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Kretzer B, Herényi L, Csík G, Supala E, Orosz Á, Tordai H, Kiss B, Kellermayer M. TMPyP binding evokes a complex, tunable nanomechanical response in DNA. Nucleic Acids Res 2024; 52:8399-8418. [PMID: 38943349 PMCID: PMC11317170 DOI: 10.1093/nar/gkae560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 07/01/2024] Open
Abstract
TMPyP is a porphyrin capable of DNA binding and used in photodynamic therapy and G-quadruplex stabilization. Despite its broad applications, TMPyP's effect on DNA nanomechanics is unknown. Here we investigated, by manipulating λ-phage DNA with optical tweezers combined with microfluidics in equilibrium and perturbation kinetic experiments, how TMPyP influences DNA nanomechanics across wide ranges of TMPyP concentration (5-5120 nM), mechanical force (0-100 pN), NaCl concentration (0.01-1 M) and pulling rate (0.2-20 μm/s). Complex responses were recorded, for the analysis of which we introduced a simple mathematical model. TMPyP binding, which is a highly dynamic process, leads to dsDNA lengthening and softening. dsDNA stability increased at low (<10 nM) TMPyP concentrations, then decreased progressively upon increasing TMPyP concentration. Overstretch cooperativity decreased, due most likely to mechanical roadblocks of ssDNA-bound TMPyP. TMPyP binding increased ssDNA's contour length. The addition of NaCl at high (1 M) concentration competed with the TMPyP-evoked nanomechanical changes. Because the largest amplitude of the changes is induced by the pharmacologically relevant TMPyP concentration range, this porphyrin derivative may be used to tune DNA's structure and properties, hence control the wide array of biomolecular DNA-dependent processes including replication, transcription, condensation and repair.
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Affiliation(s)
- Balázs Kretzer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Levente Herényi
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Gabriella Csík
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Eszter Supala
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Ádám Orosz
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Hedvig Tordai
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
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Sharma K, Ghiffary MR, Lee G, Kim HU. Efficient production of an antitumor precursor actinocin and other medicinal molecules from kynurenine pathway in Escherichia coli. Metab Eng 2024; 81:144-156. [PMID: 38043641 DOI: 10.1016/j.ymben.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
Kynurenine pathway has a potential to convert L-tryptophan into multiple medicinal molecules. This study aims to explore the biosynthetic potential of kynurenine pathway for the efficient production of actinocin, an antitumor precursor selected as a proof-of-concept target molecule. Kynurenine pathway is first constructed in Escherichia coli by testing various combinations of biosynthetic genes from four different organisms. Metabolic engineering strategies are next performed to improve the production by inhibiting a competing pathway, and enhancing intracellular supply of a cofactor S-adenosyl-L-methionine, and ultimately to produce actinocin from glucose. Metabolome analysis further suggests additional gene overexpression targets, which finally leads to the actinocin titer of 719 mg/L. E. coli strain engineered to produce actinocin is further successfully utilized to produce 350 mg/L of kynurenic acid, a neuroprotectant, and 1401 mg/L of 3-hydroxyanthranilic acid, an antioxidant, also from glucose. These competitive production titers demonstrate the biosynthetic potential of kynurenine pathway as a source of multiple medicinal molecules. The approach undertaken in this study can be useful for the sustainable production of molecules derived from kynurenine pathway, which are otherwise chemically synthesized.
