title: Synthesis of a novel 4H-pyran analog as minor groove binder to DNA using ethidium bromide as fluorescence probe.
abstract: In the present work, isopropyl-6-amino-4-(3,5-bis(trifluoromethyl)phenyl)-5-cyano-2-methyl-4H-pyran-3-carboxylate (4H-pyran analog) has been synthesized by a three component reaction catalyzed by CsOH/γ-Al2O3 and characterized. The interaction of 4H-pyran analog with herring sperm DNA (hs DNA) under physiological conditions (phosphate buffer of pH 7.2) was investigated by UV absorption, FT-IR, fluorescence, (31)P NMR and circular dichroism (CD) spectroscopy. Fluorescence quenching results reveal that static quenching mechanism is involved in binding between 4H-pyran analog and hs DNA. The calculated thermodynamic parameters (ΔH° and ΔS°) indicate that hydrogen bonding plays a major role in binding between them. UV absorption and fluorescence shows the binding mode of 4H-pyran analog with hs DNA as non-intercalative. According to the IR spectroscopy, 4H-pyran analog binds to guanine, thymine, adenine bases of hs DNA but not to phosphate backbone of hs DNA which is also in good agreement with (31)P NMR results. CD and competitive binding experiment results confirms the minor groove binding of 4H-pyran analog to hs DNA.
authors.affiliation: Department of Chemistry, University of Mumbai, Vidyanagari, Santacruz (E), Mumbai 400 098, India. Electronic address: ramanammv@yahoo.com.
authors.forename: M M V
authors.initials: MM
authors.lastname: Ramana
authors.affiliation: Department of Chemistry, University of Mumbai, Vidyanagari, Santacruz (E), Mumbai 400 098, India.
authors.forename: Rahul
authors.initials: R
authors.lastname: Betkar
authors.affiliation: Department of Chemistry, University of Mumbai, Vidyanagari, Santacruz (E), Mumbai 400 098, India.
authors.forename: Amey
authors.initials: A
authors.lastname: Nimkar
authors.affiliation: Department of Chemistry, University of Mumbai, Vidyanagari, Santacruz (E), Mumbai 400 098, India.
authors.forename: Prasanna
authors.initials: P
authors.lastname: Ranade
authors.affiliation: Department of Chemistry, University of Mumbai, Vidyanagari, Santacruz (E), Mumbai 400 098, India.
authors.forename: Balaji
authors.initials: B
authors.lastname: Mundhe
authors.affiliation: Department of Chemistry, University of Mumbai, Vidyanagari, Santacruz (E), Mumbai 400 098, India.
authors.forename: Sachin
authors.initials: S
authors.lastname: Pardeshi
mesh_terms: D000818:Animals; D001665:Binding Sites; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004996:Ethidium / Q000737:chemistry; D005399:Fishes; D005456:Fluorescent Dyes / Q000737:chemistry; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011714:Pyrans / Q000737:chemistry / Q000378:metabolism*; D013050:Spectrometry, Fluorescence; D013056:Spectrophotometry, Ultraviolet; D017550:Spectroscopy, Fourier Transform Infrared; D013816:Thermodynamics
chemical_list: D005456:Fluorescent Dyes; D011714:Pyrans; D004247:DNA; D004996:Ethidium
keywords: 4H-pyran analog; Hs DNA; Hydrogen bonding; Minor groove binding; Static quenching