12 字母额外 DNA 的酶法合成与纳米孔测序。

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

机构信息

Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.

Department of Physics, University of Washington, Seattle, WA, 98195, USA.

出版信息

Nat Commun. 2023 Oct 26;14(1):6820. doi: 10.1038/s41467-023-42406-z.

Abstract

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.

摘要

自然界中发现的 4 字母 DNA 字母表(A、T、G、C)是存储、传输和进化生物信息问题的一种优雅而又非穷尽的解决方案。在这里,我们报告了使用多达 12 个字母(A、T、G、C、B、S、P、Z、X、K、J、V)组成的扩展字母表进行 DNA 读写的策略。在写入方面,我们设计了一种酶促策略,使用 2'-脱氧-xenonucleoside 三磷酸作为底物将单个正交 xenonucleic acid (XNA) 碱基对插入标准 DNA 序列中。将这种策略与在芯片上生成的组合寡核苷酸相结合,我们构建了包含单个 XNA 碱基的文库,用于参数化商业可用的纳米孔测序的 kmer 碱基调用模型。这些基本步骤被组合起来合成和测序含有 12 个字母的 DNA——这是在电中性、规范碱基配对框架内可访问的上限。通过引入低势垒合成和测序策略,这项工作克服了以前的障碍,为广泛使用扩展字母铺平了道路。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/504c/10603101/9cc87bbc4819/41467_2023_42406_Fig1_HTML.jpg

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