title: Energetic basis of molecular recognition in a DNA aptamer.
abstract: The thermal stability and ligand binding properties of the L-argininamide-binding DNA aptamer (5'-GATCGAAACGTAGCGCCTTCGATC-3') were studied by spectroscopic and calorimetric methods. Differential calorimetric studies showed that the uncomplexed aptamer melted in a two-state reaction with a melting temperature T(m)=50.2+/-0.2 degrees C and a folding enthalpy DeltaH(0)(fold)=-49.0+/-2.1 kcal mol(-1). These values agree with values of T(m)=49.6 degrees C and DeltaH(0)(fold)=-51.2 kcal mol(-1) predicted for a simple hairpin structure. Melting of the uncomplexed aptamer was dependent upon salt concentration, but independent of strand concentration. The T(m) of aptamer melting was found to increase as L-argininamide concentrations increased. Analysis of circular dichroism titration data using a single-site binding model resulted in the determination of a binding free energy DeltaG(0)(bind)=-5.1 kcal mol(-1). Isothermal titration calorimetry studies revealed an exothermic binding reaction with DeltaH(0)(bind)=-8.7 kcal mol(-1). Combination of enthalpy and free energy produce an unfavorable entropy of -TDeltaS(0)=+3.6 kcal mol(-1). A molar heat capacity change of -116 cal mol(-1) K(-1) was determined from calorimetric measurements at four temperatures over the range of 15-40 degrees C. Molecular dynamics simulations were used to explore the structures of the unligated and ligated aptamer structures. From the calculated changes in solvent accessible surface areas of these structures a molar heat capacity change of -125 cal mol(-1) K(-1) was calculated, a value in excellent agreement with the experimental value. The thermodynamic signature, along with the coupled CD spectral changes, suggest that the binding of L-argininamide to its DNA aptamer is an induced-fit process in which the binding of the ligand is thermodynamically coupled to a conformational ordering of the nucleic acid.
authors.affiliation: Department of Chemistry and Biochemistry, Mississippi College, 200 S. Capitol St., Clinton, MS 39058, USA. rbishop@mc.edu
authors.forename: G Reid
authors.initials: GR
authors.lastname: Bishop
authors.forename: Jinsong
authors.initials: J
authors.lastname: Ren
authors.forename: Brandon C
authors.initials: BC
authors.lastname: Polander
authors.forename: Benjamin D
authors.initials: BD
authors.lastname: Jeanfreau
authors.forename: John O
authors.initials: JO
authors.lastname: Trent
authors.forename: Jonathan B
authors.initials: JB
authors.lastname: Chaires
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001120:Arginine / Q000031:analogs & derivatives* / Q000737:chemistry; D001483:Base Sequence; D002152:Calorimetry, Differential Scanning; D006358:Hot Temperature; D009690:Nucleic Acid Conformation; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D044366:Transition Temperature
chemical_list: D052157:Aptamers, Nucleotide; C518912:L-argininamide-binding DNA aptamer; D012997:Solvents; C069339:argininamide; D001120:Arginine