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Affiliation(s)
- Komal Sharma
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Mohammad Rifqi Ghiffary
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - GaRyoung Lee
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; Graduate School of Engineering Biology, KAIST, Daejeon, 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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Kumar R, Keshri R, Prodhan K, Shaikh K, Draksharapu A. A tetranuclear Mn-diamond core complex as a functional mimic of both catechol oxidase and phenoxazinone synthase enzymes. Dalton Trans 2023; 52:15412-15419. [PMID: 37226832 DOI: 10.1039/d3dt00761h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Through dioxygen activation, a tetranuclear Mn(II,III,III,II) diamond core, [Mn4(HPTP*)2(μ-O)2(H2O)4](ClO4)4 (1) complex, has been synthesised using a suitably designed septadentate ligand framework (HPTP*H = 1,3-bis(bis((4-methoxy-3,5-dimethylpyridin-2-yl)methyl)amino)propan-2-ol). The newly prepared complex 1 was characterised using multiple spectroscopic techniques and X-ray crystallography. 1 exhibits excellent catalytic oxidation reactivity for the model substrates, namely, 3,5-di-tert-butylcatechol (3,5-DTBC) and 2-aminophenol, efficiently mimicking the enzymes catechol oxidase and phenoxazinone synthase, respectively. Remarkably, we employed aerial oxygen to catalyze the oxidation of these model substrates, 3,5-DTBC and 2-aminophenol, with turnover numbers of 835 and 14, respectively. A tetranuclear Mn-diamond core complex that mimics both catechol oxidase and phenoxazinone synthase could pave the way for further research into its potential as a multi-enzymatic functional mimic.
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Affiliation(s)
- Rakesh Kumar
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur - 208016, India.
| | - Rahul Keshri
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur - 208016, India.
| | - Koushik Prodhan
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur - 208016, India.
| | - Kanchan Shaikh
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur - 208016, India.
| | - Apparao Draksharapu
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur - 208016, India.
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Satange R, Kao SH, Chien CM, Chou SH, Lin CC, Neidle S, Hou MH. Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism. Nucleic Acids Res 2022; 50:8867-8881. [PMID: 35871296 PMCID: PMC9410880 DOI: 10.1093/nar/gkac629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/24/2022] [Accepted: 07/22/2022] [Indexed: 12/12/2022] Open
Abstract
The use of multiple drugs simultaneously targeting DNA is a promising strategy in cancer therapy for potentially overcoming single drug resistance. In support of this concept, we report that a combination of actinomycin D (ActD) and echinomycin (Echi), can interact in novel ways with native and mismatched DNA sequences, distinct from the structural effects produced by either drug alone. Changes in the former with GpC and CpG steps separated by a A:G or G:A mismatch or in a native DNA with canonical G:C and C:G base pairs, result in significant asymmetric backbone twists through staggered intercalation and base pair modulations. A wobble or Watson–Crick base pair at the two drug-binding interfaces can result in a single-stranded ‘chair-shaped’ DNA duplex with a straight helical axis. However, a novel sugar-edged hydrogen bonding geometry in the G:A mismatch leads to a ‘curved-shaped’ duplex. Two non-canonical G:C Hoogsteen base pairings produce a sharply kinked duplex in different forms and a four-way junction-like superstructure, respectively. Therefore, single base pair modulations on the two drug-binding interfaces could significantly affect global DNA structure. These structures thus provide a rationale for atypical DNA recognition via multiple DNA intercalators and a structural basis for the drugs’ potential synergetic use.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University , Taichung 402, Taiwan
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University , Taichung 402, Taiwan
| | - Shih-Hao Kao
- Institute of Biotechnology, National Chung Hsing University , Taichung 402, Taiwan
| | - Ching-Ming Chien
- Institute of Genomics and Bioinformatics, National Chung Hsing University , Taichung 402, Taiwan
| | - Shan-Ho Chou
- Institute of Biochemistry, National Chung Hsing University , Taichung 402, Taiwan
| | - Chi-Chien Lin
- Institute of Biomedical Science, National Chung Hsing University , Taichung 402, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London , London WC1N 1AX, United Kingdom
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University , Taichung 402, Taiwan
- Ph.D. Program in Medical Biotechnology, National Chung Hsing University , Taichung 402, Taiwan
- Institute of Biotechnology, National Chung Hsing University , Taichung 402, Taiwan
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Murade CU, Chaudhuri S, Nabti I, Fahs H, Refai FSM, Xie X, Pearson YE, Gunsalus KC, Shubeita GT. FRET-Based Probe for High-Throughput DNA Intercalator Drug Discovery and In Vivo Imaging. ACS Sens 2021; 6:2233-2240. [PMID: 34029461 DOI: 10.1021/acssensors.1c00167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecules that bind DNA by intercalating its bases remain among the most potent cancer therapies and antimicrobials due to their interference with DNA-processing proteins. To accelerate the discovery of novel intercalating drugs, we designed a fluorescence resonance energy transfer (FRET)-based probe that reports on DNA intercalation, allowing rapid and sensitive screening of chemical libraries in a high-throughput format. We demonstrate that the method correctly identifies known DNA intercalators in approved drug libraries and discover previously unreported intercalating compounds. When introduced in cells, the oligonucleotide-based probe rapidly distributes in the nucleus, allowing direct imaging of the dynamics of drug entry and its interaction with DNA in its native environment. This enabled us to directly correlate the potency of intercalators in killing cultured cancer cells with the ability of the drug to penetrate the cell membrane. The combined capability of the single probe to identify intercalators in vitro and follow their function in vivo can play a valuable role in accelerating the discovery of novel DNA-intercalating drugs or repurposing approved ones.
