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Tripathi AK. Binding interaction of N-acetylated acridine conjugate with ct-DNA and β-cyclodextrin: Synthesis and photophysical studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 205:497-502. [PMID: 30059876 DOI: 10.1016/j.saa.2018.07.069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/03/2018] [Accepted: 07/23/2018] [Indexed: 05/17/2023]
Abstract
In the present work we are reporting the synthesis and binding interaction of a saturated fatty acid containing 9-aminoacridine derivative (AC-PA) with ct-DNA and β-cyclodextrin (β-CD). From Steady-state fluorescence experiments this newly synthesized 9-aminoacridine derivative, AC-PA, shows more efficient binding interaction with ct-DNA as compared to the 9-aminoacridine (AC). The extent of interaction of AC-PA and AC with ct-DNA was found out by calculating the fluorescence quenching by using Stern-Volmer quenching equation. The calculated quenching constants of AC-PA and AC are (4.5 ± 0.5) × 103M-1 (3.7 ± 0.5) × 103M-1 respectively. The mechanism of fluorescence quenching of AC-PA and AC, were understand by using Stern-Volmer plots as well as time-resolved fluorescence experiments. The fluorescence quenching of AC-PA and AC by ct-DNA are static in nature and take place by formation of ground state complexes. The binding mode between AC-PA and AC were understood by DNA melting analysis experiment. The DNA melting analysis experiments were reveals that the binding interactions between fluorophores (AC-PA and AC) with ct-DNA are intercalative in nature. The melting temperature and mode of binding intercalative mode of binding between AC-PA and AC were further confirmed by DSC and CD experiments. The steady-state and time-resolved fluorescence parameters of AC-PA are quite sensitive towards the formation of inclusion complexes between AC-PA and β-CD. Long hydrophobic tail containing acridine conjugate (AC-PA) shows more efficient binding interactions with the β-CD and the calculated binding constants value of AC-PA is 0.51 × 102M-1. Whereas, the parent molecule, AC not showing any binding interactions with β-CD.
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Affiliation(s)
- Alok Kumar Tripathi
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, India.
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Saha M, Nandy P, Chakraborty M, Das P, Das S. The importance of pK a in an analysis of the interaction of compounds with DNA. Biophys Chem 2018; 236:15-21. [PMID: 29525503 DOI: 10.1016/j.bpc.2018.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/27/2018] [Accepted: 02/04/2018] [Indexed: 01/29/2023]
Abstract
pKa of a compound is crucial for determining the contributions of different forms of it towards overall binding with DNA. Hence it is important to use correct pKa values in DNA interaction studies. This study takes a look at the importance of pKa values to realize binding of compounds with DNA. Since pKa of a compound determined in the presence of DNA is quite different from that determined in its absence hence, presence of different forms of a compound during interaction with DNA is different from that realized if the determination of pKa is done in normal aqueous solution in absence of DNA. Hence, calculations determining contributions of different forms of a compound interacting with DNA are affected accordingly. Two simple analogues of anthracyclines, alizarin and purpurin, were used to investigate the influence DNA has on pKa values. Indeed, they were different in presence of DNA than when determined in normal aqueous solution. pKa1 for alizarin and purpurin determined in the absence and presence of calf thymus DNA were used in equations that determine contributions of two forms (neutral and anionic) towards overall binding with DNA. The study concludes that correct pKa values, determined correctly i.e. under appropriate conditions, must be used for DNA binding experiments to evaluate contributions of individual forms.
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Affiliation(s)
- Mouli Saha
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India
| | - Promita Nandy
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India
| | | | - Piyal Das
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India
| | - Saurabh Das
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India.
