51
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Chan DSH, Yang H, Kwan MHT, Cheng Z, Lee P, Bai LP, Jiang ZH, Wong CY, Fong WF, Leung CH, Ma DL. Structure-based optimization of FDA-approved drug methylene blue as a c-myc G-quadruplex DNA stabilizer. Biochimie 2011; 93:1055-64. [DOI: 10.1016/j.biochi.2011.02.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 02/24/2011] [Indexed: 12/20/2022]
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52
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Won BY, Shin S, Baek S, Jung YL, Li T, Shin SC, Cho DY, Lee SB, Park HG. Investigation of the signaling mechanism and verification of the performance of an electrochemical real-time PCR system based on the interaction of methylene blue with DNA. Analyst 2011; 136:1573-9. [DOI: 10.1039/c0an00695e] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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53
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Hosseini SS, Bhadbhade M, Clarke RJ, Rutledge PJ, Rendina LM. Synthesis, carbohydrate- and DNA-binding studies of cationic 2,2′:6′,2′′-terpyridineplatinum(ii) complexes containing N- and S-donor boronic acid ligands. Dalton Trans 2011; 40:506-13. [DOI: 10.1039/c0dt00892c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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54
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Zięba A, Sochanik A, Szurko A, Rams M, Mrozek A, Cmoch P. Synthesis and in vitro antiproliferative activity of 5-alkyl-12(H)-quino[3,4-b] [1,4]benzothiazinium salts. Eur J Med Chem 2010; 45:4733-9. [DOI: 10.1016/j.ejmech.2010.07.035] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 06/28/2010] [Accepted: 07/18/2010] [Indexed: 11/25/2022]
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55
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Chowdhury SR, Islam MM, Kumar GS. Binding of the anticancer alkaloid sanguinarine to double stranded RNAs: insights into the structural and energetics aspects. MOLECULAR BIOSYSTEMS 2010; 6:1265-76. [PMID: 20442937 DOI: 10.1039/b927001a] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Elucidation of the molecular aspects of small molecule-RNA complexation is of prime importance for rational RNA targeted drug design strategies. Towards this, the interaction of the cytotoxic plant alkaloid sanguinarine to three double stranded ribonucleic acids, poly (A).poly(U), poly(I).poly(C) and poly(C).poly(G) was studied using various biophysical and thermodynamic techniques. Absorbance and fluorescence studies showed that the alkaloid bound cooperatively to these RNAs with binding affinities of the order 10(4) M(-1). Fluorescence quenching and hydrodynamic studies gave evidence for intercalation of sanguinarine to these RNA duplexes. Isothermal titration calorimetric studies revealed that the binding was characterized by negative enthalpy and positive entropy changes and the affinity constants derived were in agreement with the overall binding affinity values obtained from spectroscopic data. The binding of sanguinarine stabilized the melting of poly(A). poly(U) and poly(I).poly(C) and the binding data evaluated from the melting data were in agreement with that obtained from other techniques. The overall binding affinity of sanguinarine to these double stranded RNAs varied in the order, poly(A).poly(U) > poly(I).poly(C) >> poly(C).poly(G). The temperature dependence of the enthalpy changes afforded negative values of heat capacity changes for the binding of sanguinarine to poly(A).poly(U) and poly(I).poly(C), suggesting substantial hydrophobic contribution in the binding process. Further, enthalpy-entropy compensation phenomena was also seen in poly(A).poly(U) and poly(I).poly(C) systems that correlated to the strong binding involving a multiplicity of weak noncovalent interactions compared to the weak binding with poly(C).poly(G). These results further advance our understanding on the binding of small molecules that are specific binders to double stranded RNA sequences.
