Department of Biological Engineering, Laboratory for Computational Biology & Biophysics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Nucleic Acids Res. 2014 Feb;42(4):2159-70. doi: 10.1093/nar/gkt1269. Epub 2013 Dec 5.
Programmed self-assembly of DNA enables the rational design of megadalton-scale macromolecular assemblies with sub-nanometer scale precision. These assemblies can be programmed to serve as structural scaffolds for secondary chromophore molecules with light-harvesting properties. Like in natural systems, the local and global spatial organization of these synthetic scaffolded chromophore systems plays a crucial role in their emergent excitonic and optical properties. Previously, we introduced a computational model to predict the large-scale 3D solution structure and flexibility of nucleic acid nanostructures programmed using the principle of scaffolded DNA origami. Here, we use Förster resonance energy transfer theory to simulate the temporal dynamics of dye excitation and energy transfer accounting both for overall DNA nanostructure architecture as well as atomic-level DNA and dye chemical structure and composition. Results are used to calculate emergent optical properties including effective absorption cross-section, absorption and emission spectra and total power transferred to a biomimetic reaction center in an existing seven-helix double stranded DNA-based antenna. This structure-based computational framework enables the efficient in silico evaluation of nucleic acid nanostructures for diverse light-harvesting and photonic applications.
DNA 可编程自组装使亚纳米级精度的兆道尔顿规模的大分子组装的合理设计成为可能。这些组装体可以被编程为具有光收集性质的二级发色团分子的结构支架。与在天然系统中一样，这些合成支架化发色团系统的局部和全局空间组织在它们的激发子和光学性质中起着至关重要的作用。以前，我们引入了一个计算模型来预测使用支架 DNA 折纸原理编程的核酸纳米结构的大规模 3D 溶液结构和灵活性。在这里，我们使用Förster 共振能量转移理论来模拟染料激发和能量转移的时间动力学，同时考虑到整个 DNA 纳米结构的架构以及原子级 DNA 和染料的化学结构和组成。结果用于计算出包括有效吸收截面、吸收和发射光谱以及传递到现有七螺旋双链 DNA 天线中仿生反应中心的总功率在内的新兴光学性质。这种基于结构的计算框架能够有效地对核酸纳米结构进行计算机评估，以用于各种光收集和光子应用。
