Interaction of Minor Groove Ligands to an AAATT/AATTT Site

Correlation of Thermodynamic Characterization and Solution Structure

Dionisios Rentzeperis, Luis A Marky, Tammy J. Dwyer, Bernhard H. Geierstanger, Jeffrey G. Pelton, David E. Wemmer

Research output: Contribution to journalArticle

118 Citations (Scopus)

Abstract

combination of circular dichroism spectroscopy, titration calorimetry, and optical melting has been used to investigate the association of the minor groove ligands netropsin and distamycin to the central A3T2 binding site of the DNA duplex d(CGCAAATTGGC).d(GCCAATTTGCG). For the complex with netropsin at 20 °C, a ligand/duplex stoichiometry of 1:1 was obtained with Kb ~ 4.3 x 107 M-1, Hh ~ -7.5 kcal mol-1, ∆Sb ~ 9.3 cal K-1 mol-1, and ∆CP ~ 0. Previous NMR studies characterized the distamycin complex with A3T2 at saturation as a dimeric side-by-side complex. Consistent with this result, we found a ligand/duplex stoichiometry of 2:1. In the current study, the relative thermodynamic contributions of the two distamycin ligands in the formation of this side-by-side complex (2:1 Dst.A3T2) were evaluated and compared with the thermodynamic characteristics of netropsin binding. The association of the first distamycin molecule of the 2:1 DSt.A3T2 complex yielded the following thermodynamic profile: Kb ~ 3.1 x 107 M-1, ∆Hb = -12.3 kcal mol-1, ∆Sb = -8 cal K-1 mol-1, and ∆Cp = -42 cal K-1 mol-1. The binding of the second distamycin molecule occurs with a lower Kb of ~ 3.3 x 106 M-1, a more favorable ∆Hb of -18.8 kcal mol-1, a more unfavorable 8Sb of -34 cal K-1 mol-1, and a higher ∆Cp of -196 cal K-1 mol-1. The latter term indicates an ordering of electrostricted and structural water molecules by the complexes. These results correlate well with the NMR titrations and are discussed in context of the solution structure of the 2:1 DSt.A3T2 complex.

Original languageEnglish (US)
Pages (from-to)2937-2945
Number of pages9
JournalBiochemistry
Volume34
Issue number9
DOIs
StatePublished - Jan 1 1995

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Thermodynamics
Netropsin
Ligands
Titration
Stoichiometry
Molecules
Nuclear magnetic resonance
Association reactions
Circular dichroism spectroscopy
Calorimetry
Circular Dichroism
Freezing
Spectrum Analysis
Melting
Binding Sites
stallimycin
Water
DNA
ganhuangenin

ASJC Scopus subject areas

  • Biochemistry

Cite this

Interaction of Minor Groove Ligands to an AAATT/AATTT Site : Correlation of Thermodynamic Characterization and Solution Structure. / Rentzeperis, Dionisios; Marky, Luis A; Dwyer, Tammy J.; Geierstanger, Bernhard H.; Pelton, Jeffrey G.; Wemmer, David E.

In: Biochemistry, Vol. 34, No. 9, 01.01.1995, p. 2937-2945.

Research output: Contribution to journalArticle

Rentzeperis, Dionisios ; Marky, Luis A ; Dwyer, Tammy J. ; Geierstanger, Bernhard H. ; Pelton, Jeffrey G. ; Wemmer, David E. / Interaction of Minor Groove Ligands to an AAATT/AATTT Site : Correlation of Thermodynamic Characterization and Solution Structure. In: Biochemistry. 1995 ; Vol. 34, No. 9. pp. 2937-2945.
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abstract = "combination of circular dichroism spectroscopy, titration calorimetry, and optical melting has been used to investigate the association of the minor groove ligands netropsin and distamycin to the central A3T2 binding site of the DNA duplex d(CGCAAATTGGC).d(GCCAATTTGCG). For the complex with netropsin at 20 °C, a ligand/duplex stoichiometry of 1:1 was obtained with Kb ~ 4.3 x 107 M-1, Hh ~ -7.5 kcal mol-1, ∆Sb ~ 9.3 cal K-1 mol-1, and ∆CP ~ 0. Previous NMR studies characterized the distamycin complex with A3T2 at saturation as a dimeric side-by-side complex. Consistent with this result, we found a ligand/duplex stoichiometry of 2:1. In the current study, the relative thermodynamic contributions of the two distamycin ligands in the formation of this side-by-side complex (2:1 Dst.A3T2) were evaluated and compared with the thermodynamic characteristics of netropsin binding. The association of the first distamycin molecule of the 2:1 DSt.A3T2 complex yielded the following thermodynamic profile: Kb ~ 3.1 x 107 M-1, ∆Hb = -12.3 kcal mol-1, ∆Sb = -8 cal K-1 mol-1, and ∆Cp = -42 cal K-1 mol-1. The binding of the second distamycin molecule occurs with a lower Kb of ~ 3.3 x 106 M-1, a more favorable ∆Hb of -18.8 kcal mol-1, a more unfavorable 8Sb of -34 cal K-1 mol-1, and a higher ∆Cp of -196 cal K-1 mol-1. The latter term indicates an ordering of electrostricted and structural water molecules by the complexes. These results correlate well with the NMR titrations and are discussed in context of the solution structure of the 2:1 DSt.A3T2 complex.",
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AB - combination of circular dichroism spectroscopy, titration calorimetry, and optical melting has been used to investigate the association of the minor groove ligands netropsin and distamycin to the central A3T2 binding site of the DNA duplex d(CGCAAATTGGC).d(GCCAATTTGCG). For the complex with netropsin at 20 °C, a ligand/duplex stoichiometry of 1:1 was obtained with Kb ~ 4.3 x 107 M-1, Hh ~ -7.5 kcal mol-1, ∆Sb ~ 9.3 cal K-1 mol-1, and ∆CP ~ 0. Previous NMR studies characterized the distamycin complex with A3T2 at saturation as a dimeric side-by-side complex. Consistent with this result, we found a ligand/duplex stoichiometry of 2:1. In the current study, the relative thermodynamic contributions of the two distamycin ligands in the formation of this side-by-side complex (2:1 Dst.A3T2) were evaluated and compared with the thermodynamic characteristics of netropsin binding. The association of the first distamycin molecule of the 2:1 DSt.A3T2 complex yielded the following thermodynamic profile: Kb ~ 3.1 x 107 M-1, ∆Hb = -12.3 kcal mol-1, ∆Sb = -8 cal K-1 mol-1, and ∆Cp = -42 cal K-1 mol-1. The binding of the second distamycin molecule occurs with a lower Kb of ~ 3.3 x 106 M-1, a more favorable ∆Hb of -18.8 kcal mol-1, a more unfavorable 8Sb of -34 cal K-1 mol-1, and a higher ∆Cp of -196 cal K-1 mol-1. The latter term indicates an ordering of electrostricted and structural water molecules by the complexes. These results correlate well with the NMR titrations and are discussed in context of the solution structure of the 2:1 DSt.A3T2 complex.

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