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Affiliation(s)
- Sebanti Roy Chowdhury
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology (CSIR), 4, Raja S. C. Mullick Road, Kolkata 700032, India
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56
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Paul P, Hossain M, Yadav RC, Kumar GS. Biophysical studies on the base specificity and energetics of the DNA interaction of photoactive dye thionine: Spectroscopic and calorimetric approach. Biophys Chem 2010; 148:93-103. [DOI: 10.1016/j.bpc.2010.02.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 02/22/2010] [Accepted: 02/23/2010] [Indexed: 12/01/2022]
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57
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Survey of the year 2008: applications of isothermal titration calorimetry. J Mol Recognit 2010; 23:395-413. [DOI: 10.1002/jmr.1025] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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58
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Chi Z, Liu R, Zhao X, Sun Y, Yang B, Gao C. Study on the genotoxic interaction of methyl violet with calf thymus DNA. APPLIED SPECTROSCOPY 2009; 63:1331-1335. [PMID: 20030976 DOI: 10.1366/000370209790109085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
By utilizing ultraviolet (UV)-visible absorption spectroscopy, circular dichroism (CD), resonance light scattering (RLS), and transmission electron microscope (TEM) techniques, the toxic interaction of methyl violet (MV) with calf thymus DNA (ctDNA) was investigated at the molecular level. The UV-visible absorption spectra results showed that MV intercalated into ctDNA base pairs at low MV concentrations, while MV was attached to the negative charged phosphate groups at higher concentrations and the binding constant (K(theta)(25 degrees C)) was 1.80 x 10(3) L mol(-1). The absorbency results showed that the genotoxic interaction of MV with ctDNA is under the electrostatic binding mode. MV had strong toxic interaction with ctDNA at 4.0 x 10(-5) mol L(-1) MV and pH 6.5. The toxic interaction of MV with ctDNA can result in the formation of massive aggregates and change of the ctDNA conformation, which showed a significant linear dose-response relationship.
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Affiliation(s)
- Zhenxing Chi
- School of Environmental Science and Engineering, Shandong University, 27# Shanda South Road, Jinan 250100, PR China
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59
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Abstract
Most of the anticancer chemotherapeutic drugs that are broadly and successfully used today are DNA-damaging agents. Targeting of DNA has been proven to cause relatively potent and selective destruction of tumor cells. However, the clinical potential of DNA-damaging agents is limited by the adverse side effects and increased risk of secondary cancers that are consequences of the agents' genotoxicity. In this review, we present evidence that those agents capable of targeting DNA without inducing DNA damage would not be limited in these ways, and may be as potent as DNA-damaging agents in the killing of tumor cells. We use as an example literature data and our own research of the well-known antimalarial drug quinacrine, which binds to DNA without inducing DNA damage, yet modulates a number of cellular pathways that impact tumor cell survival.
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Affiliation(s)
- Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA.
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60
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Passeri R, Aloisi GG, Elisei F, Latterini L, Caronna T, Fontana F, Sora IN. Photophysical properties of N-alkylated azahelicene derivatives as DNA intercalators: counterion effects. Photochem Photobiol Sci 2009; 8:1574-82. [PMID: 19862416 DOI: 10.1039/b9pp00015a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, three compounds having the same organic moiety (N-methyl-5-azahelicenium salts) but different counterions (I-, NO3- and COOCF3-) have been investigated in buffered aqueous solutions and in the presence of DNA to give information on the counterion effects on the binding. In particular, the absorption spectra, fluorescence quantum yields and fluorescence lifetimes in aqueous solution for free organic molecules have been determined by steady-state and time-resolved spectrofluorimetric measurements. The obtained values are compared with those of the chromophores in the presence of increasing concentrations of DNA. The results allow determination of the association constants (K(a)) and the number of base couples per chromophore molecule (n) by means of the McGhee Von Hippel model. The binding parameters are strongly affected by the nature of counterions since the highest K(a) value was determined for the compound having COOCF3-; on the other hand the NO3- derivative is able to interact with the highest number of binding sites. The morphology and structural properties of the DNA-chromophore complexes were investigated by circular dichroism (CD) and atomic force microscopy (AFM). The data revealed that I- and COOCF3- derivatives preferentially form intercalation complexes, while the NO3- salt is able to form intercalation and grove binding complexes at the same time.