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3
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Chemical structures and biological activities of bis- and tetrakis-acridine derivatives: A review. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.05.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Wong PT, Tang K, Coulter A, Tang S, Baker JR, Choi SK. Multivalent Dendrimer Vectors with DNA Intercalation Motifs for Gene Delivery. Biomacromolecules 2014; 15:4134-45. [DOI: 10.1021/bm501169s] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Pamela T. Wong
- Michigan Nanotechnology Institute for Medicine
and Biological Sciences and ‡Department of
Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Kenny Tang
- Michigan Nanotechnology Institute for Medicine
and Biological Sciences and ‡Department of
Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Alexa Coulter
- Michigan Nanotechnology Institute for Medicine
and Biological Sciences and ‡Department of
Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Shengzhuang Tang
- Michigan Nanotechnology Institute for Medicine
and Biological Sciences and ‡Department of
Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - James R. Baker
- Michigan Nanotechnology Institute for Medicine
and Biological Sciences and ‡Department of
Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Seok Ki Choi
- Michigan Nanotechnology Institute for Medicine
and Biological Sciences and ‡Department of
Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
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5
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Quantitative structure–property relationship study on the intercalation of anticancer drugs with ct-DNA. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0716-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Csuk R, Barthel A, Raschke C, Kluge R, Ströhl D, Trieschmann L, Böhm G. Synthesis of Monomeric and Dimeric Acridine Compounds as Potential Therapeutics in Alzheimer and Prion Diseases. Arch Pharm (Weinheim) 2009; 342:699-709. [DOI: 10.1002/ardp.200900065] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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7
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Hvastkovs EG, Buttry DA. Electrochemical Detection of DNA Hybridization via Bis-Intercalation of a Naphthylimide-Functionalized Viologen Dimer. Anal Chem 2007; 79:6922-6. [PMID: 17696404 DOI: 10.1021/ac070358e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis and DNA binding properties of a bis-naphthyl imide tetracationic diviologen compound NI(CH2)3V(2+)(CH2)6V(2+)(CH2)3NI (where V(2+) = 4,4'-bipyridinium and NI = naphthyl imide, NIV) are described. Binding to thiolated ssDNA and dsDNA immobilized at Au electrodes was characterized using the electrochemical response for reduction of the V(2+) state to the V+ (viologen radical cation) state. Isotherms and binding constants for this molecule to both forms of immobilized DNA were generated in this fashion. The character of the binding isotherm for dsDNA suggests bis-intercalation. Under high saline conditions, the diviologen molecule dissociated 160 times slower from dsDNA compared to ssDNA. Slow dissociation kinetics from dsDNA (kd =7.0 x 10-5 s(-1)) allow this molecule to be used as an effective DNA hybridization indicator.
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Affiliation(s)
- Eli G Hvastkovs
- Department of Chemistry (3838), University of Wyoming, 1000 East University Avenue, Laramie, Wyoming 82070, USA
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Tarasov SG, Casas-Finet JR, Cholody WM, Kosakowska-Cholody T, Gryczynski ZK, Michejda CJ. Bisimidazoacridones: 2. Steady-state and Time-resolved Fluorescence Studies of Their Diverse Interactions with DNA¶§. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2003)0780313bsatfs2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Park MS, Swamy K, Lee YJ, Lee HN, Jang YJ, Moon YH, Yoon J. A new acridine derivative as a fluorescent chemosensor for zinc ions in an 100% aqueous solution: a comparison of binding property with anthracene derivative. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.09.029] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Cholody WM, Kosakowska-Cholody T, Hollingshead MG, Hariprakasha HK, Michejda CJ. A New Synthetic Agent with Potent but Selective Cytotoxic Activity against Cancer. J Med Chem 2005; 48:4474-81. [PMID: 15974599 DOI: 10.1021/jm048946x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of novel unsymmetrical bifunctional antitumor agents was accomplished by linking an imidazoacridone moiety to another polycyclic heteroaromatic moiety via linkers of various length and rigidity. These compounds bind to cellular DNA, but it is hypothesized that biological effects become manifested when the drug-DNA complexes interact with critical DNA binding proteins that are involved in repair and transcription. The most promising compound of the series, 4ad (WMC79), consists of an imidazoacridone linked to a 3-nitronaphthalimide moiety via a 1,4-dipropanopiperazine linker. It was found to be potently, but selectively, cytotoxic against colon cancers (GI(50) = 0.5 nM, LC(50) = 32 nM) and leukemias (GI(50) = 3.5 nM, LC(50) = 33 nM). Compound 4ad, which appears to be a candidate for further development as an anticancer drug, kills sensitive cells by induction of apoptosis. It also showed significant in vivo activity against HCT-116 colon cancer xenografts in nude mice. Other compounds in the series also exhibited antitumor properties, but they were significantly lower than that of 4ad.
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Affiliation(s)
- Wieslaw M Cholody
- Molecular Aspects of Drug Design, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland 21702, USA
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Woodhouse SL, Ziolkowski EJ, Rendina LM. Synthesis and anti-cancer activity of dinuclear platinum(ii) complexes containing bis(thioalkyl)dicarba-closo-dodecaborane(12) ligands. Dalton Trans 2005:2827-9. [PMID: 16094469 DOI: 10.1039/b508340k] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of novel, dinuclear (2,2':6',2''-terpyridine)platinum(ii) complexes containing bis(thioalkyl)-dicarba-closo-dodecaborane(12)(carborane) ligands were prepared and characterised, and their preliminary anti-cancer characteristics have been determined in vitro; the complexes are the first examples of bis-intercalator complexes containing a boron-rich carborane cage.
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Affiliation(s)
- Susan L Woodhouse
- School of Chemistry and Physics, The University of Adelaide, Adelaide, South Australia 5005, Australia
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12
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Interactions of acyclic and cyclic bis-phenanthridinium derivatives with ss- and ds-polynucleotides. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.05.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Tarasov SG, Casas-Finet JR, Cholody WM, Kosakowska-Cholody T, Gryczynski ZK, Michejda CJ. Bisimidazoacridones: 2. Steady-state and Time-resolved Fluorescence Studies of Their Diverse Interactions with DNA¶§. Photochem Photobiol 2003; 78:313-22. [PMID: 14626657 DOI: 10.1562/0031-8655(2003)078<0313:bsatfs>2.0.co;2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Several bisimidazoacridones (BIA) are potent, selective antineoplastic agents, whereas others have potent anti-human immunodeficiency virus activity. BIA are bifunctional agents that consist of two imidazoacridone (IA) chromophores held together by various linkers. Interaction of BIA with DNA has been postulated to be required for their biological activity. Fluorescence data on free and bound BIA suggest that the binding of BIA and similar drugs to DNA is driven by a transfer of hydrophobic molecules from aqueous media to the more amphiphilic DNA environment. Binding to DNA was sensitive to sequence and depended on the length and rigidity of the linker. Time-resolved fluorescence measurements showed that BIA adopt an extended conformation upon binding and that all of the molecules are tightly associated with DNA. Gel-shift and melting assays indicated that one of the aromatic residues of BIA is intercalated, whereas the other, together with a linker, resides in a groove, probably the minor groove. A continuum of structures may be possible where intercalation and classical minor groove binding are limiting structures. In general, the hypothesis for the mechanism of action of BIA wherein the unintercalated residue, accessible for additional interactions, captures a critical protein involved in repair or transcription, is consistent with this model.
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Affiliation(s)
- Sergey G Tarasov
- Molecular Aspects of Drug Design Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick, Frederick, MD, USA.
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Girault S, Grellier P, Berecibar A, Maes L, Mouray E, Lemière P, Debreu MA, Davioud-Charvet E, Sergheraert C. Antimalarial, antitrypanosomal, and antileishmanial activities and cytotoxicity of bis(9-amino-6-chloro-2-methoxyacridines): influence of the linker. J Med Chem 2000; 43:2646-54. [PMID: 10893302 DOI: 10.1021/jm990946n] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Forty bis(9-amino-6-chloro-2-methoxyacridines), in which acridine moieties are joined by alkanediamines, polyamines, or polyamines substituted by a side chain, were synthesized and tested for their in vitro activity upon the erythrocytic stage of Plasmodium falciparum, trypomastigote stage of Trypanosoma brucei, and amastigote stage of Trypanosoma cruzi and Leishmania infantum as well as for their cytotoxic effects upon MRC-5 cells. Results clearly showed the importance of the nature of the linker and of its side chain for antiparasitic activity, cytotoxicity, and cellular localization. Among several compounds devoid of cytotoxic effects at 25 microM upon MRC-5 cells, one displayed IC(50) values ranging from 8 to 18 nM against different P. falciparum strains while three others totally inhibited T. brucei at 1.56 microM.
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Affiliation(s)
- S Girault
- UMR 8525 CNRS, Université de Lille II, Institut de Biologie et Institut Pasteur de Lille, 1 rue du Professeur Calmette, BP 447, 59021 Lille, France
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Abstract
A quantitative technique for the nondestructive visualization of nanometer scale intermolecular separations in a living system is described. A calibration procedure for the acquisition and analysis of resonance energy transfer (RET) image data is outlined. The factors limiting RET imaging of biological samples are discussed. Measurements required for the calibration include: (a) the spectral sensitivity of the image intensifier (or camera); (b) the transmission spectra of the emission filters; and (c) the quantum distribution functions of the energy transfer pair measured in situ. Resonance energy transfer imaging is demonstrated for two DNA specific dyes. The Förster critical distance for energy transfer between Hoechst 33342 (HO) and acridine orange (AO) is 4.5 +/- 0.7 nm. This distance is slightly greater than the distance of a single turn of the DNA helix (3.5 nm or approximately 10 base pairs), and is well below the optical diffraction limit. Timed sequences of intracellular energy transfer reveal nuclear structure, strikingly similar to that observed with confocal and electron microscopy, and may show the spatial distribution of eu- and hetero- chromatin in the interphase nuclei.
