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Kang J, Voothuluru P, Hoyos-Miernyk E, Alexander D, Oliver MJ, Sharp RE. Antioxidant Metabolism Underlies Different Metabolic Strategies for Primary Root Growth Maintenance under Water Stress in Cotton and Maize. Antioxidants (Basel) 2022; 11:antiox11050820. [PMID: 35624684 PMCID: PMC9137980 DOI: 10.3390/antiox11050820] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 01/24/2023] Open
Abstract
The divergence of metabolic responses to water stress in the elongation zone of cotton and maize primary roots was investigated by establishing water-deficit conditions that generated steady root elongation at equivalent tissue water potentials. In water-stressed cotton roots, cell elongation was maintained in the apical 3 mm but was progressively inhibited with further displacement from the apex. These responses are similar to previous findings in maize, providing the foundation for comparisons of metabolic responses in regions of growth maintenance and inhibition between the species. Metabolomics analyses showed region-specific and species-specific changes in metabolite abundance in response to water stress, revealing both conserved responses including osmolyte accumulation, and key differences in antioxidative and sulfur metabolism. Quantitative assessment showed contrasting glutathione responses in the root elongation zone between the species, with glutathione levels declining in cotton as stress duration progressed, whereas in maize, glutathione levels remained elevated. Despite the lesser glutathione response in cotton, hydrogen peroxide levels were low in water-stressed cotton compared with maize roots and were associated with higher catalase, ascorbate peroxidase, and superoxide dismutase activities in cotton. The results indicate alternative metabolic strategies underlying the responses of primary root growth to water stress between cotton and maize.
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Affiliation(s)
- Jian Kang
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA; (J.K.); (E.H.-M.); (M.J.O.)
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
| | - Priyamvada Voothuluru
- Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN 37996, USA;
| | - Elizabeth Hoyos-Miernyk
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA; (J.K.); (E.H.-M.); (M.J.O.)
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
| | | | - Melvin J. Oliver
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA; (J.K.); (E.H.-M.); (M.J.O.)
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
| | - Robert E. Sharp
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA; (J.K.); (E.H.-M.); (M.J.O.)
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
- Correspondence: ; Tel.: +1-573-882-1841
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2
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Chan KX, Wirtz M, Phua SY, Estavillo GM, Pogson BJ. Balancing metabolites in drought: the sulfur assimilation conundrum. TRENDS IN PLANT SCIENCE 2013; 18:18-29. [PMID: 23040678 DOI: 10.1016/j.tplants.2012.07.005] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 05/18/2023]
Abstract
A key plant response to drought is the accumulation of specific sets of metabolites that act as osmoprotectants, osmolytes, antioxidants, and/or stress signals. An emerging question is: how do plants regulate metabolism to balance the 'competing interests' between metabolites during stress? Recent research connects primary sulfur metabolism (e.g., sulfate transport in the vasculature, its assimilation in leaves, and the recycling of sulfur-containing compounds) with the drought stress response. In this review, we highlight key steps in sulfur metabolism that play significant roles in drought stress signaling and responses. We propose that a complex balancing act is required to coordinate primary and secondary sulfur metabolism during the drought stress response in plants.