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Affiliation(s)
| | - Samata Chaudhuri
- Physics Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ibtissem Nabti
- Physics Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Hala Fahs
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Fatima S. M. Refai
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Xin Xie
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Yanthe E. Pearson
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Kristin C. Gunsalus
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 10003, United States
| | - George T. Shubeita
- Physics Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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Paramanathan T, Vladescu I, McCauley MJ, Rouzina I, Williams MC. Force spectroscopy reveals the DNA structural dynamics that govern the slow binding of Actinomycin D. Nucleic Acids Res 2012; 40:4925-32. [PMID: 22328730 PMCID: PMC3367174 DOI: 10.1093/nar/gks069] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Actinomycin D (ActD) is a small molecule with strong antibiotic and anticancer activity. However, its biologically relevant DNA-binding mechanism has never been resolved, with some studies suggesting that the primary binding mode is intercalation, and others suggesting that single-stranded DNA binding is most important. To resolve this controversy, we develop a method to quantify ActD’s equilibrium and kinetic DNA-binding properties as a function of stretching force applied to a single DNA molecule. We find that destabilization of double stranded DNA (dsDNA) by force exponentially facilitates the extremely slow ActD-dsDNA on and off rates, with a much stronger effect on association, resulting in overall enhancement of equilibrium ActD binding. While we find the preferred ActD–DNA-binding mode to be to two DNA strands, major duplex deformations appear to be a pre-requisite for ActD binding. These results provide quantitative support for a model in which the biologically active mode of ActD binding is to pre-melted dsDNA, as found in transcription bubbles. DNA in transcriptionally hyperactive cancer cells will therefore likely efficiently and rapidly bind low ActD concentrations (∼10 nM), essentially locking ActD within dsDNA due to its slow dissociation, blocking RNA synthesis and leading to cell death.
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Sajid I, Shaaban KA, Hasnain S. Antitumour compounds from a saline soil isolate,Streptomyces griseoincarnatusCTF15. Nat Prod Res 2011; 25:549-59. [DOI: 10.1080/14786419.2010.534993] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Actinomycins like anti-cancer photo-sensitizers. J Fluoresc 2011; 21:1417-20. [PMID: 21274606 DOI: 10.1007/s10895-010-0825-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 12/29/2010] [Indexed: 10/18/2022]
Abstract
Spectroscopic and microscopic study on application of actinomycins as anti-tumor photo-sensitizing drugs was carried out in this work. It has been shown that 7-aminoactinomycin (7AAMD) and actinomycin D (AMD) inside cells of line HeLa bind not only with DNA, but also with proteins. Fluorescence of 7AAMD in HeLa cells and destruction of these cells by photosensitizing with actinomycin D were detected. When photo-destruction occurs, the antibiotic is released out from destroyed cells.
