ArticleJournal of the American Chemical Society2009
Molecular dynamics of water-mediated interactions of a linear benzimidazole-biphenyl diamidine with the DNA minor groove.
Article in Journal of the American Chemical Society, 2009. 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, 44 citations in OpenAlex.
- Alternative Approach to Sequence-Specific Recognition of DNA: Cooperative Stacking of Dication Dimers─Sensitivity to Compound Curvature, Aromatic Structure, and DNA Sequence.ACS chemical biology · 2025Article
- X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences.ACS bio & med chem Au · 2023Article
- Binding to the DNA Minor Groove by Heterocyclic Dications: from AT Specific to GC Recognition Compounds.Current protocols · 2023Review
- Drug design and DNA structural research inspired by the Neidle laboratory: DNA minor groove binding and transcription factor inhibition by thiophene diamidines.Bioorganic & medicinal chemistry · 2022Article
- Thermodynamic Factors That Drive Sequence-Specific DNA Binding of Designed, Synthetic Minor Groove Binding Agents.Life (Basel, Switzerland) · 2022Article
- Engineered modular heterocyclic-diamidines for sequence-specific recognition of mixed AT/GC base pairs at the DNA minor groove.Chemical science · 2021Article
- Extending the σ-Hole Motif for Sequence-Specific Recognition of the DNA Minor Groove.Biochemistry · 2020Article
- Small Sequence-Sensitive Compounds for Specific Recognition of the G⋅C Base Pair in DNA Minor Groove.Chemistry (Weinheim an der Bergstrasse, Germany) · 2020Article
- A New Generation of Minor-Groove-Binding-Heterocyclic Diamidines That Recognize G·C Base Pairs in an AT Sequence Context.Molecules (Basel, Switzerland) · 2019Review
- Heterocyclic Diamidine DNA Ligands as HOXA9 Transcription Factor Inhibitors: Design, Molecular Evaluation, and Cellular Consequences in a HOXA9-Dependant Leukemia Cell Model.Journal of medicinal chemistry · 2019Article
- Bound Compound, Interfacial Water, and Phenyl Ring Rotation Dynamics of a Compound in the DNA Minor Groove.Biochemistry · 2018Article
- Facile construction of fused benzimidazole-isoquinolinones that induce cell-cycle arrest and apoptosis in colorectal cancer cells.Bioorganic & medicinal chemistry · 2018Article
- A modular design for minor groove binding and recognition of mixed base pair sequences of DNA.Chemical communications (Cambridge, England) · 2017Article
- Sequence-specific recognition of DNA minor groove by an NIR-fluorescence switch-on probe and its potential applications.Nucleic acids research · 2015Article
- Molecular basis for sequence-dependent induced DNA bending.Chembiochem : a European journal of chemical biology · 2013Article
- 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
- Microscopic rearrangement of bound minor groove binders detected by NMR.The journal of physical chemistry. B · 2012Article
- Water-mediated binding of agents that target the DNA minor groove.Journal of the American Chemical Society · 2011Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
DB921 has a benzimidazole-biphenyl system with terminal amidines that gives the compound a linear conformation with a radius of curvature that does not match the DNA minor groove shape. Surprisingly, the compound binds in the groove with an unusually high equilibrium constant [Miao, Y.; Lee, M. P. H.; Parkinson, G. N.; Batista-Parra, A.; Ismail, M. A.; Neidle, S.; Boykin, D. W.; Wilson, W. D. Biochemistry 2005, 44, 14701-14708]. X-ray crystallographic analysis of DB921 bound to -AATT- in d(CGCGAATTCGCG)(2) showed that the benzimidazole is in position to directly interact with bases at the floor of the groove, while the phenylamidine of DB921 forms indirect contacts with the bases through an interfacial water. The DB921-water pair forms a curved, flexible module with a high K(a) (or a low K(d)) value of binding. To better understand the dynamics of the DB921-DNA complex and how water can be used in the design of compounds to recognize DNA, a 100 ns molecular dynamics simulation of the complex was conducted. In addition to the X-ray conformation, some significantly variant, dynamic conformations, which had additional interfacial water molecules between DB921 and DNA, appeared in the MD simulation. The benzimidazole contacts remained relatively constant through the entire simulation. The biphenylamidine end of the bound molecule, however, undergoes much larger changes in orientation relative to the floor of the groove as well as variations in the type of water interactions. The results provide an understanding of how water couples the linear DB921 compound to the minor groove for tight binding, without a large unfavorable contribution to the entropy of binding.
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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.