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Affiliation(s)
- Kai Xun Chan
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
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3
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Pavan GM, Kostiainen MA, Danani A. Computational Approach for Understanding the Interactions of UV-Degradable Dendrons with DNA and siRNA. J Phys Chem B 2010; 114:5686-93. [DOI: 10.1021/jp911439q] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Giovanni M. Pavan
- Mathematical and Physical Sciences Research Unit (SMF), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
| | - Mauri A. Kostiainen
- Mathematical and Physical Sciences Research Unit (SMF), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
| | - Andrea Danani
- Mathematical and Physical Sciences Research Unit (SMF), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
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4
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Pavan GM, Danani A, Pricl S, Smith DK. Modeling the Multivalent Recognition between Dendritic Molecules and DNA: Understanding How Ligand “Sacrifice” and Screening Can Enhance Binding. J Am Chem Soc 2009; 131:9686-94. [DOI: 10.1021/ja901174k] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Giovanni M. Pavan
- Molecular Simulations Engineering (MOSE) Laboratory, Department of Chemical Engineering (DICAMP), University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy, Institute of Computer Integrated Manufacturing for Sustainable Innovation (ICIMSI), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
| | - Andrea Danani
- Molecular Simulations Engineering (MOSE) Laboratory, Department of Chemical Engineering (DICAMP), University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy, Institute of Computer Integrated Manufacturing for Sustainable Innovation (ICIMSI), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
| | - Sabrina Pricl
- Molecular Simulations Engineering (MOSE) Laboratory, Department of Chemical Engineering (DICAMP), University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy, Institute of Computer Integrated Manufacturing for Sustainable Innovation (ICIMSI), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
| | - David K. Smith
- Molecular Simulations Engineering (MOSE) Laboratory, Department of Chemical Engineering (DICAMP), University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy, Institute of Computer Integrated Manufacturing for Sustainable Innovation (ICIMSI), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
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5
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Huang Y, Keen JC, Pledgie A, Marton LJ, Zhu T, Sukumar S, Park BH, Blair B, Brenner K, Casero RA, Davidson NE. Polyamine analogues down-regulate estrogen receptor alpha expression in human breast cancer cells. J Biol Chem 2006; 281:19055-63. [PMID: 16679312 PMCID: PMC3623667 DOI: 10.1074/jbc.m600910200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The critical role of polyamines in cell growth has led to the development of a number of agents that interfere with polyamine metabolism including a novel class of polyamine analogues, oligoamines. Here we demonstrate that oligoamines specifically suppress the mRNA and protein expression of estrogen receptor alpha (ERalpha) and ERalpha target genes in ER-positive human breast cancer cell lines, whereas neither ERbeta nor other steroid hormonal receptors are affected by oligoamines. The constitutive expression of a cytomegalovirus promoter-driven exogenous ERalpha in ER-negative MDA-MB-231 human breast cancer cells was not altered by oligoamines, suggesting that oligoamines specifically suppress ERalpha transcription rather than affect mRNA or protein stability. Further analysis demonstrated that oligoamines disrupted the DNA binding activity of Sp1 transcription factor family members to an ERalpha minimal promoter element containing GC/CA-rich boxes. Treatment of MDA-MB-231 cells with the JNK-specific inhibitor SP600125 or expression of the c-Jun dominant negative inhibitor TAM67 blocked the oligoamine-activated JNK/c-Jun pathway and enhanced oligoamine-inhibited ERalpha expression, suggesting that AP-1 is a positive regulator of ERalpha expression and that oligoamine-activated JNK/AP-1 activity may antagonize the down-regulation of ERalpha induced by oligoamines. Taken together, these results suggest a novel antiestrogenic mechanism for specific polyamine analogues in human breast cancer cells.
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Affiliation(s)
- Yi Huang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Judith C. Keen
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Allison Pledgie
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | | | - Tao Zhu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Saraswati Sukumar
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Ben Ho Park
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Brian Blair
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Keith Brenner
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Robert A. Casero
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Nancy E. Davidson
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
- To whom correspondence should be addressed: Breast Cancer Program, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 1650 Orleans St., Rm. 409, Baltimore, MD 21231. Tel.: 410-955-8489; Fax: 410-614-4073;
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6
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Khalid S, Hannon MJ, Rodger A, Rodger PM. Simulations of DNA Coiling around a Synthetic Supramolecular Cylinder That Binds in the DNA Major Groove. Chemistry 2006; 12:3493-506. [PMID: 16496427 DOI: 10.1002/chem.200501168] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In this work we present the results of a molecular simulation study of the interaction between a tetracationic bis iron(II) supramolecular cylinder, [Fe2(C25H20N4)3]4+, and DNA. This supramolecular cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA. The simulations have been designed to elucidate the interactions that lead the cylinder to target the major groove and that drive the subsequent DNA conformational changes. Three sets of multi-nanosecond simulations have been performed: one of the uncomplexed d(CCCCCTTTTTCC) d(GGAAAAAGGGGG) dodecamer; one of this DNA complexed with the cylinder molecule; and one of this DNA complexed with a neutralised version of the cylinder. Coiling of the DNA was observed in the DNA-cylinder simulations, giving insight into the molecular level nature of the supramolecular coiling observed experimentally. The cylinder charge was found not to be essential for the DNA coiling, which implies that the DNA response is moderated by the short range interactions that define the molecular shape. Cylinder charge did, however, affect the integrity of the DNA duplex, to the extent that, under some circumstances, the tetracationic cylinder induced defects in the DNA base pairing at locations adjacent to the cylinder binding site.
