-1), K(spm-PAMAM-G4) = 6.6 × 10(4) M(-1), K(spmd-mPEG-G3) = 1.0 × 10(5) M(-1), K(spmd-mPEG-PAMAM-G4) = 5.5 × 10(4) M(-1), K(spmd-PAMAM-G4) = 9.2 × 10(4) M(-1), K(BE-333-mPEG-G3) = 4.2 × 10(4) M(-1), K(Be-333-mPEG-PAMAM-G4) = 3.2 × 10(4) M(-1), K(BE-333-PAMAM-G4) = 3.6 × 10(4) M(-1), K(BE-3333-mPEG-G3) = 2.2 × 10(4) M(-1), K(Be-3333-mPEG-PAMAM-G4) = 2.4 × 10(4) M(-1), K(BE-3333-PAMAM-G4) = 2.3 × 10(4) M(-1). Biogenic polyamines showed stronger affinity toward dendrimers than those of synthetic polyamines, while weaker interaction was observed as polyamine cationic charges increased. The free binding energies calculated from docking studies were: -3.2 (spermine), -3.5 (spermidine) and -3.03 (BE-3333) kcal/mol, with the following order of binding affinity: spermidine-PAMAM-G-4>spermine-PAMMAM-G4>BE-3333-PAMAM-G4 consistent with spectroscopic data. Our results suggest that dendrimers can act as carrier vehicles for delivering antitumor polyamine analogues to target tissues.
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Affiliation(s)
- Jean-Sebastian Mandeville
- Département de Chimie-Biologie, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Phillipe Bourassa
- Département de Chimie-Biologie, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Thekkumkattil John Thomas
- Department of Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
- The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
| | - Heidar-Ali Tajmir-Riahi
- Département de Chimie-Biologie, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
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