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11
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Chen YC, Huang JTB, Jeng KCG, Yang RCK, Liao MK, Chen CS, Chien WJ, Wey MT, Kan LS, Sheh L. Determination of Allosteric Effects and Interstrand Bidentate Interactions in DNA-Peptide Molecular Recognition. J CHIN CHEM SOC-TAIP 2010. [DOI: 10.1002/jccs.201000041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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12
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Huang JTB, Chen YC, Chang JC, Jeng KCG, Kao KKL, Yang RCK, Kan LS, Wey MT, Waring MJ, Chen CS, Chien WJ, Sheh L. Novel DNA-peptide interaction networks. Bioorg Med Chem 2010; 18:2575-85. [PMID: 20338768 DOI: 10.1016/j.bmc.2010.02.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 02/19/2010] [Accepted: 02/19/2010] [Indexed: 10/19/2022]
Abstract
Allostery in the binding of peptides to DNA has been studied by quantitative DNase I footprinting using four newly designed peptides containing the XP(Hyp)RK motif and N-methylpyrrole (Py) moieties. Apparent binding constants in the micromolar range as well as Hill coefficients were determined for each peptide. The results, together with previous studies on five other peptides support the proposal that interaction network cooperativity is highly preferred in DNA-peptide interactions that involve multiple recognition sites. It is envisaged that interstrand bidentate interactions participate in the relay of conformational changes between recognition sites on the complementary strands. Models for interpreting DNA allostery based upon interaction networks are outlined. Circular dichroism experiments involving the titration of peptides against a short oligonucleotide duplex indicate that some of these peptides bind in a dimeric manner to DNA via the minor groove, inducing characteristic conformational changes. These insights should prompt the design of new DNA-binding peptides for investigating allosteric interactions between peptides and DNA, as well as novel interaction networks, and ultimately may shed light upon the fundamental chemical rules that govern allostery in more complex biological process such as DNA-protein interaction networks.
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Affiliation(s)
- Jonathan T B Huang
- Department of Chemistry and Life Science Research Center, Tunghai Christian University, Taichung 407, Taiwan, ROC
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Hudson JS, Brooks SC, Graves DE. Interactions of actinomycin D with human telomeric G-quadruplex DNA. Biochemistry 2009; 48:4440-7. [PMID: 19348506 DOI: 10.1021/bi900203z] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The G-quadruplex structural motif of DNA has emerged as a novel and exciting target for anticancer drug discovery. The human telomeric G-quadruplex consists of a single strand repeat of d[AGGG(TTAGGG)(3)] that can fold into higher-order DNA structures. Small molecules that selectively target and stabilize the G-quadruplex structure(s) may serve as potential therapeutic agents and have garnered significant interest in recent years. In the work presented here, the anticancer agent, actinomycin D, is demonstrated to bind to and induce changes in both structure and stability in both the Na(+) and K(+) forms of the G-quadruplex DNA. The binding of actinomycin D to the G-quadruplex DNAs is characterized by intrinsic association constants of approximately 2 x 10(5) M(-1) (strand) and 2:1 molecularity, and are shown to be enthalpically driven with binding enthalpies of approximately -7 kcal/mol. The free Na(+) or K(+) forms of the quadruplex structures differ in melting temperatures by approximately 8 degrees C (60 and 68 degrees C, respectively), whereas both forms, when complexed with actinomycin D are stabilized with melting temperatures of approximately 79 degrees C. The induced CD signals observed for the actinomycin D-G-quadruplex complexes may indicate that the phenoxazone ring of actinomycin D is stacked on the G-tetrad rather than intercalated between adjacent G-tetrads. Complex formation with actinomycin D results in changes to both the Na(+) or K(+) structural isoforms to ligand-bound complexes having similar structural properties and stabilities.
