Enzymatic synthesis and nanopore sequencing of 12-letter supernumerary DNA.

Autor: Kawabe H; Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA., Thomas CA; Department of Physics, University of Washington, Seattle, WA, 98195, USA., Hoshika S; Foundation for Applied Molecular Evolution, Alachua, FL, 32615, USA.; Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA., Kim MJ; Foundation for Applied Molecular Evolution, Alachua, FL, 32615, USA.; Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA., Kim MS; Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA., Miessner L; Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA., Kaplan N; Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA., Craig JM; Department of Physics, University of Washington, Seattle, WA, 98195, 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., Benner SA; Foundation for Applied Molecular Evolution, Alachua, FL, 32615, USA.; Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA., Marchand JA; Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA. jmarcha@uw.edu.; Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, USA. jmarcha@uw.edu.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2023 Oct 26; Vol. 14 (1), pp. 6820. Date of Electronic Publication: 2023 Oct 26.
DOI: 10.1038/s41467-023-42406-z
Abstrakt: The 4-letter DNA alphabet (A, T, G, C) as found in Nature is an elegant, yet non-exhaustive solution to the problem of storage, transfer, and evolution of biological information. Here, we report on strategies for both writing and reading DNA with expanded alphabets composed of up to 12 letters (A, T, G, C, B, S, P, Z, X, K, J, V). For writing, we devise an enzymatic strategy for inserting a singular, orthogonal xenonucleic acid (XNA) base pair into standard DNA sequences using 2'-deoxy-xenonucleoside triphosphates as substrates. Integrating this strategy with combinatorial oligos generated on a chip, we construct libraries containing single XNA bases for parameterizing kmer basecalling models for commercially available nanopore sequencing. These elementary steps are combined to synthesize and sequence DNA containing 12 letters - the upper limit of what is accessible within the electroneutral, canonical base pairing framework. By introducing low-barrier synthesis and sequencing strategies, this work overcomes previous obstacles paving the way for making expanded alphabets widely accessible.
(© 2023. The Author(s).)
Databáze: MEDLINE
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