ArticleAccounts of chemical research2009
A role for water molecules in DNA-ligand minor groove recognition.
Article in Accounts of chemical research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 127 citations in OpenAlex.
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- Direct amidinium-phosphate interactions guide AT-selective DNA binding by a potent antileishmanial drug.Communications chemistry · 2026Article
- 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
- 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
- Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA.RNA (New York, N.Y.) · 2023Article
- Binding to the DNA Minor Groove by Heterocyclic Dications: from AT Specific to GC Recognition Compounds.Current protocols · 2023Review
- Multiassay Profiling of a Focused Small Molecule Library Reveals Predictive Bidirectional Modulation of the lncRNA MALAT1 Triplex StabilityACS chemical biology · 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
- Solvent Vibrations as a Proxy of the Telomere G-Quadruplex Rearrangements across Thermal Unfolding.International journal of molecular sciences · 2022Article
- Thermodynamic Factors That Drive Sequence-Specific DNA Binding of Designed, Synthetic Minor Groove Binding Agents.Life (Basel, Switzerland) · 2022Article
- Probing the Hydrogen-Bonding Environment of Individual Bases in DNA Duplexes with Isotope-Edited Infrared Spectroscopy.The journal of physical chemistry. B · 2021Article
- Water spines and networks in G-quadruplex structures.Nucleic acids research · 2021Article
- Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org.Acta crystallographica. Section D, Structural biology · 2020Article
- Gold-Hybridized Zinc Oxide Nanorods as Real-Time Low-Cost NanoBiosensors for Detection of virulent DNA signature of HPV-16 in Cervical Carcinoma.Scientific reports · 2019Article
- Canonical DNA minor groove insertion of bisbenzamidine-Ru(ii) complexes with chiral selectivity.Chemical science · 2019Article
- Bound Compound, Interfacial Water, and Phenyl Ring Rotation Dynamics of a Compound in the DNA Minor Groove.Biochemistry · 2018Article
- Dynamic self-assembly of DNA minor groove-binding ligand DB921 into nanotubes triggered by an alkali halide.Nanoscale · 2018Article
- Using Genome Sequence to Enable the Design of Medicines and Chemical Probes.Chemical reviews · 2018Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Targeting the minor groove of DNA through binding to a small molecule has long been considered an important molecular-recognition strategy in biology. A wide range of synthetic heterocyclic molecules bind noncovalently in the minor groove of the double helix and are also effective against a number of human and animal diseases. A classic structural concept, the isohelicity principle, has guided much of this work: such heterocyclic molecules require a shape that complements the convex surface of the minor groove. Researchers have used this principle to design molecules that can read DNA sequences. This principle also predicts that molecules that lack the complementary shape requirement would only bind weakly to DNA. Recently, however, researchers have unexpectedly found that some essentially linear compounds, which do not have this feature, can have high DNA affinity. In this Account, we discuss an alternative recognition concept based on these new findings. We demonstrate that highly structured water molecules can play a key role in mediating between the ligand and DNA minor groove without loss of binding affinity. Combined structural and thermodynamic approaches to understanding the behavior of these molecules have shown that there are different categories of bound water in their DNA complexes. For example, application of this water-bridging concept to the phenylamidine platform has resulted in the discovery of molecules with high levels of biological activity and low nonspecific toxicity. Some of these molecules are now in advanced clinical trials.
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