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DNA minor-groove binder Hoechst 33258 destabilizes base-pairing adjacent to its binding site
- Source :
- Communications Biology, Vol 3, Iss 1, Pp 1-9 (2020), Communications Biology
- Publication Year :
- 2020
- Publisher :
- Nature Publishing Group, 2020.
-
Abstract
- Understanding the dynamic interactions of ligands to DNA is important in DNA-based nanotechnologies. By structurally tracking the dissociation of Hoechst 33258-bound DNA (d(CGCAAATTTGCG)2) complex (H-DNA) with T-jump 2D-IR spectroscopy, the ligand is found to strongly disturb the stability of the three C:G base pairs adjacent to A:T the binding site, with the broken base pairs being more than triple at 100 ns. The strong stabilization effect of the ligand on DNA duplex makes this observation quite striking, which dramatically increases the melting temperature and dissociation time. MD simulations demonstrate an important role of hydration water and counter cations in maintaining the separation of terminal base pairs. The hydrogen bonds between the ligand and thymine carbonyls are crucial in stabilizing H-DNA, whose breaking signal appearing prior to the complete dissociation. Thermodynamic analysis informs us that H-DNA association is a concerted process, where H cooperates with DNA single strands in forming H-DNA.<br />Using T-jump 2D-IR spectroscopy, Zhang et al. show that DNA minor-groove binder Hoechst 33258 strongly destabilizes its complex with DNA (H-DNA). This study suggests that the association of H-DNA is a concerted process, where Hoechst 33258 cooperates with DNA single strands in forming H-DNA.
- Subjects :
- Base pair
Medicine (miscellaneous)
Nucleic Acid Denaturation
010402 general chemistry
01 natural sciences
Article
General Biochemistry, Genetics and Molecular Biology
Dissociation (chemistry)
chemistry.chemical_compound
Biophysical chemistry
Spectroscopy, Fourier Transform Infrared
Binding site
Spectroscopy
lcsh:QH301-705.5
Binding Sites
010405 organic chemistry
Ligand
Hydrogen bond
DNA Breaks
Hydrogen Bonding
DNA
0104 chemical sciences
Thymine
Crystallography
chemistry
lcsh:Biology (General)
Bisbenzimidazole
Thermodynamics
General Agricultural and Biological Sciences
Subjects
Details
- Language :
- English
- ISSN :
- 23993642
- Volume :
- 3
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- Communications Biology
- Accession number :
- edsair.doi.dedup.....ecc16e0118a9b39418484f8626461085