ArticleNucleic acids research2008
Pyrrole-imidazole hairpin polyamides with high affinity at 5'-CGCG-3' DNA sequence; influence of cytosine methylation on binding.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 53 citations in OpenAlex.
- RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Single position substitution of hairpin pyrrole-imidazole polyamides imparts distinct DNA-binding profiles across the human genome.PloS one · 2020Article
- TAMRA-polypyrrole for A/T sequence visualization on DNA molecules.Nucleic acids research · 2018Article
- Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin).Journal of visualized experiments : JoVE · 2016Article
- Mapping polyamide-DNA interactions in human cells reveals a new design strategy for effective targeting of genomic sites.Angewandte Chemie (International ed. in English) · 2014Article
- Controlling gene networks and cell fate with precision-targeted DNA-binding proteins and small-molecule-based genome readers.The Biochemical journal · 2014Review
- Design of sequence-specific DNA binding molecules for DNA methyltransferase inhibition.Journal of the American Chemical Society · 2014Article
- DNA Binding Polyamides and the Importance of DNA Recognition in their use as Gene-Specific and Antiviral Agents.Medicinal chemistry · 2014Article
- Pyrrole-imidazole polyamides distinguish between double-helical DNA and RNA.Angewandte Chemie (International ed. in English) · 2013Article
- Strategies to modulate heritable epigenetic defects in cellular machinery: lessons from nature.Pharmaceuticals (Basel, Switzerland) · 2012Article
- Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants.Nucleic acids research · 2012Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To investigate the binding of 5'-CpG-3' sequences by small molecules, two pyrrole (Py)-imidazole (Im) hairpin polyamides, PyImPyIm-gamma-PyImPyIm-beta-Dp (1) and PyIm-beta-Im-gamma-PyIm-beta-Im-beta-Dp (2), which recognize the sequence 5'-CGCG-3', were synthesized. The binding affinities of the 5'-CGCG-3' sequence to the Py-Im hairpin polyamides were measured by surface plasmon resonance (SPR) analysis. SPR data revealed that dissociation equilibrium constants (K(d)) of polyamides 1 and 2 were 1.1 (+/- 0.3) x 10(-6) M and 1.7 (+/- 0.4) x 10(-8) M, respectively. Polyamide 2 possesses great binding affinity for this sequence, 65-fold higher than polyamide 1. Moreover, when all cytosines in 5'-CpGpCpG-3' were replaced with 5-methylcytosines ((m)Cs), the K(d) value of polyamide 2 increased to 5.8 (+/- 0.7) x 10(-9) (M), which indicated about 3-fold higher binding than the unmethylated 5'-CGCG-3' sequence. These results suggest that polyamide 2 would be suitable to target CpG-rich sequences in the genome.
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