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Vlaho D, Fakhoury JF, Damha MJ. Structural Studies and Gene Silencing Activity of siRNAs Containing Cationic Phosphoramidate Linkages. Nucleic Acid Ther 2017; 28:34-43. [PMID: 29195060 DOI: 10.1089/nat.2017.0702] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A series of siRNA duplexes containing cationic non-bridging 3',5'-linked phosphoramidate (PN) linkages was designed and synthesized using a combination of phosphoramidite and H-phosphonate chemistries. Modified oligonucleotides were assayed for their thermal stability, helical structure, and ability to modulate the expression of firefly luciferase. We demonstrate that PN modifications of siRNAs are, in general, minimally destabilizing with respect to duplex thermal stability; destabilization can be mitigated through the incorporation of 2'-modified RNA-like residues or PN conjugates containing ionizable pendant moieties. We also demonstrate that single cationic dimethylethylenediamine PN linkages have little effect on siRNA potency, whether located in the passenger or guide strand of the duplex. Highly modified siRNA passenger strands were further modified with up to four cationic PN linkages, with little effect on duplex potency or helical structure. We envision that PN modifications could be useful in the production of therapeutic siRNAs with optimal biological properties.
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Affiliation(s)
- Danielle Vlaho
- Department of Chemistry, McGill University , Montreal, Canada
| | | | - Masad J Damha
- Department of Chemistry, McGill University , Montreal, Canada
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2
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Bag SS, Talukdar S, Das SK, Pradhan MK, Mukherjee S. Donor/acceptor chromophores-decorated triazolyl unnatural nucleosides: synthesis, photophysical properties and study of interaction with BSA. Org Biomol Chem 2016; 14:5088-108. [DOI: 10.1039/c6ob00500d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report the syntheses and photophysical properties of some triazolyl donor/acceptor unnatural nucleosides and studies on the interaction of one of the fluorescent nucleosides with BSA.
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Affiliation(s)
- Subhendu Sekhar Bag
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Sangita Talukdar
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Suman Kalyan Das
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Manoj Kumar Pradhan
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
| | - Soumen Mukherjee
- Bio-organic Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Technology Guwahati-781039
- India
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Bhowmik D, Buzzetti F, Fiorillo G, Lombardi P, Suresh Kumar G. Spectroscopic studies on the binding interaction of novel 13-phenylalkyl analogs of the natural alkaloid berberine to nucleic acid triplexes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 120:257-264. [PMID: 24184628 DOI: 10.1016/j.saa.2013.09.081] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/13/2013] [Accepted: 09/25/2013] [Indexed: 06/02/2023]
Abstract
In this study we have characterized the capability of six 13-phenylalkyl analogs of berberine to stabilize nucleic acid triplex structures, poly(rA)⋅2poly(rU) and poly(dA)⋅2poly(dT). Berberine analogs bind to the RNA and DNA triplexes non-cooperatively. As the chain length of the substitution increased beyond CH2, the affinity enhanced up to critical length of (CH2)4, there after which the binding affinity decreased for both the triplexes. A remarkably stronger intercalative binding of the analogs compared to berberine to the triplexes was confirmed from ferrocyanide fluorescence quenching, fluorescence polarization and viscosity results. Circular dichroism results had indicated strong conformational changes in the triplexes on binding of the analogs. The analogs enhanced the stability of the Hoogsteen base paired third strand of both the triplexes while no significant change in the high-temperature duplex-to-single strand transitions was observed. Energetics of the interaction revealed that as the alkyl chain length increased, the binding was more entropy driven. This study demonstrates that phenylalkyl substitution at the 13-position of berberine increased the triplex binding affinity of berberine but a threshold length of the side chain is critical for the strong intercalative binding to occur.
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Affiliation(s)
- Debipreeta Bhowmik
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR - Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Franco Buzzetti
- Naxopharma srl, Via G. Di Vittorio, 70, 20026 Novate Milanese (MI), Italy
| | - Gaetano Fiorillo
- Naxopharma srl, Via G. Di Vittorio, 70, 20026 Novate Milanese (MI), Italy
| | - Paolo Lombardi
- Naxopharma srl, Via G. Di Vittorio, 70, 20026 Novate Milanese (MI), Italy
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR - Indian Institute of Chemical Biology, Kolkata 700 032, India.