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Affiliation(s)
- Syma Khalid
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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7
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Lindemose S, Nielsen PE, Møllegaard NE. Polyamines preferentially interact with bent adenine tracts in double-stranded DNA. Nucleic Acids Res 2005; 33:1790-803. [PMID: 15788751 PMCID: PMC1069516 DOI: 10.1093/nar/gki319] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Revised: 03/03/2005] [Accepted: 03/03/2005] [Indexed: 11/29/2022] Open
Abstract
Polyamines, such as putrescine, spermidine and spermine, have indirectly been linked with the regulation of gene expression, and their concentrations are typically increased in cancer cells. Although effects on transcription factor binding to cognate DNA targets have been demonstrated, the mechanisms of the biological action of polyamines is poorly understood. Employing uranyl photo-probing we now demonstrate that polyamines at submillimolar concentrations bind preferentially to bent adenine tracts in double-stranded DNA. These results provide the first clear evidence for the sequence-specific binding of polyamines to DNA, and thereby suggest a mechanism by which the cellular effects of polyamines in terms of differential gene transcriptional activity could, at least partly, be a direct consequence of sequence-specific interactions of polyamines with promoters at the DNA sequence level.
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Affiliation(s)
- Søren Lindemose
- Department of Medical Biochemistry and Genetics, The Panum Institute, University of CopenhagenBlegdamsvej 3C, 2200 Copenhagen N, Denmark
| | - Peter E. Nielsen
- Department of Medical Biochemistry and Genetics, The Panum Institute, University of CopenhagenBlegdamsvej 3C, 2200 Copenhagen N, Denmark
| | - Niels Erik Møllegaard
- Department of Medical Biochemistry and Genetics, The Panum Institute, University of CopenhagenBlegdamsvej 3C, 2200 Copenhagen N, Denmark
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8
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Real AN, Greenall RJ. Influence of Spermine on DNA Conformation in a Molecular Dynamics Trajectory of d(CGCGAATTCGCG)2: Major Groove Binding by One Spermine Molecule Delays the A→B Transition. J Biomol Struct Dyn 2004; 21:469-88. [PMID: 14692792 DOI: 10.1080/07391102.2004.10506941] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The effect of spermine on the A-DNA to B-DNA transition in d(CGCGAATTCGCG)(2) has been investigated by five A-start molecular dynamics simulations, using the Cornell et al. potential. In the absence of spermine an A-->B transition is initiated immediately and the DNA becomes equidistant from the A- and B-forms at 200ps. In three DNA-spermine simulations, when a spermine is located across the major groove of A-DNA in one of three different initial locations, the time taken to reach equidistance from the A- and B-forms is delayed until 800, 950 or 1000ps. In each case the A-form appears to be temporarily stabilized by spermine's electrostatic interactions with phosphates on both sides of the major groove. The onset of the A-->B transition can be correlated with the spermine losing contact with phosphates on one side of the groove and with A-like --> B-like sugar pucker transitions in the vicinity of the spermine bridge. However in the fifth trajectory, in which the spermine initially threads from the major groove via the backbone into the minor groove, the B-->A transition occurs rapidly once again and the DNA is equidistant between the A- and B-forms within 300ps. This indicates that the mere presence of spermine is insufficient to delay the transition and that major groove binding stabilizes A-DNA.
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Affiliation(s)
- Alan N Real
- Department of Physics, University of York, York, YO10 5DD, United Kingdom
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9
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HOWARD BRIANJ, GRANT GUYH. (William) Graham Richards. Mol Phys 2003. [DOI: 10.1080/00268970310001605741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Bryson K, Greenall RJ. Binding sites of the polyamines putrescine, cadaverine, spermidine and spermine on A- and B-DNA located by simulated annealing. J Biomol Struct Dyn 2000; 18:393-412. [PMID: 11149516 DOI: 10.1080/07391102.2000.10506676] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Molecular dynamics simulations with simulated annealing are performed on polyamine-DNA systems in order to determine the binding sites of putrescine, cadaverine, spermidine and spermine on A- and B-DNA. The simulations either contain no additional counterions or sufficient Na+ ions, together with the charge on the polyamine, to provide 73% neutralisation of the charges on the DNA phosphates. The stabilisation energies of the complexes indicate that all four polyamines should stabilise A-DNA in preference to B-DNA, which is in agreement with experiment in the case of spermine and spermidine, but not in the case of putrescine or cadaverine. The major groove is the preferred binding site on A-DNA of all the polyamines. Putrescine and cadaverine tend to bind to the sugar-phosphate backbone of B-DNA, whereas spermidine and spermine occupy more varied sites, including binding along the backbone and bridging both the major and minor grooves.