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Affiliation(s)
- Jason S Hudson
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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Kostyukov VV, Khomutova NM, Evstigneev MP. Contribution of changes in translational, rotational, and vibrational degrees of freedom to the energy of complex formation of aromatic ligands with DNA. Biophysics (Nagoya-shi) 2009. [DOI: 10.1134/s0006350909040058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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Singhal G, Rajeswari MR. Interaction of actinomycin D with promoter element of c-met and its inhibitory effect on the expression of c-Met. J Biomol Struct Dyn 2009; 26:625-36. [PMID: 19236112 DOI: 10.1080/07391102.2009.10507277] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
c-Met, the tyrosine kinase receptor for hepatocyte growth factor plays a pivotal role in normal cellular signaling and overexpression of c-Met protein is reported in several human cancers. Thus, transcriptional regulation of c-met appears to be an attractive target for chemotherapy. Therefore, we selected a 24mer GC rich sequence (24R) from the c-met promoter located at -142 to -119 from transcription start site and studied its interaction with anticancer drug, Actinomycin D. Spectroscopic analysis demonstrated a strong complexation between ActD and 24RY as shown by: (i) a high binding constant, K of 4-5 x 10(5) M(-1) with DeltaDeltaG of -47 +/- 1.5 Kcalmol(-1); (ii) marked increase by +10 degrees C in melting temperature of 24RY; and (iii) significant changes in circular dichroic spectra of both ActD and 24RY. Molecular modeling revealed the preference of ActD to the Sp1 binding site, GGCGGG, in 24RY. Expression of the c-Met was checked in HepG2 cells, a human hepatocellular carcinoma cell line by using western blotting and immunocytochemistry. Downregulation of c-Met expression by as much as 50% was observed in the presence of 20ng/ml (IC(50)) of ActD. Taking into account of the binding studies also, we feel that the down regulation of c-Met perhaps involves binding of ActD to the promoter site of c-met. Therefore, c-met could be a challenging and promising target for therapeutic strategies in combating cancer.
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Affiliation(s)
- Garima Singhal
- Department of Biochemistry, All India Institute of Medical Science, New Delhi, India
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Chen H, Dou C, Wu Y, Xi X, Gao W, Yang P. The terminal binding of base mismatched oligonucleotide d(CCGAATGAGG)2 by [Co(phen)2(DPQ)]Cl3. INORG CHEM COMMUN 2009. [DOI: 10.1016/j.inoche.2008.11.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Adamcik J, Valle F, Witz G, Rechendorff K, Dietler G. The promotion of secondary structures in single-stranded DNA by drugs that bind to duplex DNA: an atomic force microscopy study. NANOTECHNOLOGY 2008; 19:384016. [PMID: 21832575 DOI: 10.1088/0957-4484/19/38/384016] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We study the behavior of single-stranded DNA (ssDNA) in the presence of well-known drugs with either an intercalating binding mode, such as daunorubicin, actinomycin D, and chloroquine, or a minor groove binding mode, such as netropsin and berenil, by atomic force microscopy (AFM). At very low salt conditions, ssDNA molecules adopt an unstructured conformation without secondary structures. We observe that under these conditions additions of drugs that bind to double-stranded DNA (dsDNA) promote the formation of secondary structures in ssDNA. Furthermore, with an increase of concentration of the drugs, the extension as well as the thermal stabilization of these hairpins was observed.
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Affiliation(s)
- Jozef Adamcik
- Laboratoire de Physique de la Matière Vivante, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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Hundt S, Zaigler A, Lange C, Soppa J, Klug G. Global analysis of mRNA decay in Halobacterium salinarum NRC-1 at single-gene resolution using DNA microarrays. J Bacteriol 2007; 189:6936-44. [PMID: 17644597 PMCID: PMC2045193 DOI: 10.1128/jb.00559-07] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA degradation is an important factor in the regulation of gene expression. It allows organisms to quickly respond to changing environmental conditions by adapting the expression of individual genes. The stability of individual mRNAs within an organism varies considerably, contributing to differential amounts of proteins expressed. In this study we used DNA microarrays to analyze mRNA degradation in exponentially growing cultures of the extremely halophilic euryarchaeon Halobacterium salinarum NRC-1 on a global level. We determined mRNA half-lives for 1,717 open reading frames, 620 of which are part of known or predicted operons. Under the tested conditions transcript stabilities ranged from 5 min to more than 18 min, with 79% of the evaluated mRNAs showing half-lives between 8 and 12 min. The overall mean half-life was 10 min, which is considerably longer than the ones found in the other prokaryotes investigated thus far. As previously observed in Escherichia coli and Saccharomyces cerevisiae, we could not detect a significant correlation between transcript length and transcript stability, but there was a relationship between gene function and transcript stability. Genes that are known or predicted to be transcribed in operons exhibited similar mRNA half-lives. These results provide initial insights into mRNA turnover in a euryarchaeon. Moreover, our model organism, H. salinarum NRC-1, is one of just two archaea sequenced to date that are missing the core subunits of the archaeal exosome. This complex orthologous to the RNA degrading exosome of eukarya is found in all other archaeal genomes sequenced thus far.