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4
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Bhowmik D, Kumar GS. Interaction of 9-O-(ω-amino) alkyl ether berberine analogs with poly(dT)·poly(dA)*poly(dT) triplex and poly(dA)·poly(dT) duplex: a comparative study. Mol Biol Rep 2013; 40:5439-50. [PMID: 23666107 DOI: 10.1007/s11033-013-2642-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 05/03/2013] [Indexed: 10/26/2022]
Abstract
Isoquinoline alkaloids and their analogs represent an important class of molecules for their broad range of clinical and pharmacological utility. These compounds are of current interest owing to their low toxicity and excellent chemo preventive properties. These alkaloids can play important role in stabilising the nucleic acid triple helices. The present study has focused on the interaction of five 9-O-(ω-amino) alkyl ether berberine analogs with the DNA triplex poly(dT)·poly(dA)*poly(dT) and the parent duplex poly(dA)·poly(dT) studied using various biophysical techniques. Scatchard analysis of the spectral data indicated that the analogs bind both to the duplex and triplex in a non-cooperative manner in contrast to the cooperative binding of berberine to the DNA triplex. Strong intercalative binding to the DNA triplex structure was revealed from ferrocyanide quenching, fluorescence polarization and viscosity results. Thermal melting studies demonstrated higher stabilization of the Hoogsteen base paired third strand of the DNA triplex compared to the Watson-Crick strand. Circular dichroism studies suggested a stronger perturbation of the DNA triplex conformation by the alkaloid analogs compared to the duplex. The binding was entropy-driven in each case and the entropy contribution to free energy increased as the length of the alkyl side chain increased. The analogs exhibited stronger binding affinity to the triple helical structure compared to the parent double helical structure.
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Affiliation(s)
- Debipreeta Bhowmik
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700 032, India
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Rahman SMA, Baba T, Kodama T, Islam MA, Obika S. Hybridizing ability and nuclease resistance profile of backbone modified cationic phosphorothioate oligonucleotides. Bioorg Med Chem 2012; 20:4098-102. [PMID: 22658536 DOI: 10.1016/j.bmc.2012.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/01/2012] [Accepted: 05/02/2012] [Indexed: 11/25/2022]
Abstract
Various stereochemically pure cationic phosphorothioate oligonucleotides bearing aminoalkyl moieties were synthesized, and their duplex-forming ability against single-stranded DNA (ssDNA), single-stranded RNA (ssRNA) and triplex-forming ability against double-stranded DNA (dsDNA) were evaluated by UV melting experiments. The cationic Rp stereoisomers showed improved duplex-forming ability against ssDNA, triplex-forming ability against dsDNA and nuclease stability.
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Affiliation(s)
- S M Abdur Rahman
- Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh.
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Park SM, Nam SJ, Jeong HS, Kim WJ, Kim BH. The effects of the 4-(4-Methylpiperazine)phenyl group on nucleosides and oligonucleotides: cellular delivery, detection, and stability. Chem Asian J 2010; 6:487-92. [PMID: 21254426 DOI: 10.1002/asia.201000574] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Indexed: 11/11/2022]
Abstract
As drug candidates, one promising way to improve the cellular delivery efficacy of oligonucleotides is to introduce a cationic group. By introducing a cationic moiety into the oligonucleotide structure, they become capable of approaching the cell surface and also of crossing the cellular membrane. In an effort to develop cell-permeable oligonucleotides, we examined the piperazinephenyl-bearing 2'-deoxyuridine ((PP)U), which can be not only cationic but also fluorescent as a cationic monomer for cationic oligonucleotides. Several modified DNA oligonucleotides with different numbers of (PP)U building blocks were synthesized and evaluated for the effect on thermal stability and conformation by the introduction of (PP)U. The cellular delivery of modified oligonucleotides was different depending on the number of (PP)U building blocks. Furthermore, these (PP)U-modified oligonucleotides had sufficient fluorescence that we were able to identify the delivery results without the use of conventional fluorescent tags. They were predominantly localized in the cell cytoplasm. In addition, they were stable enough after 3 hours in the presence of nuclease. These results showed that a piperazinephenyl moiety that is conjugated with nucleobase is able to deliver and detect the oligonucleotides, which suggests that this concept of 'dual-function oligonucleotides' might be utilized in diagnostics, therapeutics, and as a convenient biological tool for probing the activity of oligonucleotides inside cells.