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Affiliation(s)
- K Bryson
- Department of Physics, University of York, United Kingdom
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11
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Rodger A, Sanders KJ, Hannon MJ, Meistermann I, Parkinson A, Vidler DS, Haworth IS. DNA structure control by polycationic species: polyamine, cobalt ammines, and di-metallo transition metal chelates. Chirality 2000; 12:221-36. [PMID: 10790193 DOI: 10.1002/(sici)1520-636x(2000)12:4<221::aid-chir9>3.0.co;2-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Many polycationic species bind to DNA and induce structural changes. The work reported here is the first phase of a program whose long-term aim is to create a class of simple and inexpensive sequence-selective compounds that will enable enhanced DNA structure control for a wide range of applications. Three classes of molecule have been included in this work: the polyamine spermine (charge: 4(+)) and spermidine (charge: 3(+)) (which are known to induce a wide range of DNA conformational changes but whose binding modes are still not well understood); cobalt (III) amine transition metal complexes as potential polyamine mimics and [Fe(H(2)O)(6)](3+); and the first member of a new class of di-metallo tris-chelated cylinders of helical structure (charge 4(+)). Temperature-dependent absorption, circular dichroism, linear dichroism, gel electrophoresis, and molecular modeling data are presented. The cobalt amines prove to be effective polyamine mimics, although their binding appears to be restricted to backbone and major groove. All the ligands stabilize the DNA, but the 4(+) di-iron tris-chelate does so comparatively weakly and seems to have a preference for single-stranded DNA. All the molecules studied bend the DNA, with the di-iron tris-chelate having a particularly dramatic effect even at very low drug load.
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Affiliation(s)
- A Rodger
- Department of Chemistry, University of Warwick, Coventry, UK.
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12
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Shamma T, Haworth IS. Spermine inhibition of the 2,5-diaziridinyl-1,4-benzoquinone (DZQ) crosslinking reaction with DNA duplexes containing poly(purine). poly(pyrimidine) tracts. Nucleic Acids Res 1999; 27:2601-9. [PMID: 10373575 PMCID: PMC148467 DOI: 10.1093/nar/27.13.2601] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Upon reduction, 2,5-diaziridinyl-1,4-benzoquinone (DZQ) can form an interstrand guanine to guanine crosslink with DNA duplexes containing a d(GC).d(GC) dinucleotide step. The reaction is enhanced by a thymine positioned 5[prime] to each guanine [i.e. in a d(TGCA). d(TGCA) duplex fragment]. Here we show that spermine can inhibit DZQ crosslink formation in duplexes of sequence d[C(N6)TGCA(M6)C]. d[G(M[prime]6)TG-CA(N[prime]6)G]. For N6= M6= GGGGGG, N6= M6= a 'random' sequence and N6= GGGGGG and M6= a 'random' sequence, spermine concentrations of 20, 1 and 3 microM, respectively, were required for 50% inhibition of the DZQ crosslink. This suggests that spermine is more strongly bound to the polyguanosine tract than the random sequence, making it less available for crosslink inhibition. When the polyguanosine tract is interrupted by N 7-deazaguanine (D) located three bases, d(CGGGDGGTGCAGGDGGGC), and four bases, d(CG-GDGGGTGCAGGGDGGC), from the d(TGCA).d(TGCA) site, 30 and 3 microM spermine, respectively, were required for 50% crosslink inhibition. We suggest that this difference is due to the relative proximity of the three-guanosine tract to the d(TGCA).d(TGCA) site. We were able to confirm these conclusions with further experiments using duplexes containing three-guanosine and two-guanosine tracts and from computer simulations of the spermine-DNA complexes.