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Affiliation(s)
- Sonja Hundt
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
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Dubail I, Bigot A, Lazarevic V, Soldo B, Euphrasie D, Dupuis M, Charbit A. Identification of an essential gene of Listeria monocytogenes involved in teichoic acid biogenesis. J Bacteriol 2006; 188:6580-91. [PMID: 16952950 PMCID: PMC1595501 DOI: 10.1128/jb.00771-06] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Listeria monocytogenes is a facultative intracellular gram-positive bacterium responsible for severe opportunistic infections in humans and animals. We had previously identified a gene encoding a putative UDP-N-acetylglucosamine 2-epimerase, a precursor of the teichoic acid linkage unit, in the genome of L monocytogenes strain EGD-e. This gene, now designated lmo2537, encodes a protein that shares 62% identity with the cognate epimerase MnaA of Bacillus subtilis and 55% identity with Cap5P of Staphylococcus aureus. Here, we addressed the role of lmo2537 in L. monocytogenes pathogenesis by constructing a conditional knockout mutant. The data presented here demonstrate that lmo2537 is an essential gene of L. monocytogenes that is involved in teichoic acid biogenesis. In vivo, the conditional mutant is very rapidly eliminated from the target organs of infected mice and thus is totally avirulent.
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Affiliation(s)
- Iharilalao Dubail
- Faculté de Médecine Necker, 156, Rue de Vaugirard, 75730 Paris Cedex 15, France
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Li H, Peng X, Leonard P, Seela F. Binding of actinomycin C1 (D) and actinomin to base-modified oligonucleotide duplexes with parallel chain orientation. Bioorg Med Chem 2006; 14:4089-100. [PMID: 16500105 DOI: 10.1016/j.bmc.2006.02.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 02/01/2006] [Accepted: 02/03/2006] [Indexed: 11/29/2022]
Abstract
The binding of actinomycin D (C1, 1) and its analog actinomin (2) was studied on base-modified oligonucleotide duplexes with parallel chain orientation (ps) and with anti-parallel chains (aps) for comparison. Actinomycin D binds not only to aps duplexes containing guanine-cytosine base pairs but also to those incorporating modified bases such as 7-deazaguanine or its 6-deoxo derivative. For this, novel phosphoramidites were prepared. The new building block of 7-deaza-2'-deoxyguanosine is significantly more stable than the one currently used and allows normal oxidation conditions during solid-phase oligonucleotide synthesis. Actinomycin binds weakly to ps duplexes containing guanine-isocytosine base pairs but not to ps-DNA incorporating pairs of isoguanine-cytosine residues. On the contrary, the actinomycin D analog actinomin, which contains positively charged side chains instead of the chiral peptide rings, is strongly bound to both ps- and aps-DNA. Guanines, isoguanine, as well as other 7-deaza derivatives are accepted as nucleobases. Apparently, the pentapeptide lacton rings of actinomycin do not fit nicely into the groove of ps-DNA thereby reducing the binding strength of the antibiotic while the groove size of ps-DNA does not affect actinomin binding notably.