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Affiliation(s)
- Sun Min Park
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, Republic of Korea
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Morvan F, Debart F, Vasseur JJ. From anionic to cationic alpha-anomeric oligodeoxynucleotides. Chem Biodivers 2010; 7:494-535. [PMID: 20232324 DOI: 10.1002/cbdv.200900220] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- François Morvan
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université Montpellier 1 and Université Montpellier 2, Place Eugène Bataillon, CC1704, FR-34095 Montpellier cedex 5, France
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8
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Using an aryl phenanthroimidazole moiety as a conjugated flexible intercalator to improve the hybridization efficiency of a triplex-forming oligonucleotide. Bioorg Med Chem 2008; 16:9937-47. [PMID: 18977149 DOI: 10.1016/j.bmc.2008.10.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 10/03/2008] [Accepted: 10/12/2008] [Indexed: 11/23/2022]
Abstract
When inserting 2-phenyl or 2-naphth-1-yl-phenanthroimidazole intercalators (X and Y, respectively) as bulges into triplex-forming oligonucleotides, both intercalators show extraordinary high thermal stability of the corresponding Hoogsteen-type triplexes and Hoogsteen-type parallel duplexes with high discrimination to Hoogsteen mismatches. Molecular modeling shows that the phenyl or the naphthyl ring stacks with the nucleobases in the TFO, while the phenanthroimidazol moiety stacks with the base pairs of the dsDNA. DNA-strands containing the intercalator X show higher thermal triplex stability than DNA-strands containing the intercalator Y. The difference can be explained by a lower degree of planarity of the intercalator in the case of naphthyl. It was also observed that triplex stability was considerably reduced when the intercalators X or Y was replaced by 2-(naphthlen-1-yl)imidazole. This confirms intercalation as the important factor for triplex stabilization and it rules out an alternative complexation of protonated imidazole with two phosphate groups. The intercalating nucleic acid monomers X and Y were obtained via a condensation reaction of 9,10-phenanthrenequinone (4) with (S)-4-(2-(2,2-dimethyl-1,3-dioxolan-4-yl)ethoxy)benzaldehyde (3a) or (S)-4-(2-(2,2-dimethyl-1,3-dioxolan-4-yl)ethoxy)-1-naphthaldehyde (3b), respectively, in the presence of acetic acid and ammonium acetate. The required monomers for DNA synthesis using amidite chemistry were obtained by standard deprotection of the hydroxy groups followed by 4,4'-dimethoxytritylation and phosphitylation.
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Duca M, Vekhoff P, Oussedik K, Halby L, Arimondo PB. The triple helix: 50 years later, the outcome. Nucleic Acids Res 2008; 36:5123-38. [PMID: 18676453 PMCID: PMC2532714 DOI: 10.1093/nar/gkn493] [Citation(s) in RCA: 265] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Triplex-forming oligonucleotides constitute an interesting DNA sequence-specific tool that can be used to target cleaving or cross-linking agents, transcription factors or nucleases to a chosen site on the DNA. They are not only used as biotechnological tools but also to induce modifications on DNA with the aim to control gene expression, such as by site-directed mutagenesis or DNA recombination. Here, we report the state of art of the triplex-based anti-gene strategy 50 years after the discovery of such a structure, and we show the importance of the actual applications and the main challenges that we still have ahead of us.
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Affiliation(s)
- Maria Duca
- LCMBA CNRS UMR6001, University of Nice-Sophia Antipolis, Parc Valrose, 06108 NICE Cedex 2, France
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Globisch D, Bomholt N, Filichev V, Pedersen E. Stability ofHoogsteen-Type Triplexes – Electrostatic Attraction between Duplex Backbone and Triplex-Forming Oligonucleotide (TFO) Using an Intercalating Conjugate. Helv Chim Acta 2008. [DOI: 10.1002/hlca.200890082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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García J, Díaz-Rodríguez A, Fernandez S, Sanghvi YS, Ferrero M, Gotor V. New Concept for the Separation of an Anomeric Mixture of α/β-d-Nucleosides through Regioselective Enzymatic Acylation or Hydrolysis Processes. J Org Chem 2006; 71:9765-71. [PMID: 17168595 DOI: 10.1021/jo062033o] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
An efficient and high yield protocol for the synthesis and separation of 3'- and/or 5'-protected alpha-2'-deoxynucleosides has been developed through regioselective acylation/deacylation processes catalyzed by enzymes. Pseudomonas cepacia lipase (PSL-C) was found to be highly chemo- and regioselective toward the 3'-position of the beta-2'-deoxynucleoside derivatives, whereas PSL-C displayed opposite selectivity toward the 5'-position for the corresponding alpha-anomer. The successful application of this protocol was demonstrated by a convenient separation of an alpha/beta-mixture of thymidine derivatives from an industrial waste stream. Furthermore, this technique was also applied for the separation of an anomeric mixture of 2'-deoxy-2'-fluoro-alpha/beta-arabinonucleosides that are useful building blocks for the antisense constructs.
