title: Single molecule investigation of Ag+ interactions with single cytosine-, methylcytosine- and hydroxymethylcytosine-cytosine mismatches in a nanopore.
abstract: Both cytosine-Ag-cytosine interactions and cytosine modifications in a DNA duplex have attracted great interest for research. Cytosine (C) modifications such as methylcytosine (mC) and hydroxymethylcytosine (hmC) are associated with tumorigenesis. However, a method for directly discriminating C, mC and hmC bases without labeling, modification and amplification is still missing. Additionally, the nature of coordination of Ag(+) with cytosine-cytosine (C-C) mismatches is not clearly understood. Utilizing the alpha-hemolysin nanopore, we show that in the presence of Ag(+), duplex stability is most increased for the cytosine-cytosine (C-C) pair, followed by the cytosine-methylcytosine (C-mC) pair, and the cytosine-hydroxymethylcytosine (C-hmC) pair, which has no observable Ag(+) induced stabilization. Molecular dynamics simulations reveal that the hydrogen-bond-mediated paring of a C-C mismatch results in a binding site for Ag(+). Cytosine modifications (such as mC and hmC) disrupted the hydrogen bond, resulting in disruption of the Ag(+) binding site. Our experimental method provides a novel platform to study the metal ion-DNA interactions and could also serve as a direct detection method for nucleobase modifications.
authors.affiliation: 1] Department of Biological Engineering and Dalton Cardiovascular Research Center University of Missouri, Columbia, MO 65211, USA [2].
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
authors.affiliation: 1] Computational Biology Center, IBM T. J. Watson Research, Yorktown Heights, NY 10598, USA [2].
authors.forename: Bin-Quan
authors.initials: BQ
authors.lastname: Luan
authors.affiliation: Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
authors.forename: Zhiyu
authors.initials: Z
authors.lastname: Yang
authors.affiliation: Department of Biological Engineering and Dalton Cardiovascular Research Center University of Missouri, Columbia, MO 65211, USA.
authors.forename: Xinyue
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Biological Engineering and Dalton Cardiovascular Research Center University of Missouri, Columbia, MO 65211, USA.
authors.forename: Brandon
authors.initials: B
authors.lastname: Ritzo
authors.affiliation: Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
authors.forename: Kent
authors.initials: K
authors.lastname: Gates
authors.affiliation: Department of Biological Engineering and Dalton Cardiovascular Research Center University of Missouri, Columbia, MO 65211, USA.
authors.forename: Li-Qun
authors.initials: LQ
authors.lastname: Gu
mesh_terms: D020137:Base Pair Mismatch; D001483:Base Sequence; D001665:Binding Sites; D003596:Cytosine / Q000031:analogs & derivatives* / Q000378:metabolism; D006460:Hemolysin Proteins / Q000737:chemistry; D006860:Hydrogen Bonding; D007477:Ions / Q000737:chemistry; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D058608:Nanopores; D009690:Nucleic Acid Conformation; D012834:Silver / Q000737:chemistry*; D044366:Transition Temperature
chemical_list: D006460:Hemolysin Proteins; D007477:Ions; D012834:Silver; D003596:Cytosine
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