Supplement: Development of a technology to certify engineered DNA molecules

项目总结 公开获得经过认证的、有充分记录的研究材料对科学进步至关重要。 质粒已经成为解决生物学中几乎任何问题的基本研究工具，并与 其他形式的工程DNA分子，对于包括基因治疗在内的临床研究应用是必不可少的， 疫苗开发和重组药物的生产。目前，两个常见的链接之间 质粒及其文档包括质粒名称和质粒序列。尽管核心作用是 质粒在生物医学研究和开发中发挥着作用，没有保证的方法来连接物理 将一个试管中的质粒化到其文档中。移液错误、标签错误、自发突变或 未经证实的对质粒的修饰是一些可能导致试管含有不同 而不是标签上所标明的。此外，没有标准化、安全的方法来 记录一个质粒的序列、功能和谱系的。因此，存在着广泛的差异。 在生命科学界循环中的质粒的物理序列和它们假设的 参考序列。这种情况造成了可再生性问题，减缓了研发工作，并显著提高了 生物技术应用的安全和安全问题。 我们建议开发一种新的数字证书技术，该技术由一个基于Web的资源实现，名为 这将在经过工程的DNA分子之间提供强大的物理联系，它们的电子 文档及其作者。这项技术将产生独特的DNA序列 可以插入到基因工程DNA分子中的加密算法。MyPlatmid.org将允许用户 通过汇总单个遗传元素的文档以及 元素的组合。此外，它还将直接将基因工程DNA序列的计算机记录联系起来 并提供了一种检索文献的方法，而无需事先知道该质粒的 身份。称为证书的短的唯一DNA序列将被插入到 经过工程处理的序列。与DNA条形码不同，证书将由加密算法使用 DNA序列本身和作者的身份作为输入，以便工程DNA分子的用户可以验证 经过认证的DNA分子的来源和完整性。本提案中描述的技术预计将 促进与半导体行业类似的转型，不同的利益相关者在半导体行业 投资开发可以很容易地组合成更大设计的电路，然后再进行制造 由不参与芯片设计的代工厂制造。通过确保序列、起源、功能和谱系 工程DNA分子被准确跟踪并传送给所有用户，所提议的技术将 提高工程DNA分子在生命科学中的重复性、实用性和潜在应用。

PROJECT SUMMARY The open availability of authenticated, well-documented research materials is essential for scientific progress. Plasmids have become essential research tools to address almost any question in biology, and together with other forms of engineered DNA molecules, are essential for clinical research applications including gene therapy, vaccine development, and the production of recombinant drugs. Currently, the two common links between a plasmid and its documentation are the plasmid names and the plasmid sequence. Despite the central role that plasmids play in biomedical research and development, there is no guaranteed way to connect a physical plasmid in a tube to its documentation. A pipetting error, a labelling error, a spontaneous mutation, or an undocumented modification of the plasmid are some of the events that could result in a tube containing a different plasmid than what is indicated on the label. In addition, there is no standardized, secure approach to documenting the sequence, function, and lineage of a plasmid. As a result, there are widespread discrepancies between the physical sequences of the plasmids in circulation in the life science community and their supposed reference sequence. This situation creates reproducibility issues, slows down R&D efforts and raises significant security and safety issues for biotechnology applications. We are proposing to develop a new digital certificate technology, enabled by a web-based resource called MyPlasmid.org, that will provide a robust, physical link between engineered DNA molecules, their electronic documentation, and their authors. This technology will produce unique DNA sequences generated by cryptographic algorithms that can be inserted into an engineered DNA molecule. MyPlasmid.org will allow users to document their genetic designs by aggregating the documentation of individual genetic elements as well as combinations of elements. In addition, it will link the computer records of the engineered DNA sequence directly to the molecule itself and provide a method to retrieve documentation without a priori knowledge of the plasmid's identity. Short unique DNA sequences called certificates will be inserted between the functional blocks of engineered sequences. Unlike DNA barcodes, certificates will be computed by cryptographic algorithms using the DNA sequence itself and the author's identity as input so that users of engineered DNA molecules can verify the origin and integrity of certified DNA molecules. The technology described in this proposal is expected to foster a transition similar what has been observed in the semi-conductor industry where different stakeholders invest in the development of circuits that can be easily combined in larger designs that can then be manufactured by foundries not involved in the chip design. By ensuring that the sequence, origin, function, and lineage of engineered DNA molecules is accurately tracked and conveyed to all users, the proposed technology will improve the reproducibility, utility, and potential application of engineered DNA molecules in the life sciences.