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Affiliation(s)
- M Ludwig
- C. W. Bill Young Marrow Donor Recruitment and Research Program, Naval Medical Research Institute, Bethesda, Maryland 20889-5055
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Pothier J, Delepierre M, Barsi MC, Garbay-Jaureguiberry C, Igolen J, Le Bret M, Roques BP. Comparison of the bis-intercalating complexes formed between either ditercalinium or a flexible analogue and d(CpGpCpG)2 or d(TpTpCpGpCpGpApA)2 minihelices: 1H- and 31P-NMR analyses. Biopolymers 1991; 31:1309-23. [PMID: 1777582 DOI: 10.1002/bip.360311109] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The 400-MHz 1H- and 162-MHz 31P-nmr have been used to study complexes constituted by (a) the d(TpTpCpGpCpGpApA)2 or the d(CpGpCpG)2 self-complementary oligonucleotides and (b) two bifunctional 7H-pyrido [4,3-c] carbazole dimer drugs, the antitumoral ditercalinium (NSC 366241), a dimer with a rigid bis-piperidine linking chain and its pharmacologically inactive analogue, a dimer with a flexible spermine-like linking chain. Nearly all proton and phosphorus signals have been assigned by two-dimensional (2D) nmr (correlated spectroscopy, homonuclear Hartmann-Hahn, nuclear Overhauser enhancement spectroscopy, 2D 31P (1H) heteronuclear correlated spectroscopy and 31P-31P chemical exchange experiments). Both drugs bis-intercalate into the two CpG sites. The complexes show small differences in the position of the 7H-pyrido [4,3-c] carbazole ring into the intercalation site and possibly in the ribose-phosphate backbone deformation. However, the inactive analogue exhibits a longer residence lifetime in octanucleotide than the ditercalinium does. All these results are discussed in terms of differences in dimer activities.
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Affiliation(s)
- J Pothier
- Département de Chimie Organique U266 INSERM, Paris, France
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Möller U, Cech D, Schubert F. P(III)-Acridinderivate als Synthesebausteine für die Festphasensynthese nichtradioaktiv markierter Oligonucleotide. ACTA ACUST UNITED AC 1990. [DOI: 10.1002/jlac.1990199001220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Coulombeau C, Gresh N. A theoretical investigation of the base sequence preferences of monointercalating polymethylene carboxamide derivatives 9-aminoacridine. Nucleic Acids Res 1990; 18:711-7. [PMID: 2315037 PMCID: PMC330317 DOI: 10.1093/nar/18.4.711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Theoretical computations are performed of the comparative binding affinities of five polymethylene carboxamide derivatives of 9-aminoacridine to a series of double-stranded hexanucleotides. The purpose of this investigation is to ascertain whether minor groove recognition of a guanine base adjacent to the intercalation site can occur, and be preferentially stabilized, for a given length of the polymethylene side chain, encompassing from n = 2 up to n = 6 methylene groups. For that purpose, several representative sequences were investigated, in which intercalation of the 9-aminoacridine chromophore occurred at a central d(CpG) or d(TpA) step. Investigated were the self-complementary sequences d(CGCGCG)2, d(GCCGGC)2, d(TATATA)2 and d(ATTAAT)2, as well as the 'mixed' sequences d(ACTAAT) .d(ATTAGT) and d(TGTATA). d(TATACA). For n = 3 up to n = 6, such a recognition was enabled only when the guanine base was located downstream of the intercalation site, i.e. with steps d(CGG) and d(TAG). It occurred by means of a bidentate interaction involving, on the one hand, H(N2) and N3 of the base, and, on the other hand, the carbonyl oxygen and the cis amino hydrogen of the terminal formamide moiety of the ligand. Because of the flexibility of the side chain, however, alternative binding modes were also found to occur competitively, involving backbone-only interactions of the side chain. On the basis of the present computations, upon binding to the sequence d(GCCGGC)2, an optimal value of n = 5 could be derived, with the corresponding acridine derivative eliciting both a significant prevalence of the bidentate over backbone only binding mode, and the most favourable energy balance within the investigated series. This privileged value of n = 5 is fully consistent with the experimental results of Markovits et al. and Gaugain et al. The very flexibility of the side chain, however, hampered any preferential recognition of a triplet sequence with a downstream guanine, such as d(CGG) or d(TAG), to be elicited over sequences such as d(TAA), d(TAT) or d(TAC).
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Affiliation(s)
- C Coulombeau
- Université J.Fourier, LEDSS VI, BP 53F, Grenoble, France
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