title: Discrimination of methylcytosine from hydroxymethylcytosine in DNA molecules.
abstract: Modified DNA bases are widespread in biology. 5-Methylcytosine (mC) is a predominant epigenetic marker in higher eukaryotes involved in gene regulation, development, aging, cancer, and disease. Recently, 5-hydroxymethylcytosine (hmC) was identified in mammalian brain tissue and stem cells. However, most of the currently available assays cannot distinguish mC from hmC in DNA fragments. We investigate here the physical properties of DNA with modified cytosines, in efforts to develop a physical tool that distinguishes mC from hmC in DNA fragments. Molecular dynamics simulations reveal that polar cytosine modifications affect internal base pair dynamics, while experimental evidence suggest a correlation between the modified cytosine's polarity, DNA flexibility, and duplex stability. On the basis of these physical differences, solid-state nanopores can rapidly discriminate among DNA fragments with mC or hmC modification by sampling a few hundred molecules in the solution. Further, the relative proportion of hmC in the sample can be determined from the electronic signature of the intact DNA fragment.
authors.affiliation: Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States. wanunu@sas.upenn.edu
authors.forename: Meni
authors.initials: M
authors.lastname: Wanunu
authors.forename: Devora
authors.initials: D
authors.lastname: Cohen-Karni
authors.forename: Robert R
authors.initials: RR
authors.lastname: Johnson
authors.forename: Lauren
authors.initials: L
authors.lastname: Fields
authors.forename: Jack
authors.initials: J
authors.lastname: Benner
authors.forename: Neil
authors.initials: N
authors.lastname: Peterman
authors.forename: Yu
authors.initials: Y
authors.lastname: Zheng
authors.forename: Michael L
authors.initials: ML
authors.lastname: Klein
authors.forename: Marija
authors.initials: M
authors.lastname: Drndic
mesh_terms: D044503:5-Methylcytosine / Q000737:chemistry* / Q000031:analogs & derivatives; D000818:Animals; D003596:Cytosine / Q000031:analogs & derivatives* / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction
chemical_list: C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine; D004247:DNA