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Affiliation(s)
- T Shamma
- Department of Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033, USA
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Andreasson B, Nordenskiöld L, Braunlin WH. An NMR self-diffusion study of the interactions between spermidine and oligonucleotides. Biopolymers 1998. [DOI: 10.1002/(sici)1097-0282(199604)38:4<505::aid-bip6>3.0.co;2-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Desiderio MA, Bergamaschi D, Mascellani E, De Feudis P, Erba E, D'Incalci M. Treatment with inhibitors of polyamine biosynthesis, which selectively lower intracellular spermine, does not affect the activity of alkylating agents but antagonizes the cytotoxicity of DNA topoisomerase II inhibitors. Br J Cancer 1997; 75:1028-34. [PMID: 9083339 PMCID: PMC2222756 DOI: 10.1038/bjc.1997.176] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Inhibitors of ornithine decarboxylase (ODC), such as alpha-difluoromethylornithine (DFMO), may influence the cytotoxicity of anti-tumour agents that interact with DNA. Intracellular levels of putrescine and spermidine were markedly reduced by ODC inhibitors while the level of spermine, which is the main polyamine in nuclei, was unchanged. By combining a novel inhibitor of ODC, such as (2R, 5R)-6-heptyne-2,5-diamine (MDL 72.175, MAP), with an inhibitor of S-adenosylmethionine decarboxylase (SAMDC), such as 5'-[[(Z)-4-aminobut-2-enyl]methylamino]-5'-deoxyadenosine (MDL 73.811, AbeAdo), spermine was selectively depleted in a human ovarian cancer cell line OVCAR-3 (i.e. spermine became almost undetectable whereas the levels of spermidine and putrescine were not affected). The depletion of spermine blocked DNA synthesis with a consequent accumulation of cells in the G1 phase of the cell cycle. Pretreatment with MAP plus AbeAdo did not change the cytotoxicity of alkylating agents, such as L-phenylalanine mustard (L-PAM), 1,4-bis(2'-chloroethyl)-1,4-diazabicyclo-[2.2.1] heptane diperchlorate (DABIS), 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU), cis-diamminedichloroplatinum (II) (cis-DDP), N-deformyl-N-[4-N-N,N-bis (2-chloroethylamino)benzoyl] (tallimustine) or CC-1065, whereas it markedly reduced the cytotoxicity of DNA topoisomerase II inhibitors, such as doxorubicin (DX) and 4'-demethylepipodophyllotoxin-5-(4,6-O)-ethylidene- beta-D-glycopyranoside (VP-16). The addition of spermine before drug treatment restored the sensitivity to the DNA topoisomerase II inhibitors, thus indicating that the reduced effect was related to the intracellular spermine level. The reason for the reduction in cytotoxicity is unclear, but it does not appear to be related to a cell cycle effect or to a decrease in the intracellular level of DNA topoisomerase II. Drugs that modify polyamine biosynthesis are under early clinical development as potential new anti-tumour agents. These findings illustrate the need for caution in combining such drugs with DNA topoisomerase II inhibitors.
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Affiliation(s)
- M A Desiderio
- Istituto di Patologia Generale, Università degli Studi di Milano, CNR,Milan, Italy
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15
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Barawkar DA, Rajeev KG, Kumar VA, Ganesh KN. Triplex formation at physiological pH by 5-Me-dC-N4-(spermine) [X] oligodeoxynucleotides: non protonation of N3 in X of X*G:C triad and effect of base mismatch/ionic strength on triplex stabilities. Nucleic Acids Res 1996; 24:1229-37. [PMID: 8614624 PMCID: PMC145769 DOI: 10.1093/nar/24.7.1229] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Oligodeoxynucleotide (ODN) directed triplex formation has therapeutic importance and depends on Hoogsteen hydrogen bonds between a duplex DNA and a third DNA strand. T*A:T triplets are formed at neutral pH and C+*G:C are favoured at acidic pH. It is demonstrated that spermine conjugation at N4 of 5-Me-dC in ODNs 1-5 (sp-ODNs) imparts zwitterionic character, thus reducing the net negative charge of ODNs 1-5. sp-ODNs form triplexes with complementary 24mer duplex 8:9 show foremost stability at neutral pH 7.3 and decrease in stability towards lower pH, unlike the normal ODNs where optimal stability is found at an acidic pH 5.5. At pH 7.3, control ODNs 6 and 7 carrying dC or 5-Me-dC, respectively, do not show any triple helix formation. The stability order of triplex containing 5-Me-dC-N4-(spermine) with normal and mismatched duplex was found to be X*G:C approximately X*A:T > X*C:G > X*T:A. The hysteresis curve of sp-ODN triplex 3*8:9 indicated a better association with complementary duplex 8:9 as compared to unmodified ODN 6 in triplex 6*8:9. pH-dependent UV difference spectra suggest that N3 protonation is not a requirement for triplex formation by sp-ODN and interstrand interaction of conjugated spermine more than compensates for loss in stability due to absence of a single Hoogsteen hydrogen bond. These results may have importance in designing oligonucleotides for antigene applications.