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Affiliation(s)
- Hong Li
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
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21
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Lewis MA, Long EC. Fluorescent intercalator displacement analyses of DNA binding by the peptide-derived natural products netropsin, actinomycin, and bleomycin. Bioorg Med Chem 2006; 14:3481-90. [PMID: 16439138 DOI: 10.1016/j.bmc.2006.01.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Revised: 01/04/2006] [Accepted: 01/04/2006] [Indexed: 11/17/2022]
Abstract
The response of the high-throughput fluorescent intercalator displacement (HT-FID) assay reported recently by Boger et al. to peptide-based DNA binding intercalators and metal complexes was examined through the study of actinomycin and Co(III).bleomycin-B2. Along with a validation of netropsin that illustrated the good laboratory-to-laboratory reproducibility of the assay, our examination of actinomycin revealed results for a four base pair cassette library of DNA hairpins that paralleled the known DNA site-selectivity of this agent and also indicated the involvement of the flanking sequences of the hairpin oligonucleotide. In addition, for Co(III).bleomycin-B2 the established cleavage site-selectivity for 5'-GT and 5'-GC sites was correlated to drug-DNA association in this binding-only assay; our results also suggest a tetranucleotide site-selectivity for metallobleomycin involving cross-strand, 'back-to-back' 5'-GT and 5'-GC sites such as 5'-ACGT and 5'-ACGC.
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Affiliation(s)
- Mark A Lewis
- Department of Chemistry and Chemical Biology, Purdue School of Science, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, USA
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22
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Kurosawa K, Bui VP, VanEssendelft JL, Willis LB, Lessard PA, Ghiviriga I, Sambandan TG, Rha CK, Sinskey AJ. Characterization of Streptomyces MITKK-103, a newly isolated actinomycin X2-producer. Appl Microbiol Biotechnol 2005; 72:145-154. [PMID: 16374634 DOI: 10.1007/s00253-005-0240-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Revised: 10/21/2005] [Accepted: 11/01/2005] [Indexed: 11/29/2022]
Abstract
A new actinomycete strain designated MITKK-103 was isolated from the soil of a flowerpot using a humic acid agar medium. The newly isolated strain was able to produce a large amount of actinomycin X2 even under nonoptimized growing conditions and serves as a promising source of this antibiotic. Actinomycin X2 has higher cytotoxicity toward cultured human leukemia (HL-60) cells than does actinomycin D, and it induces cell death via apoptosis. A nearly complete 16S ribosomal DNA (rDNA) sequence from the isolate was determined and found to have high identity (98.5-100%) with Streptomyces galbus, Streptomyces griseofuscus, and Streptomyces padanus, indicating that MITKK-103 belongs to the genus Streptomyces. The isolate clustered with species belonging to the S. padanus clade in a 16S-rDNA-based phylogenetic tree and showed 75% overall homology to S. padanus ATCC 25646 in DNA-DNA relatedness analysis. Although the growth of the isolate was somewhat different from the three species mentioned, the strain MITKK-103 most closely resembles S. padanus on the basis of the morphological and phenotypic characteristics, phylogenetic analysis, and genotypic data. As such, this is the first report of a strain of S. padanus capable of producing actinomycins.
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MESH Headings
- Bacterial Typing Techniques
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Dactinomycin/analogs & derivatives
- Dactinomycin/biosynthesis
- Dactinomycin/toxicity
- HL-60 Cells
- Humans
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- Pigments, Biological/biosynthesis
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
- Streptomyces/classification
- Streptomyces/isolation & purification
- Streptomyces/metabolism
- Streptomyces/ultrastructure
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Affiliation(s)
- K Kurosawa
- Department of Biology, Building 68-370, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - V P Bui
- Department of Biology, Building 68-370, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - J L VanEssendelft
- Department of Biology, Building 68-370, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - L B Willis
- Department of Biology, Building 68-370, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - P A Lessard
- Department of Biology, Building 68-370, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - I Ghiviriga
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - T G Sambandan
- Biomaterials Science and Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - C K Rha
- Biomaterials Science and Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - A J Sinskey
- Department of Biology, Building 68-370, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Department of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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