Accelerating Self-Assembly of Crisscross Slat Systems

IF 4.7 2区 生物学 Q1 GENETICS & HEREDITY Mobile DNA Pub Date : 2023-01-01 DOI:10.4230/LIPIcs.DNA.29.7
David Doty, Hunter Fleming, Daniel Hader, Matthew J. Patitz, Lukas A. Vaughan
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引用次数: 1

Abstract

We present an abstract model of self-assembly of systems composed of “crisscross slats”, which have been experimentally implemented as a single-stranded piece of DNA [21] or as a complete DNA origami structure [28]. We then introduce a more physically realistic “kinetic” model and show how important constants in the model were derived and tuned, and compare simulation-based results to experimental results [21,28]. Using these models, we show how we can apply optimizations to designs of slat systems in order to lower the numbers of unique slat types required to build target structures. In general, we apply two types of techniques to achieve greatly reduced numbers of slat types. Similar to the experimental work implementing DNA origami-based slats, in our designs the slats oriented in horizontal and vertical directions are each restricted to their own plane and sets of them overlap each other in square regions which we refer to as macrotiles . Our first technique extends their previous work of reusing slat types within macrotiles and requires analyses of binding domain patterns to determine the potential for errors consisting of incorrect slat types attaching at undesired translations and reflections. The second technique leverages the power of algorithmic self-assembly to efficiently reuse entire macrotiles which self-assemble in patterns following designed algorithms that dictate the dimensions and patterns of growth. Using these designs, we demonstrate that in kinetic simulations the systems with reduced numbers of slat types self-assemble more quickly than those with greater numbers. This provides evidence that such optimizations will also result in greater assembly speeds in experimental systems. Furthermore, the reduced numbers of slat types required have the potential to vastly reduce the cost and number of lab steps for crisscross assembly experiments.
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加速交叉板系的自组装
我们提出了一个由“交叉板条”组成的系统自组装的抽象模型,该模型已被实验实现为单链DNA[21]或完整的DNA折纸结构[28]。然后,我们引入了一个更现实的“动力学”模型,并展示了模型中重要的常数是如何推导和调整的,并将基于模拟的结果与实验结果进行了比较[21,28]。使用这些模型,我们展示了如何将优化应用于板条系统的设计,以减少构建目标结构所需的独特板条类型的数量。一般来说,我们采用两种技术来大大减少板条类型的数量。类似于基于DNA折纸的板条的实验工作,在我们的设计中,水平方向和垂直方向的板条都被限制在自己的平面上,并且它们的集合在我们称之为宏块的方形区域中相互重叠。我们的第一项技术扩展了他们之前在宏块中重用板条类型的工作,需要对绑定域模式进行分析,以确定在不需要的翻译和反射上附着不正确的板条类型所构成的潜在错误。第二种技术利用算法自组装的能力,有效地重用整个宏块,这些宏块按照指定增长的维度和模式的设计算法以模式进行自组装。利用这些设计,我们证明了在动力学模拟中,具有较少数量的板条类型的系统比具有较多数量的系统自组装速度更快。这提供的证据表明,这种优化也将导致更大的组装速度在实验系统。此外,所需的板条类型数量的减少有可能大大降低交叉组装实验的成本和实验室步骤的数量。
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来源期刊
Mobile DNA
Mobile DNA GENETICS & HEREDITY-
CiteScore
8.20
自引率
6.10%
发文量
26
审稿时长
11 weeks
期刊介绍: Mobile DNA is an online, peer-reviewed, open access journal that publishes articles providing novel insights into DNA rearrangements in all organisms, ranging from transposition and other types of recombination mechanisms to patterns and processes of mobile element and host genome evolution. In addition, the journal will consider articles on the utility of mobile genetic elements in biotechnological methods and protocols.
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