2D-IR spectroscopy shows that optimised DNA minor groove binding of Hoechst33258 follows an induced fit model

Lennart A. I. Ramakers, Gordon Hithell, John J. May, Gregory M. Greetham, Paul M. Donaldson, Michael Towrie, Anthony W. Parker, Glenn Burley, Neil Hunt

Research output: Contribution to journalArticle

  • 4 Citations

Abstract

The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced non-covalent interactions between ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a sub-optimal alternating A-T sequence. Results from 2-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region. This induced fit maximizes favourable ligand-DNA enthalpic contributions in the optimal binding case and demonstrates that controlling the molecular details that induce subtle changes in DNA structure may hold the key to designing next-generation DNA-binding molecules.
LanguageEnglish
JournalJournal of Physical Chemistry B
Early online date19 Jan 2017
DOIs
StateE-pub ahead of print - 19 Jan 2017

Fingerprint

grooves
Infrared spectroscopy
DNA
deoxyribonucleic acid
Molecules
spectroscopy
Ligands
Biomolecules
Propellers
molecules
Hydration
Molecular structure
ligands
propellers
spine
Proteins
determinants
hydration
molecular structure
infrared spectroscopy

Keywords

  • spectroscopy
  • DNA
  • Hoechst33258
  • minor groove binding
  • induced fit
  • non-covalent interactions
  • ligand
  • biomolecule
  • molecule-DNA binding

Cite this

Ramakers, Lennart A. I. ; Hithell, Gordon ; May, John J. ; Greetham, Gregory M. ; Donaldson, Paul M. ; Towrie, Michael ; Parker, Anthony W. ; Burley, Glenn ; Hunt, Neil. / 2D-IR spectroscopy shows that optimised DNA minor groove binding of Hoechst33258 follows an induced fit model. In: Journal of Physical Chemistry B. 2017
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title = "2D-IR spectroscopy shows that optimised DNA minor groove binding of Hoechst33258 follows an induced fit model",
abstract = "The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced non-covalent interactions between ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a sub-optimal alternating A-T sequence. Results from 2-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region. This induced fit maximizes favourable ligand-DNA enthalpic contributions in the optimal binding case and demonstrates that controlling the molecular details that induce subtle changes in DNA structure may hold the key to designing next-generation DNA-binding molecules.",
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2D-IR spectroscopy shows that optimised DNA minor groove binding of Hoechst33258 follows an induced fit model. / Ramakers, Lennart A. I.; Hithell, Gordon; May, John J.; Greetham, Gregory M.; Donaldson, Paul M.; Towrie, Michael; Parker, Anthony W.; Burley, Glenn; Hunt, Neil.

In: Journal of Physical Chemistry B, 19.01.2017.

Research output: Contribution to journalArticle

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AU - Ramakers,Lennart A. I.

AU - Hithell,Gordon

AU - May,John J.

AU - Greetham,Gregory M.

AU - Donaldson,Paul M.

AU - Towrie,Michael

AU - Parker,Anthony W.

AU - Burley,Glenn

AU - Hunt,Neil

N1 - “This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry B, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/acs.jpcb.7b00345.

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Y1 - 2017/1/19

N2 - The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced non-covalent interactions between ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a sub-optimal alternating A-T sequence. Results from 2-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region. This induced fit maximizes favourable ligand-DNA enthalpic contributions in the optimal binding case and demonstrates that controlling the molecular details that induce subtle changes in DNA structure may hold the key to designing next-generation DNA-binding molecules.

AB - The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced non-covalent interactions between ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a sub-optimal alternating A-T sequence. Results from 2-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region. This induced fit maximizes favourable ligand-DNA enthalpic contributions in the optimal binding case and demonstrates that controlling the molecular details that induce subtle changes in DNA structure may hold the key to designing next-generation DNA-binding molecules.

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