ArticleJournal of the American Chemical Society2013
Small-molecule binding to the DNA minor groove is mediated by a conserved water cluster.
Article in Journal of the American Chemical Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 79 citations in OpenAlex.
- Direct amidinium-phosphate interactions guide AT-selective DNA binding by a potent antileishmanial drug.Communications chemistry · 2026Article
- Auxiliary Discrminator Sequence Generative Adversarial Networks for Few Sample Molecule Generation.Journal of chemical information and modeling · 2025Article
- Water-Mediated Chiral Resolution of Ag-NHC(Nucleobase) Complexes.Inorganic chemistry · 2025Article
- Solvation free energy in governing equations for DNA hybridization, protein-ligand binding, and protein folding.FEBS open bio · 2024Article
- Single GC base pair recognition by a heterocyclic diamidine: structures, affinities, and dynamics.RSC advances · 2024Article
- Targeting DNA junction sites by bis-intercalators induces topological changes with potent antitumor effects.Nucleic acids research · 2024Article
- On Water Arrangements in Right- and Left-Handed DNA Structures.Molecules (Basel, Switzerland) · 2024Review
- X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences.ACS bio & med chem Au · 2023Article
- The Novel DNA Binding Mechanism of Ridinilazole, a PrecisionAntimicrobial agents and chemotherapy · 2023Article
- Identification of Photocatalytic Alkaloids from Coptidis Rhizome by an Offline HPLC/CC/SCD Approach.Molecules (Basel, Switzerland) · 2022Article
- 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
- Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks.Acta crystallographica. Section D, Structural biology · 2022Article
- Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications.RSC chemical biology · 2022Review
- Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction.Nucleic acids research · 2021Article
- Water spines and networks in G-quadruplex structures.Nucleic acids research · 2021Article
- Modeling antimalarial and antihuman African trypanosomiasis compounds: a ligand- and structure-based approaches.Molecular diversity · 2020Article
- Small molecule binders recognize DNA microstructural variations via an induced fit mechanism.Physical chemistry chemical physics : PCCP · 2019Article
- CoInternational journal of molecular sciences · 2018Article
- Investigation of the electrostatic and hydration properties of DNA minor groove-binding by a heterocyclic diamidine by osmotic pressure.Biophysical chemistry · 2017Article
- Pharmacological inhibition of the transcription factor PU.1 in leukemia.The Journal of clinical investigation · 2017Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
High-resolution crystal structures of the DNA duplex sequence d(CGCGAATTCGCG)(2) complexed with three minor-groove ligands are reported. A highly conserved cluster of 11 linked water molecules has been found in the native and all 3 ligand-bound structures, positioned at the boundary of the A/T and G/C regions where the minor groove widens. This cluster appears to play a key structural role in stabilizing noncovalently binding small molecules in the AT region of the B-DNA minor groove. The cluster extends from the backbone phosphate groups along the mouth of the groove and links to DNA and ligands by a network of hydrogen bonds that help to maintain the ligands in position. This arrangement of water molecules is distinct from, but linked by, hydrogen bonding to the well-established spine of hydration, which is displaced by bound ligands. Features of the water cluster and observed differences in binding modes help to explain the measured binding affinities and thermodynamic characteristics of these ligands on binding to AT sites in DNA.
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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.