A mechanistic model of the BLADE platform predicts performance characteristics of 256 different synthetic DNA recombination circuits.
A mechanistic model of the BLADE platform predicts performance characteristics of 256 different synthetic DNA recombination circuits.
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DOI：
10.1371/journal.pcbi.1007849
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发表时间：
2020-12
影响因子：
4.3
通讯作者：
Bates DG
中科院分区：
文献类型：
--
作者：
Bowyer JE;Ding C;Weinberg BH;Wong WW;Bates DG
通过DNA切除的布尔逻辑和算术（BLADE）是最近开发的用于在哺乳动物细胞中实施对基因表达的诱导和逻辑控制的平台，其具有革命性细胞工程治疗应用的潜力。这个2输入2输出平台可以实现256个不同的逻辑电路，利用DNA重组的特异性和稳定性。在这里，我们开发了第一个机械数学模型的2输入BLADE平台的基础上Cre和Flp介导的DNA切除。校准模型的实验数据从两个电路后，我们证明了密切的协议模型输出和数据的其他111个电路，迄今为止已经实验构建使用2输入刀片平台。其余143个电路的模型模拟尚未进行实验测试，预测在可能的电路范围内的2输入刀片平台的优异性能。来自测试和未测试子集的电路表现不佳，由大量的STOP序列组成。模型预测表明，电路性能下降，重组酶表达的减少，并产生新的实验数据，证实了这种关系。合成生物学的一个主要目标是可预测地设计和构建遗传电路来控制细胞功能。尽管近年来在这一目标上取得了许多进展，但合成生物学仍然主要是一门以微生物为中心的学科，目前哺乳动物细胞中缺乏高性能的遗传电路。位点特异性DNA重组酶Cre、Flp是最强大的基因组工程工具之一，并通过DNA切除（BLADE）形成布尔逻辑和算术的基础，该平台有可能彻底改变哺乳动物细胞治疗应用的细胞工程。在这里，我们开发了第一个机械的数学模型的2-输入刀片平台，并通过模拟113个不同的电路，已被构造和实验测试的性能，应用它。我们通过模拟143个有待测试的电路的性能来展示我们模型的预测能力。我们的模型也能够测试实验假设，揭示了合成BLADE电路的性能对重组酶表达水平敏感。我们能够通过生成新的实验数据来确认这一计算结果。
Boolean logic and arithmetic through DNA excision (BLADE) is a recently developed platform for implementing inducible and logical control over gene expression in mammalian cells, which has the potential to revolutionise cell engineering for therapeutic applications. This 2-input 2-output platform can implement 256 different logical circuits that exploit the specificity and stability of DNA recombination. Here, we develop the first mechanistic mathematical model of the 2-input BLADE platform based on Cre- and Flp-mediated DNA excision. After calibrating the model on experimental data from two circuits, we demonstrate close agreement between model outputs and data on the other 111 circuits that have so far been experimentally constructed using the 2-input BLADE platform. Model simulations of the remaining 143 circuits that have yet to be tested experimentally predict excellent performance of the 2-input BLADE platform across the range of possible circuits. Circuits from both the tested and untested subsets that perform less well consist of a disproportionally high number of STOP sequences. Model predictions suggested that circuit performance declines with a decrease in recombinase expression and new experimental data was generated that confirms this relationship. A major objective in synthetic biology is to predictably design and construct genetic circuits to control cellular functions. Although recent years have seen numerous advances towards this goal, Synthetic Biology is still mostly a microbial-centric discipline, and high performance genetic circuits are currently lacking in mammalian cells. Site-specific DNA recombinases Cre, Flp are among the most powerful genome engineering tools and form the basis of Boolean logic and arithmetic through DNA excision (BLADE), a platform that has the potential to revolutionise cell engineering for therapeutic applications in mammalian cells. Here, we develop the first mechanistic mathematical model of the 2-input BLADE platform and apply it by simulating the performance of 113 different circuits that have been constructed and tested experimentally. We demonstrate the predictive power of our model by simulating the performance of the 143 circuits that are yet to be tested. Our model is also capable of testing experimental hypotheses, revealing that the performance of synthetic BLADE circuits is sensitive to recombinase expression levels. We were able to confirm this computational result by generating new experimental data.
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影响因子：
4.8
作者：
Ghosh, K;Van Duyne, GD
通讯作者：
Van Duyne, GD
DOI：
10.1073/pnas.0711649105
发表时间：
2008-03-04
影响因子：
11.1
作者：
Ghosh, Pallavi;Bibb, Lori A.;Hatfull, Graham F.
通讯作者：
Hatfull, Graham F.
影响因子：
5.6
作者：
Bowyer JE;Lc de Los Santos E;Styles KM;Fullwood A;Corre C;Bates DG
通讯作者：
Bates DG
DOI：
10.1073/pnas.090527097
发表时间：
2000-05-23
影响因子：
11.1
作者：
Groth, AC;Olivares, EC;Calos, MP
通讯作者：
Calos, MP
影响因子：
3.4
作者：
Bartley, Bryan A.;Kim, Kyung;Sauro, Herbert M.
通讯作者：
Sauro, Herbert M.