Interaction of minor groove ligands with G-quadruplexes

Thermodynamic contributions of the number of quartets, T-U substitutions, and conformation

Iztok Prislan, Irine Khutsishvili, Luis A Marky

Research output: Contribution to journalArticle

5 Citations (Scopus)

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 2T 2G 2TGTG 2T 2G 2), G2, d(G 3T 2G 3TGTG 3T 2G 3), G3, their analogs where T is replaced with U, G2-U and G3-U, and r(G 2U 2G 2UGUG 2U 2G 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.

Original languageEnglish (US)
Pages (from-to)1341-1350
Number of pages10
JournalBiochimie
Volume93
Issue number8
DOIs
StatePublished - Aug 1 2011

Fingerprint

G-Quadruplexes
Thermodynamics
Conformations
Substitution reactions
Ligands
Enthalpy
Guanine
Netropsin
Oligonucleotides
Stoichiometry
Cotton
Metal ions
Entropy
Nucleotides
Binding Sites
DNA
Metals
Ions

Keywords

  • CD
  • DSC
  • G-quadruplexes
  • ITC
  • Minor groove binding ligands

ASJC Scopus subject areas

  • Biochemistry

Cite this

Interaction of minor groove ligands with G-quadruplexes : Thermodynamic contributions of the number of quartets, T-U substitutions, and conformation. / Prislan, Iztok; Khutsishvili, Irine; Marky, Luis A.

In: Biochimie, Vol. 93, No. 8, 01.08.2011, p. 1341-1350.

Research output: Contribution to journalArticle

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AU - Marky, Luis A

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N2 - 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 2T 2G 2TGTG 2T 2G 2), G2, d(G 3T 2G 3TGTG 3T 2G 3), G3, their analogs where T is replaced with U, G2-U and G3-U, and r(G 2U 2G 2UGUG 2U 2G 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.

AB - 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 2T 2G 2TGTG 2T 2G 2), G2, d(G 3T 2G 3TGTG 3T 2G 3), G3, their analogs where T is replaced with U, G2-U and G3-U, and r(G 2U 2G 2UGUG 2U 2G 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.

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KW - ITC

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