Folding of the thrombin aptamer into a G-quadruplex with Sr2+: Stability, heat, and hydration

B. I. Kankia, Luis A Marky

Research output: Contribution to journalArticle

230 Citations (Scopus)

Abstract

It has been shown that the DNA aptamer d(G2T2G2TGTG2T2G 2) adopts an intramolecular G-quadruplex structure in the presence of K+. Its affinity for trombin has been associated with the inhibition of thrombin-catalyzed fibrin clot formation. In this work, we used a combination of spectroscopy, calorimetry, density, and ultrasound techniques to determine the spectral characteristics, thermodynamics, and hydration effects for the formation of G-quadruplexes with a variety of monovalent and divalent metal ions. The formation of cation-aptamer complexes is relatively fast and highly reproducible. The comparison of their CD spectra and melting profiles as a function of strand concentration shows that K+, Rb+, NH4+, Sr2+, and Ba2+ form intramolecular cation-aptamer complexes with transition temperatures above 25 °C. However, the cations Li+, Na+, Cs+, Mg2+, and Ca2+ form weaker complexes at very low temperatures. This is consistent with the observation that metal ions with ionic radii in the range 1.3-1.5 Å fit well within the two G-quartets of the complex, while the other cations cannot. The comparison of thermodynamic unfolding profiles of the Sr2+-aptamer and K+-aptamer complexes shows that the Sr2+-aptamer complex is more stable, by ∼18 °C, and unfolds with a lower endothermic heat of 8.3 kcal/mol. This is in excellent agreement with the exothermic heats of -16.8 kcal/mol and -25.7 kcal/mol for the binding of Sr2+ and K+ to the aptamer, respectively. Furthermore, volume and compressibility parameters of cation binding show hydration effects resulting mainly from two contributions: the dehydration of both cation and guanine atomic groups and water uptake upon the folding of a single-strand into a G- quadruplex structure.

Original languageEnglish (US)
Pages (from-to)10799-10804
Number of pages6
JournalJournal of the American Chemical Society
Volume123
Issue number44
DOIs
StatePublished - Nov 7 2001

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G-Quadruplexes
Hydration
Cations
Hot Temperature
Positive ions
Thermodynamics
Metal ions
Metals
Nucleotide Aptamers
Ions
Calorimetry
Transition Temperature
Guanine
Fibrin
Dehydration
Compressibility
Thrombin
Freezing
Superconducting transition temperature
thrombin aptamer

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

Folding of the thrombin aptamer into a G-quadruplex with Sr2+ : Stability, heat, and hydration. / Kankia, B. I.; Marky, Luis A.

In: Journal of the American Chemical Society, Vol. 123, No. 44, 07.11.2001, p. 10799-10804.

Research output: Contribution to journalArticle

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abstract = "It has been shown that the DNA aptamer d(G2T2G2TGTG2T2G 2) adopts an intramolecular G-quadruplex structure in the presence of K+. Its affinity for trombin has been associated with the inhibition of thrombin-catalyzed fibrin clot formation. In this work, we used a combination of spectroscopy, calorimetry, density, and ultrasound techniques to determine the spectral characteristics, thermodynamics, and hydration effects for the formation of G-quadruplexes with a variety of monovalent and divalent metal ions. The formation of cation-aptamer complexes is relatively fast and highly reproducible. The comparison of their CD spectra and melting profiles as a function of strand concentration shows that K+, Rb+, NH4+, Sr2+, and Ba2+ form intramolecular cation-aptamer complexes with transition temperatures above 25 °C. However, the cations Li+, Na+, Cs+, Mg2+, and Ca2+ form weaker complexes at very low temperatures. This is consistent with the observation that metal ions with ionic radii in the range 1.3-1.5 {\AA} fit well within the two G-quartets of the complex, while the other cations cannot. The comparison of thermodynamic unfolding profiles of the Sr2+-aptamer and K+-aptamer complexes shows that the Sr2+-aptamer complex is more stable, by ∼18 °C, and unfolds with a lower endothermic heat of 8.3 kcal/mol. This is in excellent agreement with the exothermic heats of -16.8 kcal/mol and -25.7 kcal/mol for the binding of Sr2+ and K+ to the aptamer, respectively. Furthermore, volume and compressibility parameters of cation binding show hydration effects resulting mainly from two contributions: the dehydration of both cation and guanine atomic groups and water uptake upon the folding of a single-strand into a G- quadruplex structure.",
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