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Affiliation(s)
- D A Barawkar
- Division of Organic Chemistry, National Chemical Laboratory, Pune, India
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16
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Abstract
Self-diffusion coefficients have been determined by pulsed field gradient nmr methods for spermidine in solutions of the oligonucleotides d(GC)4 and d(GGAATTCC). The self-diffusion behavior of spermidine in solution of d(GC)4 is very similar to that observed previously for methylspermidine (completely N-methylated spermidine). Moreover, the self-diffusion behaviors of spermidine in solutions of d(GC)4 and d(GGAATTCC) are also quite similar, indicating that there is no significant influenceon on self-diffusion of oligonucleotide base composition. Furthermore, self-diffusion coefficients of the oligonucleotide d(GC)8 show only a small dependence on oligonucleotide concentration, and no measurable dependence on sodium ion or magnesium ion concentration.
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Affiliation(s)
- B Andreasson
- Division of Physical Chemistry, Stockholm University, Sweden
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17
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Abstract
In neutral solutions polyamines are fully protonated, and hence are really polyammonium cations (PAC). Spermine, for example, carries four positive charges in a linear system, H3N+(CH2)3N+H2(CH2)4N+H2 (CH2)3N+H3. There is a very powerful coulombic interaction between aqueous DNA and such cations, thus the cations are attracted to the DNA over large distances, and once close to the DNA normally remain there for long periods. A key issue is; are the cations mobile, or do they remain at one preferred site for significant periods? The latter is the currently preferred concept, but NMR and EPR evidence will be presented in favour of the former. If the former is correct, then PACs may be able to act as good drug delivery systems. In its simple form the concept is that any drug that acts directly on DNA can be chemically bound to a PAC. Once in the cell, this PAC-drug complex (PAC-D) will be carried to DNA and will move very rapidly along the exposed strands until it recognises the site of action. This may be some special base sequence region, a damaged site, or the PAC-D unit may simply be present prior to potential damage, so that this can be repaired very rapidly. Some of our current studies on these systems are described.
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Affiliation(s)
- M C Symons
- Department of Chemistry, University of Essex, Colchester, UK
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18
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Johnson F, Loew GH, Du P. Homology models of two isozymes of manganese peroxidase: prediction of a Mn(II) binding site. Proteins 1994; 20:312-9. [PMID: 7731950 DOI: 10.1002/prot.340200404] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The three-dimensional structures of two isozymes of manganese peroxidase (MnP) have been predicted from homology modeling using lignin peroxidase as a template. Although highly homologous, MnP differs from LiP by the requirement of Mn(II) as an intermediate in its oxidation of substrates. The Mn(II) site is absent in LiP and unique to the MnP family of peroxidases. The model structures were used to identify the unique Mn(II) binding sites, to determine to what extent they were conserved in the two isozymes, and to provide insight into why this site is absent in LiP. For each isozyme of MnP, three candidate Mn(II) binding sites were identified. Energy optimizations of the three possible Mn(II) enzyme complexes allowed the selection of the most favorable Mn(II) binding site as one with the most anionic oxygen moieties best configured to act as ligands for the Mn(II). At the preferred site, the Mn(II) is coordinated to the carboxyl oxygens of Glu-35, Glu-39, and Asp-179, and a propionate group of the heme. The predicted Mn(II) binding site is conserved in both isozymes. Comparison between the residues at this site in MnP and the corresponding residues in LiP shows that two of the three anionic residues in MnP are replaced by neutral residues in LiP, explaining why LiP does not bind Mn(II).
