ArticleNucleic acids research2023
Decoding complexity in biomolecular recognition of DNA i-motifs with microarrays.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 23 citations in OpenAlex.
- RNA functional modulation by Mitoxantrone via RNA structural ensemble repartitioning.Nature communications · 2026Article
- High-throughput measurement and prediction of the i-motif DNA stability landscape.Nucleic acids research · 2026Article
- Mechanistic insights into PCBP1-driven unfolding of selected i-motif DNA at GNature communications · 2026Article
- i-Motif, not G-quadruplex, stability regulates insulin expression.Nucleic acids research · 2026Article
- Integrative gene expression and heterologous functional analysis identify candidate regulators of apomixis inFrontiers in plant science · 2026Article
- Chemically modified CRISPR-Cas9 enables targeting of individual G-quadruplex and i-motif structures, revealing ligand-dependent transcriptional perturbation.Nature communications · 2025Article
- The iMab antibody selectively binds to intramolecular and intermolecular i-motif structures.Nucleic acids research · 2025Article
- Modulation of Nrf2 expression by targeting i-motif DNA.Communications chemistry · 2025Article
- Sequence-based prioritization of i-Motif candidates in the human genome.Frontiers in bioinformatics · 2025Article
- Human genomic DNA is widely interspersed with i-motif structures.The EMBO journal · 2024Article
- Structural insights into i-motif DNA structures in sequences from the insulin-linked polymorphic region.Nature communications · 2024Article
- iMab antibody binds single-stranded cytosine-rich sequences and unfolds DNA i-motifs.Nucleic acids research · 2024Article
- Prediction of DNA i-motifs via machine learning.Nucleic acids research · 2024Article
- In-cell NMR suggests that DNA i-motif levels are strongly depleted in living human cells.Nature communications · 2024Article
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7 authors at 1 institution in 1 country.
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Abstract
DNA i-motifs (iMs) are non-canonical C-rich secondary structures implicated in numerous cellular processes. Though iMs exist throughout the genome, our understanding of iM recognition by proteins or small molecules is limited to a few examples. We designed a DNA microarray containing 10976 genomic iM sequences to examine the binding profiles of four iM-binding proteins, mitoxantrone and the iMab antibody. iMab microarray screens demonstrated that pH 6.5, 5% BSA buffer was optimal, and fluorescence was correlated with iM C-tract length. hnRNP K broadly recognizes diverse iM sequences, favoring 3-5 cytosine repeats flanked by thymine-rich loops of 1-3 nucleotides. Array binding mirrored public ChIP-Seq datasets, in which 35% of well-bound array iMs are enriched in hnRNP K peaks. In contrast, other reported iM-binding proteins had weaker binding or preferred G-quadruplex (G4) sequences instead. Mitoxantrone broadly binds both shorter iMs and G4s, consistent with an intercalation mechanism. These results suggest that hnRNP K may play a role in iM-mediated regulation of gene expression in vivo, whereas hnRNP A1 and ASF/SF2 are possibly more selective in their binding preferences. This powerful approach represents the most comprehensive investigation of how biomolecules selectively recognize genomic iMs to date.
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