Minor-Groove Binding Drugs: Where Is the Second Hoechst 33258 Molecule?

Louise H. Fornander, Lisha Wu, Martin Billeter, Per Lincoln, Bengt Nordén

Research output: Contribution to journalArticlepeer-review

45 Scopus citations


Hoechst 33258 binds with high affinity into the minor groove of AT-rich sequences of double-helical DNA. Despite extensive studies of this and analogous DNA binding molecules, there still remains uncertainty concerning the interactions when multiple ligand molecules are accommodated within close distance. Albeit not of direct concern for most biomedical applications, which are at low drug concentrations, interaction studies for higher drug binding are important as they can give fundamental insight into binding mechanisms and specificity, including drug self-stacking interactions that can provide base-sequence specificity. Using circular dichroism (CD), isothermal titration calorimetry (ITC), and proton nuclear magnetic resonance (1H NMR), we examine the binding of Hoechst 33258 to three oligonucleotide duplexes containing AT regions of different lengths: [d(CGCGAATTCGCG)]2 (A2T2), [d(CGCAAATTTGCG)]2 (A3T 3), and [d(CGAAAATTTTCG)]2 (A4T4). We find similar binding geometries in the minor groove for all oligonucleotides when the ligand-to-duplex ratio is less than 1:1. At higher ratios, a second ligand can be accommodated in the minor groove of A4T4 but not A2T2 or A3T3. We conclude that the binding of the second Hoechst to A4T4 is not cooperative and that the molecules are sitting with a small separation apart, one after the other, and not in a sandwich structure as previously proposed. © 2013 American Chemical Society.
Original languageEnglish (US)
Pages (from-to)5820-5830
Number of pages11
JournalThe Journal of Physical Chemistry B
Issue number19
StatePublished - May 6 2013
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): KUK-11-008-23
Acknowledgements: We acknowledge support from King Abdullah University of Science and Technology (KAUST, KUK-11-008-23) and the European Research Council (ERC-2008-AdG 227700). L.W. and M.B. thank the Swedish NMR center for instrumental time and support.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.


Dive into the research topics of 'Minor-Groove Binding Drugs: Where Is the Second Hoechst 33258 Molecule?'. Together they form a unique fingerprint.

Cite this