Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
The Biodesign Institute and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
Sci Adv. 2019 Jan 4;5(1):eaav0655. doi: 10.1126/sciadv.aav0655. eCollection 2019 Jan.
Scaffolded DNA origami offers the unique ability to organize molecules in nearly arbitrary spatial patterns at the nanometer scale, with wireframe designs further enabling complex 2D and 3D geometries with irregular boundaries and internal structures. The sequence design of the DNA staple strands needed to fold the long scaffold strand to the target geometry is typically performed manually, limiting the broad application of this materials design paradigm. Here, we present a fully autonomous procedure to design all DNA staple sequences needed to fold any free-form 2D scaffolded DNA origami wireframe object. Our algorithm uses wireframe edges consisting of two parallel DNA duplexes and enables the full autonomy of scaffold routing and staple sequence design with arbitrary network edge lengths and vertex angles. The application of our procedure to geometries with both regular and irregular external boundaries and variable internal structures demonstrates its broad utility for nanoscale materials science and nanotechnology.
有支架的 DNA 折纸提供了独特的能力，可以在纳米尺度上几乎任意空间模式下组织分子，而线框设计进一步实现了具有不规则边界和内部结构的复杂 2D 和 3D 几何形状。为了将长支架链折叠成目标几何形状，需要设计支架链的 DNA 短链序列，通常是手动完成的，这限制了这种材料设计模式的广泛应用。在这里，我们提出了一种完全自主的程序，可以设计任何自由形式的 2D 有支架 DNA 折纸线框对象所需的所有 DNA 短链序列。我们的算法使用由两条平行 DNA 双链组成的线框边缘，并能够实现支架布线和短链序列设计的完全自主，具有任意的网络边缘长度和顶点角度。我们的程序应用于具有规则和不规则外部边界以及可变内部结构的几何形状，证明了它在纳米尺度材料科学和纳米技术中的广泛用途。
