Basic Science Program, SAIC-Frederick, Inc., NCI at Frederick, Frederick, MD 21702, United States.
Methods. 2011 Jun;54(2):239-50. doi: 10.1016/j.ymeth.2010.12.010. Epub 2010 Dec 14.
In the emerging field of RNA-based nanotechnology there is a need for automation of the structure design process. Our goal is to develop computer methods for aiding in this process. Towards that end, we created the RNA junction database, which is a repository of RNA junctions, i.e. internal, multi-branch and kissing loops with emanating stem stubs, extracted from the larger RNA structures stored in the PDB database. These junctions can be used as building blocks for nanostructures. Two programs developed in our laboratory, NanoTiler and RNA2D3D, can combine such building blocks with idealized fragments of A-form helices to produce desired 3D nanostructures. Initially, the building blocks are treated as rigid objects and the resulting geometry is tested against the design objectives. Experimental data, however, shows that RNA accommodates its shape to the constraints of larger structural contexts. Therefore we are adding analysis of the flexibility of our building blocks to the full design process. Here we present an example of RNA-based nanostructure design, putting emphasis on the need to characterize the structural flexibility of the building blocks to induce ring closure in the automated exploration. We focus on the use of kissing loops (KL) in nanostructure design, since they have been shown to play an important role in RNA self-assembly. By using an experimentally proven system, the RNA tectosquare, we show that considering the flexibility of the KLs as well as distortions of helical regions may be necessary to achieve a realistic design.
在新兴的 RNA 纳米技术领域，需要实现结构设计过程的自动化。我们的目标是开发辅助这一过程的计算机方法。为此，我们创建了 RNA 连接数据库，它是从 PDB 数据库中存储的较大 RNA 结构中提取的 RNA 连接，即内部、多分支和吻环以及发出茎干的连接。这些连接可以用作纳米结构的构建块。我们实验室开发的两个程序，NanoTiler 和 RNA2D3D，可以将这些构建块与理想化的 A 型螺旋片段结合起来，生成所需的 3D 纳米结构。最初，构建块被视为刚性物体，并且所得到的几何形状会根据设计目标进行测试。然而，实验数据表明，RNA 会根据较大结构环境的限制来调整其形状。因此，我们将对构建块的灵活性进行分析，将其纳入完整的设计过程中。这里我们展示了一个基于 RNA 的纳米结构设计的例子，重点强调了在自动探索中需要对构建块的结构灵活性进行特征描述，以诱导环闭合。我们专注于在纳米结构设计中使用吻环（KL），因为它们已被证明在 RNA 自组装中发挥重要作用。通过使用经过实验验证的系统，即 RNA tectosquare，我们表明考虑 KL 的灵活性以及螺旋区域的扭曲可能是实现真实设计所必需的。