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Affiliation(s)
- Rosita Passeri
- Dipartimento di Chimica and Centro di Eccellenza Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto, 8, 06123, Perugia, Italy
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61
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Hossain M, Suresh Kumar G. DNA intercalation of methylene blue and quinacrine: new insights into base and sequence specificity from structural and thermodynamic studies with polynucleotides. MOLECULAR BIOSYSTEMS 2009; 5:1311-22. [PMID: 19823747 DOI: 10.1039/b909563b] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding of the known DNA intercalators methylene blue and quinacrine with four sequence specific polynucleotides, viz. poly(dG-dC).poly(dG-dC), poly(dG).poly(dC), poly(dA-dT).poly(dA-dT) and poly(dA).poly(dT), have been compared using absorbance, fluorescence, competition dialysis and thermal melting and the thermodynamic aspects of the interaction studied. In all the cases, non-cooperative binding phenomena obeying neighbor exclusion principle was observed though the affinity was remarkably higher for quinacrine and the nature of the binding was characterized to be true intercalation. The data on the salt dependence of binding derived from the plot of log Kvs. log[Na(+)] revealed a slope of around 1.0, consistent with the values predicted by the theories for the binding of monovalent cations, and contained contributions from polyelectrolytic and non-polyelectrolytic forces. The bindings were characterized by strong stabilization of the polynucleotides against thermal strand separation in both optical melting as well as differential scanning calorimetry studies. The data analyzed from the thermal melting and isothermal titration calorimetry studies were in close proximity to those obtained from absorption spectral titration data. Isothermal titration calorimetry results revealed the bindings to poly(dG-dC).poly(dG-dC), poly(dG).poly(dC) and poly(dA-dT).poly(dA-dT) to be exothermic and favoured by both negative enthalpy and large favourable positive entropy changes, while that to poly(dA).poly(dT) was endothermic and entropy driven. The heat capacity changes obtained from temperature dependence of enthalpy gave negative values to all polynucleotides. New insights on the molecular aspects of interaction of these molecules to DNA have emerged from these studies.
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Affiliation(s)
- Maidul Hossain
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology (Council of Scientific and Industrial Research), 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
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Gao JT, Liu SH, Yan YE, Wu Y, Wu HT, Xing C, Ge XM, Wang H, Zhao YQ, Fan M. Quinacrine protects neuronal cells against heat-induced injury. Cell Biol Int 2009; 33:874-81. [PMID: 19427915 DOI: 10.1016/j.cellbi.2009.04.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Revised: 03/18/2009] [Accepted: 04/14/2009] [Indexed: 11/16/2022]
Abstract
The effects of quinacrine (QA) on heat-induced neuronal injury have been explored, with the intention of understanding the mechanisms of QA protection. Primary cultivated striatum neurons from newborn rats were treated with QA 1h before heat treatment at 43 degrees C which lasted for another 1h, and necrosis and apoptosis were detected by Annexin-V-FITC and propidium iodide (PI) double staining. Neuronal apoptosis was determined using terminal deoxynucleotidyl transferase-mediated biotinylated UTP nick end labeling (TUNEL) techniques. Cell membrane fluidity, activity of cytosolic phospholipase A(2) (cPLA(2)) and the level of arachidonic acid (AA) were also examined. Membrane surface ultrastructure of striatum neurons was investigated by atomic force microscopy (AFM). Results showed that heat treatment induced great striatum neurons death, with many dying neurons undergoing necrosis rather than apoptosis. QA alone had little effect on the survival of striatum neurons, while QA pretreatment before heat treatment decreased necrosis. Heat treatment also resulted in decreased membrane fluidity and increased cPLA(2) activity as well as arachidonic acid level; these effects were reversed by QA pretreatment. QA pretreatment also significantly prevented damage to the membrane surface ultrastructure of heat-treated neurons. These results suggest that QA protects striatum neurons against heat-induced neuronal necrosis, and also demonstrate that inhibition of cPLA(2) activity and stabilization of membranes may contribute to protective effect of quinacrine.
