ArticleNucleic acids research2016
Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 25 citations in OpenAlex.
- Characterization of the enzyme for 5-hydroxymethyluridine production and its role in silencing transposable elements in dinoflagellates.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome.Genome biology · 2024Article
- Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in thebioRxiv : the preprint server for biology · 2023Article
- DNA Glycosylases Define the Outcome of Endogenous Base Modifications.International journal of molecular sciences · 2023Review
- Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.Sensors (Basel, Switzerland) · 2020Review
- Analysis of Modified Nucleotide Aptamer Library Generated by Thermophilic DNA Polymerases.Chembiochem : a European journal of chemical biology · 2020Article
- Translesion DNA Synthesis Across Lesions Induced by Oxidative Products of Pyrimidines: An Insight into the Mechanism by Microscale Thermophoresis.International journal of molecular sciences · 2019Article
- Microfluidic epigenomic mapping technologies for precision medicine.Lab on a chip · 2019Review
- Type II Restriction of Bacteriophage DNA With 5hmdU-Derived Base Modifications.Frontiers in microbiology · 2019Article
- tRNA Modification Detection Using Graphene Nanopores: A Simulation Study.Biomolecules · 2017Article
- Interrogation of Base Pairing of the Spiroiminodihydantoin Diastereomers Using the α-Hemolysin Latch.Biochemistry · 2017Article
- Quantifying mammalian genomic DNA hydroxymethylcytosine content using solid-state nanopores.Scientific reports · 2016Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Oxidation of a DNA thymine to 5-hydroxymethyluracil is one of several recently discovered epigenetic modifications. Here, we report the results of nanopore translocation experiments and molecular dynamics simulations that provide insight into the impact of this modification on the structure and dynamics of DNA. When transported through ultrathin solid-state nanopores, short DNA fragments containing thymine modifications were found to exhibit distinct, reproducible features in their transport characteristics that differentiate them from unmodified molecules. Molecular dynamics simulations suggest that 5-hydroxymethyluracil alters the flexibility and hydrophilicity of the DNA molecules, which may account for the differences observed in our nanopore translocation experiments. The altered physico-chemical properties of DNA produced by the thymine modifications may have implications for recognition and processing of such modifications by regulatory DNA-binding proteins.
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