ArticleNucleic acids research2004
Influence of structural variation on nuclear localization of DNA-binding polyamide-fluorophore conjugates.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
47 citing papers in PubMed.
- Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics.Scientific reports · 2021Article
- Modulating DNA by polyamides to regulate transcription factor PU.1-DNA binding interactions.Biochimie · 2019Article
- A Polyamide Inhibits Replication of Vesicular Stomatitis Virus by Targeting RNA in the Nucleocapsid.Journal of virology · 2018Article
- Structural basis of DNA duplex distortion induced by thiazole-containing hairpin polyamides.Nucleic acids research · 2018Article
- Modulation of topoisomerase IIα expression and chemosensitivity through targeted inhibition of NF-Y:DNA binding by a diamino p-anisyl-benzimidazole (Hx) polyamide.Biochimica et biophysica acta. Gene regulatory mechanisms · 2017Article
- Reprogramming cell fate with a genome-scale library of artificial transcription factors.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- RNA polymerase II senses obstruction in the DNA minor groove via a conserved sensor motif.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Sequence-specific recognition of DNA minor groove by an NIR-fluorescence switch-on probe and its potential applications.Nucleic acids research · 2015Article
- Article
- Tumor xenograft uptake of a pyrrole-imidazole (Py-Im) polyamide varies as a function of cell line grafted.Journal of medicinal chemistry · 2014Article
- Replication stress by Py-Im polyamides induces a non-canonical ATR-dependent checkpoint response.Nucleic acids research · 2014Article
- A C-14 labeled Py-Im polyamide localizes to a subcutaneous prostate cancer tumor.Bioorganic & medicinal chemistry · 2014Article
- Article
- Programmable DNA-binding small molecules.Bioorganic & medicinal chemistry · 2013Review
- Activity of a Py-Im polyamide targeted to the estrogen response element.Molecular cancer therapeutics · 2013Article
- Pyrrole-imidazole polyamides distinguish between double-helical DNA and RNA.Angewandte Chemie (International ed. in English) · 2013Article
- Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Characterization and solubilization of pyrrole-imidazole polyamide aggregates.Journal of medicinal chemistry · 2012Article
- Microwave assisted synthesis of Py-Im polyamides.Organic letters · 2012Article
- Enhancing the cellular uptake of Py-Im polyamides through next-generation aryl turns.Nucleic acids research · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
A pivotal step forward in chemical approaches to controlling gene expression is the development of sequence-specific DNA-binding molecules that can enter live cells and traffic to nuclei unaided. DNA-binding polyamides are a class of programmable, sequence-specific small molecules that have been shown to influence a wide variety of protein-DNA interactions. We have synthesized over 100 polyamide-fluorophore conjugates and assayed their nuclear uptake profiles in 13 mammalian cell lines. The compiled dataset, comprising 1300 entries, establishes a benchmark for the nuclear localization of polyamide-dye conjugates. Compounds in this series were chosen to provide systematic variation in several structural variables, including dye composition and placement, molecular weight, charge, ordering of the aromatic and aliphatic amino-acid building blocks and overall shape. Nuclear uptake does not appear to be correlated with polyamide molecular weight or with the number of imidazole residues, although the positions of imidazole residues affect nuclear access properties significantly. Generally negative determinants for nuclear access include the presence of a beta-Ala-tail residue and the lack of a cationic alkyl amine moiety, whereas the presence of an acetylated 2,4-diaminobutyric acid-turn is a positive factor for nuclear localization. We discuss implications of these data on the design of polyamide-dye conjugates for use in biological systems.
Indexed as
Identifiers
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.