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Affiliation(s)
- Jun-Tao Gao
- Department of Neurobiology, Capital Medical University, Beijing 100069, China
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63
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Islam MM, Pandya P, Kumar S, Kumar GS. RNA targeting through binding of small molecules: Studies on t-RNA binding by the cytotoxic protoberberine alkaloidcoralyne. ACTA ACUST UNITED AC 2009; 5:244-54. [DOI: 10.1039/b816480k] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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64
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Bhadra K, Maiti M, Kumar GS. DNA-Binding Cytotoxic Alkaloids: Comparative Study of the Energetics of Binding of Berberine, Palmatine, and Coralyne. DNA Cell Biol 2008; 27:675-85. [DOI: 10.1089/dna.2008.0779] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Kakali Bhadra
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | - Motilal Maiti
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
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65
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Binding of DNA-binding alkaloids berberine and palmatine to tRNA and comparison to ethidium: Spectroscopic and molecular modeling studies. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.04.043] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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66
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Berberine-DNA complexation: new insights into the cooperative binding and energetic aspects. Biochim Biophys Acta Gen Subj 2008; 1780:1054-61. [PMID: 18549823 DOI: 10.1016/j.bbagen.2008.05.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 05/16/2008] [Accepted: 05/16/2008] [Indexed: 01/31/2023]
Abstract
The equilibrium binding of the cytotoxic plant alkaloid berberine to various DNAs and energetics of the interaction have been studied. At low ratios of bound alkaloid to base pair, the binding exhibited cooperativity to natural DNAs having almost equal proportions of AT and GC sequences. In contrast, the binding was non-cooperative to DNAs with predominantly high AT or GC sequences. Among the synthetic DNAs, cooperative binding was observed with poly(dA).poly(dT) and poly(dG).poly(dC) while non-cooperative binding was seen with poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC). Both cooperative and non-cooperative bindings were remarkably dependent on the salt concentration of the media. Linear plots of ln K(a) versus [Na(+)] for poly(dA).poly(dT) and poly(dA-dT).poly(dA-dT) showed the release of 0.56 and 0.75 sodium ions respectively per bound alkaloid. Isothermal titration calorimetry results revealed the binding to be exothermic and favoured by both enthalpy and entropy changes in all DNAs except the two AT polymers and AT rich DNA, where the same was predominantly entropy driven. Heat capacity values (DeltaCp(o)) of berberine binding to poly(dA).poly(dT), poly(dA-dT).poly(dA-dT), Clostridium perfringens and calf thymus DNA were -98, -140, -120 and -110 cal/mol K respectively. This study presents new insights into the binding dependent base pair heterogeneity in DNA conformation and the first complete thermodynamic profile of berberine binding to DNAs.
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67
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Giri P, Kumar GS. Self-structure induction in single stranded poly(A) by small molecules: Studies on DNA intercalators, partial intercalators and groove binding molecules. Arch Biochem Biophys 2008; 474:183-92. [PMID: 18387354 DOI: 10.1016/j.abb.2008.03.013] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 03/13/2008] [Accepted: 03/15/2008] [Indexed: 11/17/2022]
Abstract
Self-structure induction in single stranded poly(A) has been one typical example of the various ways that could be used to modulate nucleic acid structural aspects through binding of small molecules. For the first time, the interaction between a series of small molecules and poly(A) has been investigated to understand the nature of the structural features in DNA binding small molecules that could be responsible for the formation of self-structure in single stranded poly(A) molecules. Classical intercalators like ethidium, coralyne, quinacrine and proflavine, partial intercalators like berberine and palmatine and classical minor groove binders like hoechst 33258 and DAPI have been chosen for this study. The binding of each of these molecules to poly(A) has been characterized by absorption spectral titration, job plot and isothermal titration calorimetry. Self-structure formation was monitored from circular dichroic melting, optical melting and differential scanning calorimetry. The results revealed that while all the intercalators studied induced self-structure formation, partial intercalators did not induce the same in poly(A). Of the two classical DNA minor groove binding molecules investigated, hoechst was effective in inducing self-structure while DAPI was ineffective. Self-structure induction in poly(A) was observed to be directly linked to the cooperative binding of the molecules to poly(A) in that all the molecules that bound cooperatively induced self-structure in poly(A). Structural and thermodynamic aspects of the interaction leading to self-structure formation are described.
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Affiliation(s)
- Prabal Giri
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
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68
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Bhadra K, Maiti M, Kumar GS. Thermodynamics of the binding of cytotoxic protoberberine molecule coralyne to deoxyribonucleic acids. Biochim Biophys Acta Gen Subj 2008; 1780:298-306. [DOI: 10.1016/j.bbagen.2007.11.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 11/14/2007] [Accepted: 11/30/2007] [Indexed: 11/15/2022]
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