Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
J Am Chem Soc. 2021 Jan 13;143(1):241-251. doi: 10.1021/jacs.0c09892. Epub 2020 Dec 23.
The emergence of nucleic acid-based constitutional dynamic networks, CDNs, from a pool of nucleic acids is a key process for the understanding and modality of the evolution of biological networks. We present a versatile method that applies a library of nucleic acids coupled to biocatalytic DNA machineries as functional modules for the emergence of CDNs of diverse composition, complexity, and structural diversity. A set of four DNA template/blocker scaffolds coupled to the polymerase/dNTP replication machinery leads, in the presence of a primer, P, to the gated replication of the scaffolds and to the displacement of four components that reconfigure into a [2 × 2] CDN. Using six template/blocker scaffolds and the polymerase/dNTPs, the P-guided emergence of a [3 × 3] CDN is demonstrated. In addition, by further engineering the template/blocker scaffolds, the hierarchical control over the composition of the P-guided emergence of [3 × 3] CDNs is accomplished. Also, sequence-engineered template/blocker scaffolds, coupled to the polymerase/dNTP machinery, lead, in the presence of two primers P and/or P, to the selective emergence of two different [2 × 2] CDNs or to a [3 × 3] CDN. Also, a set of six appropriately engineered template/blocker scaffolds, coupled to the polymerase/dNTP machinery, leads to the emergence of a CDN composed of four equilibrated DNA tetrahedra constituents. Finally, by further sequence engineering of the set of template/blocker scaffolds and their coupling to a nicking/polymerization/dNTP replication machinery, the amplified high-throughput emergence of CDNs is demonstrated.
核酸构象动态网络（CDNs）是从核酸库中出现的关键过程，是理解和模拟生物网络进化的关键。我们提出了一种通用方法，该方法将核酸库与生物催化 DNA 机器偶联作为功能模块，用于出现具有不同组成、复杂性和结构多样性的 CDN。一组四个 DNA 模板/阻滞剂支架与聚合酶/dNTP 复制机制偶联，在引物 P 的存在下，导致支架的门控复制，并置换四个重新配置成 [2×2] CDN 的组件。使用六个模板/阻滞剂支架和聚合酶/dNTP，证明了在 P 引导下出现 [3×3] CDN。此外，通过进一步工程化模板/阻滞剂支架，可以实现对 P 引导的 [3×3] CDN 组成的分层控制。此外，与聚合酶/dNTP 机制偶联的序列工程化模板/阻滞剂支架，在存在两个引物 P 和/或 P 的情况下，导致选择性出现两个不同的 [2×2] CDN 或 [3×3] CDN。此外，一组六个经过适当工程化的模板/阻滞剂支架，与聚合酶/dNTP 机制偶联，导致出现由四个平衡 DNA 四面体组成的 CDN。最后，通过进一步对模板/阻滞剂支架集进行序列工程化，并将其与缺口/聚合酶/dNTP 复制机制偶联，证明了 CDN 的放大高通量出现。