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Affiliation(s)
- F Johnson
- Molecular Research Institute, Palo Alto, California 94304
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19
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Adlam G, Blagbrough IS, Taylor S, Latham HC, Haworth IS, Rodger A. Multiple binding modes with DNA of anthracene-9-carbonyl-N1-spermine probed by LD, CD, normal absorption, and molecular modelling compared with those of spermidine and spermine. Bioorg Med Chem Lett 1994. [DOI: 10.1016/s0960-894x(01)80405-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Abstract
Interaction and binding geometries of complexes of Methyl green with poly(dA-dT)2, poly(dA).poly(dT), and triplex poly(dA).2poly(dT) complexes have been studied by linear dichroism. For both of the complexes with double helical DNAs, the z symmetry axis of Methyl green is found to be approximately parallel to the DNA bases while the x symmetry axis lies at 40-44 degrees relative to the local DNA helix axis, in agreement with a groove binding mode. However, in contrast to minor-groove binders (such as DAPI and Hoechst 33258) Methyl green is found to be excluded from binding to the triple helical poly(dA).2poly(dT) in which the major groove is filled by the third strand. While most so far studied groove-binding dyes bind in the minor groove of DNA, Methyl green thus appears to be an exception.
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Affiliation(s)
- S K Kim
- Department of Physical Chemistry, Chalmers University of Technology, Gothenburg, Sweden
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21
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Haworth IS, Rodger A, Richards WG. A molecular dynamics simulation of a polyamine-induced conformational change of DNA. A possible mechanism for the B to Z transition. J Biomol Struct Dyn 1992; 10:195-211. [PMID: 1418741 DOI: 10.1080/07391102.1992.10508638] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A 75ps molecular dynamics simulation has been performed on a fully solvated complex of spermine with the B DNA decamer (dGdC)5.(dGdC)5. The simulation indicates a possible mechanism by which polyamines might induce the formation of a left-handed helix, the B to Z transition. Spermine was initially located in the major groove, hydrogen bonded to the helix. During the simulation the ligand migrates deeper into the DNA, maintaining strong hydrogen bonding to the central guanine bases and destroying the Watson-Crick base pairing with their respective cytosines. Significant rotation of these and other cytosine bases was observed, in part due to interactions of the helix with the aminopropyl chains of spermine. An intermediate BII conformation might be of importance in this process.
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Affiliation(s)
- I S Haworth
- School of Pharmacy, University of Southern California, Los Angeles 90033
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22
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Abstract
A systematic theoretical study of the CD of double-stranded poly(dG-dC) and its complexes with small molecules is presented. The intrinsic CD of the polymer and the induced CD of a transition belonging to a molecule bound to DNA are calculated using the matrix method. The calculations show considerable differences between pyrimidine-purine and purine-pyrimidine binding sites, and we find that the induced CD of a groove bound molecule is one order of magnitude stronger than that of an intercalated molecule. The results form a sound basis for interpreting the CD of ligand-DNA systems in terms of molecular geometry, interactions, and spectroscopy.
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Affiliation(s)
- R Lyng
- Department of Physical Chemistry, Chalmers University of Technology, Gothenburg, Sweden
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23
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Haworth IS, Elcock AH, Freeman J, Rodger A, Richards WG. Sequence selective binding to the DNA major groove: tris(1,10-phenanthroline) metal complexes binding to poly(dG-dC) and poly(dA-dT). J Biomol Struct Dyn 1991; 9:23-44. [PMID: 1781946 DOI: 10.1080/07391102.1991.10507891] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molecular modelling and energy minimisation calculations that incorporate solvent effects have been used to investigate the complexation of delta and lambda-[Ru(1,10-phenanthroline]2+ to DNA. The most stable binding geometry for both enantiomers is one in which a phenanthroline chelate is positioned in the major groove. The chelate is partially inserted between neighbouring base pairs, but is not intercalated. For delta, though not for lambda, a geometry with two chelates in the major groove is only slightly less favourable. Minor groove binding is shown to be no more favourable than external electrostatic binding. The optimised geometries of the DNA/[Ru(1,10-phenanthroline]2+ complexes enable published linear dichroism spectra to be used to determine the percentage of each enantiomer in the two most favourable major groove sites. For delta 57 +/- 15% and for lambda 82 +/- 7% of bound molecules are in the partially inserted site.
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Affiliation(s)
- I S Haworth
- Physical Chemistry Laboratory, Oxford, England
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