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Nanopores map the acid-base properties of a single site in a single DNA molecule.
Smith, Drew C; Thomas, Christopher A; Craig, Jonathan M; Brinkerhoff, Henry; Abell, Sarah J; Franzi, Michaela C; Carrasco, Jessica D; Hoshika, Shuichi; Benner, Steven A; Gundlach, Jens H; Laszlo, Andrew H.
Afiliación
  • Smith DC; Department of Physics, University of Washington, Seattle, WA 98195, USA.
  • Thomas CA; Department of Physics, University of Washington, Seattle, WA 98195, USA.
  • Craig JM; Department of Physics, University of Washington, Seattle, WA 98195, USA.
  • Brinkerhoff H; Department of Physics, University of Washington, Seattle, WA 98195, USA.
  • Abell SJ; Department of Physics, University of Washington, Seattle, WA 98195, USA.
  • Franzi MC; Department of Physics, University of Washington, Seattle, WA 98195, USA.
  • Carrasco JD; Department of Physics, University of Washington, Seattle, WA 98195, USA.
  • Hoshika S; Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA.
  • Benner SA; Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA.
  • Gundlach JH; Department of Physics, University of Washington, Seattle, WA 98195, USA.
  • Laszlo AH; Department of Physics, University of Washington, Seattle, WA 98195, USA.
Nucleic Acids Res ; 52(13): 7429-7436, 2024 Jul 22.
Article en En | MEDLINE | ID: mdl-38884270
ABSTRACT
Nanopores are increasingly powerful tools for single molecule sensing, in particular, for sequencing DNA, RNA and peptides. This success has spurred efforts to sequence non-canonical nucleic acid bases and amino acids. While canonical DNA and RNA bases have pKas far from neutral, certain non-canonical bases, natural RNA modifications, and amino acids are known to have pKas near neutral pHs at which nanopore sequencing is typically performed. Previous reports have suggested that the nanopore signal may be sensitive to the protonation state of an individual moiety. We sequenced ion currents with the MspA nanopore using a single stranded DNA containing a single non-canonical DNA base (Z) at various pH conditions. The Z-base has a near-neutral pKa ∼ 7.8. We find that the measured ion current is remarkably sensitive to the protonation state of the Z-base. We demonstrate how nanopores can be used to localize and determine the pKa of individual moieties along a polymer. More broadly, these experiments provide a path to mapping different protonation sites along polymers and give insight in how to optimize sequencing of polymers that contain moieties with near-neutral pKas.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: ADN de Cadena Simple / Nanoporos Idioma: En Revista: Nucleic Acids Res Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: ADN de Cadena Simple / Nanoporos Idioma: En Revista: Nucleic Acids Res Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido