title: Interaction of minor groove ligands with G-quadruplexes: thermodynamic contributions of the number of quartets, T-U substitutions, and conformation.
abstract: In the presence of specific metal ions, DNA oligonucleotides containing guanine repeat sequences can adopt G-quadruplex structures. In this work, we used a combination of spectroscopic and calorimetric techniques to investigate the conformation and unfolding thermodynamics of the K(+)-form of five G-quadruplexes with sequences: d(G(2)T(2)G(2)TGTG(2)T(2)G(2)), G2, d(G(3)T(2)G(3)TGTG(3)T(2)G(3)), G3, their analogs where T is replaced with U, G2-U and G3-U, and r(G(2)U(2)G(2)UGUG(2)U(2)G(2)), rG2. These G-quadruplexes show CD spectra characteristic of the "chair" conformation (G2 and G2-U), or "basket" conformation (rG2); or a mixture of these two conformers (G3 and G3-U). Thermodynamic profiles show that the favorable folding of each G-quadruplex results from the typical compensation of a favorable enthalpy and unfavorable entropy contributions. G-quadruplex stability increase in the following order (in ΔG°(20)): rG2 (-1.3 kcal/mol) < G2 < G2-U <G3-U (chair) < G3 (chair) <G3-U (basket) < G3 (basket) (-8.6 kcal/mol), due to favorable enthalpy contribution from the stacking of G-quartets. We used ITC to determine thermodynamic binding profiles for the interaction of the minor groove ligands, netropsin and distamycin, with each G-quadruplex. Both ligands bind with high exothermic enthalpies (~ -10.8 kcal/mol), 1:1 stoichiometries, and weak affinities (~8 × 10(4) M(-1)). The similarity of the binding thermodynamic profiles, together with the absence of induced Cotton effects, indicates a surface or outside binding mode. We speculate that the top and bottom surfaces of the G-quadruplex comprise the potential MGBL binding sites, where the ligand lies on the surface forming van der Waals interactions with the guanines of the G-quartets and loop nucleotides.
authors.affiliation: Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA.
authors.forename: Iztok
authors.initials: I
authors.lastname: Prislan
authors.forename: Irine
authors.initials: I
authors.lastname: Khutsishvili
authors.forename: Luis A
authors.initials: LA
authors.lastname: Marky
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D002151:Calorimetry; D002152:Calorimetry, Differential Scanning; D002942:Circular Dichroism; D004214:Distamycins / Q000737:chemistry / Q000378:metabolism; D054856:G-Quadruplexes; D006147:Guanine / Q000737:chemistry; D008024:Ligands; D009429:Netropsin / Q000737:chemistry / Q000378:metabolism; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry; D014498:Uracil / Q000737:chemistry
chemical_list: D052157:Aptamers, Nucleotide; D004214:Distamycins; D008024:Ligands; C081676:thrombin aptamer; D014498:Uracil; D006147:Guanine; D009429:Netropsin; C030000:stallimycin; D013941:Thymine