ArticleNucleic acids research2001
Induced fit DNA recognition by a minor groove binding analogue of Hoechst 33258: fluctuations in DNA A tract structure investigated by NMR and molecular dynamics simulations.
Article in Nucleic acids research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 53 citations in OpenAlex.
- Direct amidinium-phosphate interactions guide AT-selective DNA binding by a potent antileishmanial drug.Communications chemistry · 2026Article
- Natural Products Beyond Inhibition: A Mechanistic Framework Spanning Pockets, Interfaces, and Kinetic Barriers.Molecules (Basel, Switzerland) · 2026Review
- Binding to the DNA Minor Groove by Heterocyclic Dications: from AT Specific to GC Recognition Compounds.Current protocols · 2023Review
- Synthesis and Biological Evaluation of Novel 1ACS omega · 2022Article
- DNA minor-groove binder Hoechst 33258 destabilizes base-pairing adjacent to its binding site.Communications biology · 2020Article
- First Structure of a Designed Minor Groove Binding Heterocyclic Cation that Specifically Recognizes Mixed DNA Base Pair Sequences.Chemistry (Weinheim an der Bergstrasse, Germany) · 2017Article
- Binding to the DNA minor groove by heterocyclic dications: from AT-specific monomers to GC recognition with dimers.Current protocols in nucleic acid chemistry · 2012Review
- Molecular dynamics simulations and binding free energy analysis of DNA minor groove complexes of curcumin.Journal of molecular modeling · 2011Article
- Molecular dynamics of water-mediated interactions of a linear benzimidazole-biphenyl diamidine with the DNA minor groove.Journal of the American Chemical Society · 2009Article
- What drives the binding of minor groove-directed ligands to DNA hairpins?Nucleic acids research · 2008Article
- Design of DNA minor groove binding diamidines that recognize GC base pair sequences: a dimeric-hinge interaction motif.Journal of the American Chemical Society · 2007Article
- Ligand binding mode to duplex and triplex DNA assessed by combining electrospray tandem mass spectrometry and molecular modeling.Journal of the American Society for Mass Spectrometry · 2007Article
- A high-throughput, high-resolution strategy for the study of site-selective DNA binding agents: analysis of a "highly twisted" benzimidazole-diamidine.Journal of the American Chemical Society · 2006Article
- A host-guest approach for determining drug-DNA interactions: an example using netropsin.Nucleic acids research · 2005Article
- Induced-fit recognition of DNA by organometallic complexes with dynamic stereogenic centers.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- Determination of DNA minor groove width in distamycin-DNA complexes by solid-state NMR.Nucleic acids research · 2003Article
- High-resolution NMR structure of an AT-rich DNA sequence.Journal of biomolecular NMR · 2002Article
- The hybridization-stabilization assay: a solution-based isothermal method for rapid screening and determination of sequence preference of ligands that bind to duplexed nucleic acids.Nucleic acids research · 2001Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
NMR analysis and molecular dynamics simulations of d(GGTAATTACC)(2) and its complex with a tetrahydropyrimidinium analogue of Hoechst 33258 suggest that DNA minor groove recognition in solution involves a combination of conformational selection and induced fit, rather than binding to a preorganised site. Analysis of structural fluctuations in the bound and unbound states suggests that the degree of induced fit observed is primarily a consequence of optimising van der Waals contacts with the walls of the minor groove resulting in groove narrowing through: (i) changes in base step parameters, including increased helical twist and propeller twist; (ii) changes to the sugar-phosphate backbone conformation to engulf the bound ligand; (iii) suppression of bending modes at the TpA steps. In contrast, the geometrical arrangement of hydrogen bond acceptors on the groove floor appears to be relatively insensitive to DNA conformation (helical twist and propeller twist). We suggest that effective recognition of DNA sequences (in this case an A tract structure) appears to depend to a significant extent on the sequence being flexible enough to be able to adopt the geometrically optimal conformation compatible with the various binding interactions, rather than involving 'lock and key' recognition.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.