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Affiliation(s)
- Javier García
- Departamento de Química OrgAnica e InorgAnica and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006-Oviedo (Asturias), Spain
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12
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Deglane G, Morvan F, Debart F, Vasseur JJ. 5-Propynylamino alpha-deoxyuridine promotes DNA duplex stabilization of anionic and neutral but not cationic alpha-oligonucleotides. Bioorg Med Chem Lett 2006; 17:951-4. [PMID: 17157020 DOI: 10.1016/j.bmcl.2006.11.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Revised: 11/14/2006] [Accepted: 11/14/2006] [Indexed: 10/23/2022]
Abstract
Incorporation of 5-propynylamino and 5-propynyl alpha-2'-deoxyuridine into alpha-oligonucleotides (alpha-ON) allows high-affinity targeting of complementary DNA for alpha-ON with anionic and neutral backbone but not for cationic alpha-ON, revealing clues on the role of the amino group of the propynylamino on the formation of DNA duplexes.
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Affiliation(s)
- Gaëlle Deglane
- LCOBS, UMR 5625 CNRS-UM II, Université Montpellier II, 34095 Montpellier, France
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13
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Deglane G, Abes S, Michel T, Prévot P, Vives E, Debart F, Barvik I, Lebleu B, Vasseur JJ. Impact of the guanidinium group on hybridization and cellular uptake of cationic oligonucleotides. Chembiochem 2006; 7:684-92. [PMID: 16518865 DOI: 10.1002/cbic.200500433] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The grafting of cationic groups to synthetic oligonucleotides (ONs) in order to reduce the charge repulsion between the negatively charged strands of a duplex or triplex, and consequently to increase a complex's stability, has been extensively studied. Guanidinium groups, which are highly basic and positively charged over a wide pH range, could be an efficient ON modification to enhance their affinity for nucleic acid targets and to improve cellular uptake. A straightforward post-synthesis method to convert amino functions attached to ONs (on sugar, nucleobase or backbone) into guanidinium tethers has been perfected. In comparison to amino groups, such cationic groups anchored to alpha-oligonucleotide phosphoramidate backbones play important roles in duplex stability, particularly with RNA targets. This high affinity could be explained by dual recognition resulting from Watson-Crick or Hoogsteen base pairing combined with cationic/anionic backbone recognition between strands involving H-bond formation and salt bridging. Molecular-dynamics simulations corroborate interactions between the cationic backbones of the alpha-ONs and the anionic backbones of the nucleic acid targets. Moreover, ONs with guanidinium modification increased cellular uptake relative to negatively charged ONs. The cellular localization of these new cationic phosphoramidate ONs is mainly cytoplasmic. The uptake of these ON analogues might occur through endocytosis.
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Affiliation(s)
- Gaëlle Deglane
- LCOBS, UMR 5625 CNRS-UMII, CC 008, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
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Ohara K, Smietana M, Vasseur JJ. Characterization of specific noncovalent complexes between guanidinium derivatives and single-stranded DNA by MALDI. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:283-91. [PMID: 16443365 DOI: 10.1016/j.jasms.2005.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Revised: 11/09/2005] [Accepted: 11/13/2005] [Indexed: 05/06/2023]
Abstract
Noncovalently bound complexes between highly basic sites of 12 guanidinium compounds and single-stranded DNA were studied using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. 6-Aza-2-thiothymine (ATT) was used as the matrix in the presence of ammonium citrate, and spectra were recorded in the positive ion mode. Detailed control experiments confirmed unambiguously the high selectivity and specificity of the guanidinium moiety for phosphate groups of DNA. The results verify the binding stoichiometry and show preferential binding of hydrophobic binders (pyrene and anthracene guanidinium derivatives) to all sequences examined. In addition, we demonstrate that electrostatic noncovalent interactions are strengthened with phosphorothioate analogs of DNA. These results clearly highlight the structure-directing role of the self-assembling organic species and strongly emphasize the significance of concentration, hydrophobicity, hydrogen-bonding, and pi-pi interactions of the artificial receptor in the formation of these noncovalent complexes. Because of the ability of DNA-binding compounds to influence gene expression, and therefore cell proliferation and differentiation, the interactions described above could be important in providing a better understanding of the mechanism of action of these noncovalent genetic regulators.
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Affiliation(s)
- Keiichiro Ohara
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, CNRS-Université Montpellier II, Montpellier, France
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