Monitoring base specific dynamics during melting of DNA-ligand complexes using temperature-jump time-resolved infrared spectroscopy

Robby Fritzsch, Gregory M. Greetham, Ian P. Clark, Lucy Minnes, Michael Towrie, Anthony W. Parker, Neil T. Hunt

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Ultrafast time-resolved infrared spectroscopy employing nanosecond temperature-jump initiation has been used to study the melting of double-stranded (ds)DNA oligomers in the presence and absence of minor groove-binding ligand Hoechst 33258. Ligand binding to ds(5′-GCAAATTTCC-3′), which binds Hoechst 33258 in the central A-tract region with nanomolar affinity, causes a dramatic increase in the timescales for strand melting from 30 to 250 μs. Ligand binding also suppresses premelting disruption of the dsDNA structure, which takes place on 100 ns timescales and includes end-fraying. In contrast, ligand binding to the ds(5′-GCATATATCC-3′) sequence, which exhibits an order of magnitude lower affinity for Hoechst 33258 than the A-tract motif, leads to an increase by only a factor of 5 in melting timescales and reduced suppression of premelting sequence perturbation and end-fraying. These results demonstrate a dynamic impact of the minor groove ligand on the dsDNA structure that correlates with binding strength and thermodynamic stabilization of the duplex. Moreover, the ability of the ligand to influence base pairs distant from the binding site has potential implications for allosteric communication mechanisms in dsDNA.

LanguageEnglish
Pages6188-6199
Number of pages12
JournalJournal of Physical Chemistry B
Volume123
Issue number29
Early online date3 Jul 2019
DOIs
Publication statusPublished - 3 Jul 2019

Fingerprint

Infrared spectroscopy
Melting
DNA
deoxyribonucleic acid
infrared spectroscopy
Ligands
melting
Bisbenzimidazole
ligands
Monitoring
grooves
Temperature
temperature
affinity
Binding sites
oligomers
Oligomers
strands
Stabilization
stabilization

Keywords

  • infrared spectroscopy
  • DNA-ligand complexes
  • melting

Cite this

Fritzsch, Robby ; Greetham, Gregory M. ; Clark, Ian P. ; Minnes, Lucy ; Towrie, Michael ; Parker, Anthony W. ; Hunt, Neil T. / Monitoring base specific dynamics during melting of DNA-ligand complexes using temperature-jump time-resolved infrared spectroscopy. In: Journal of Physical Chemistry B. 2019 ; Vol. 123, No. 29. pp. 6188-6199.
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Monitoring base specific dynamics during melting of DNA-ligand complexes using temperature-jump time-resolved infrared spectroscopy. / Fritzsch, Robby; Greetham, Gregory M.; Clark, Ian P.; Minnes, Lucy; Towrie, Michael; Parker, Anthony W.; Hunt, Neil T.

In: Journal of Physical Chemistry B, Vol. 123, No. 29, 03.07.2019, p. 6188-6199.

Research output: Contribution to journalArticle

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AU - Greetham, Gregory M.

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AB - Ultrafast time-resolved infrared spectroscopy employing nanosecond temperature-jump initiation has been used to study the melting of double-stranded (ds)DNA oligomers in the presence and absence of minor groove-binding ligand Hoechst 33258. Ligand binding to ds(5′-GCAAATTTCC-3′), which binds Hoechst 33258 in the central A-tract region with nanomolar affinity, causes a dramatic increase in the timescales for strand melting from 30 to 250 μs. Ligand binding also suppresses premelting disruption of the dsDNA structure, which takes place on 100 ns timescales and includes end-fraying. In contrast, ligand binding to the ds(5′-GCATATATCC-3′) sequence, which exhibits an order of magnitude lower affinity for Hoechst 33258 than the A-tract motif, leads to an increase by only a factor of 5 in melting timescales and reduced suppression of premelting sequence perturbation and end-fraying. These results demonstrate a dynamic impact of the minor groove ligand on the dsDNA structure that correlates with binding strength and thermodynamic stabilization of the duplex. Moreover, the ability of the ligand to influence base pairs distant from the binding site has potential implications for allosteric communication mechanisms in dsDNA.

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