ArticleJournal of the American Chemical Society2012
Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing.
Article in Journal of the American Chemical Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
27 citing papers in PubMed, 72 citations in OpenAlex.
- Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review.Methods (San Diego, Calif.) · 2024Review
- Site-Specific Arrangement and Structure Determination of Minor Groove Binding Molecules in Self-Assembled Three-Dimensional DNA Crystals.Journal of the American Chemical Society · 2023Article
- Domain-Selective BET Ligands Yield Next-Generation Synthetic Genome Readers/Regulators with Nonidentical Cellular Functions.Journal of the American Chemical Society · 2023Article
- Chem-map profiles drug binding to chromatin in cells.Nature biotechnology · 2023Article
- Article
- Strong and Specific Recognition of CAG/CTG Repeat DNA (5'-dWGCWGCW-3') by a Cyclic Pyrrole-Imidazole Polyamide.Chembiochem : a European journal of chemical biology · 2022Article
- High-Fidelity Sequence-Selective Duplex Formation by Recognition-Encoded Melamine Oligomers.Journal of the American Chemical Society · 2021Article
- Single position substitution of hairpin pyrrole-imidazole polyamides imparts distinct DNA-binding profiles across the human genome.PloS one · 2020Article
- Estimating genome-wide off-target effects for pyrrole-imidazole polyamide binding by a pathway-based expression profiling approach.PloS one · 2019Article
- H-Bonded Duplexes based on a Phenylacetylene Backbone.Journal of the American Chemical Society · 2018Article
- β-Alanine and N-terminal cationic substituents affect polyamide-DNA binding.Organic & biomolecular chemistry · 2017Article
- Sequence-Selective Formation of Synthetic H-Bonded Duplexes.Journal of the American Chemical Society · 2017Article
- H-Bond Self-Assembly: Folding versus Duplex Formation.Journal of the American Chemical Society · 2017Article
- Synthetic genome readers target clustered binding sites across diverse chromatin states.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Interactions of two large antiviral polyamides with the long control region of HPV16.Biochimie · 2016Article
- Deciphering the genomic targets of alkylating polyamide conjugates using high-throughput sequencing.Nucleic acids research · 2016Article
- Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin).Journal of visualized experiments : JoVE · 2016Article
- Identification of Binding Targets of a Pyrrole-Imidazole Polyamide KR12 in the LS180 Colorectal Cancer Genome.PloS one · 2016Article
- Mixed up minor groove binders: Convincing A·T specific compounds to recognize a G·C base pair.Bioorganic & medicinal chemistry letters · 2015Article
- A sequence-specific DNA binding small molecule triggers the release of immunogenic signals and phagocytosis in a model of B-cell lymphoma.Quarterly reviews of biophysics · 2015Review
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 3 countries.
Funding
Abstract
Genomic applications of DNA-binding molecules require an unbiased knowledge of their high affinity sites. We report the high-throughput analysis of pyrrole-imidazole polyamide DNA-binding specificity in a 10(12)-member DNA sequence library using affinity purification coupled with massively parallel sequencing. We find that even within this broad context, the canonical pairing rules are remarkably predictive of polyamide DNA-binding specificity. However, this approach also allows identification of unanticipated high affinity DNA-binding sites in the reverse orientation for polyamides containing β/Im pairs. These insights allow the redesign of hairpin polyamides with different turn units capable of distinguishing 5'-WCGCGW-3' from 5'-WGCGCW-3'. Overall, this study displays the power of high-throughput methods to aid the optimal targeting of sequence-specific minor groove binding molecules, an essential underpinning for biological and nanotechnological applications.
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What OpenQuestion holds
Registered trials
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.