title: Role of Mg²⁺ ions in flavin recognition by RNA aptamer.
abstract: The role of Mg(2+) ion in flavin (flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN)) recognition by RNA aptamer has been explored through steady state and time-resolved fluorescence, circular dichroism (CD), thermal melting (TM) and isothermal titration calorimetry (ITC) studies. A strong quenching of flavin emission is detected due to stacking interaction with the nucleobases in the mismatched region of aptamer, and it enhances manifold with increasing Mg(2+) concentrations. A comparatively lower binding affinity toward FAD compared to FMN is attributed to the presence of intramolecular 'stack' conformer of FAD, which cannot participate in the intermolecular stacking interactions with the nucleobases. CD and TM studies predict that flavin detection causes structural reformation of RNA aptamer. ITC results indicate that flavin detection is thermodynamically feasible and highly enthalpy driven.
authors.affiliation: Department of Chemistry, Mendeleev Block, Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, Maharashtra, India.
authors.forename: Abhigyan
authors.initials: A
authors.lastname: Sengupta
authors.affiliation: Department of Chemistry, Mendeleev Block, Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, Maharashtra, India.
authors.forename: Krishna
authors.initials: K
authors.lastname: Gavvala
authors.affiliation: Department of Chemistry, Mendeleev Block, Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, Maharashtra, India.
authors.forename: Raj Kumar
authors.initials: RK
authors.lastname: Koninti
authors.affiliation: Department of Chemistry, Mendeleev Block, Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, Maharashtra, India. Electronic address: p.hazra@iiserpune.ac.in.
authors.forename: Partha
authors.initials: P
authors.lastname: Hazra
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000378:metabolism*; D005486:Flavin Mononucleotide / Q000378:metabolism; D005415:Flavins / Q000378:metabolism*; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D044366:Transition Temperature
chemical_list: D052157:Aptamers, Nucleotide; D005415:Flavins; D005486:Flavin Mononucleotide; D008274:Magnesium
keywords: Flavins; Molecular recognition; RNA-aptamer; Thermodynamics parameters