Bombelli Francesca Baldelli, Gambinossi Filippo, Lagi Marco, Berti Debora, Caminati Gabriella, Brown Tom, Sciortino Francesco, Norden Bengt, Baglioni Piero
Department of Chemistry and CSGI, University of Florence, Via della Lastruccia 3 - Sesto Fiorentino, 50019 Florence, Italy.
J Phys Chem B. 2008 Dec 4;112(48):15283-94. doi: 10.1021/jp804544u.
DNA nanoconstructs are obtained in solution by using six unique 42-mer DNA oligonucleotides, whose sequences have been designed to form a pseudohexagonal structure. The required flexibility is provided by the insertion of two non-base-paired thymines in the middle of each sequence that work as flexible hinges and constitute the corners of the nanostructure when formed. We show that hexagonally shaped nanostructures of about 7 nm diameter and their corresponding linear open constructs are formed by self-assembly of the specifically designed linear oligonucleotides. The structural and dynamical characterization of the nanostructure is obtained in situ for the first time by using dynamic light scattering (DLS), a noninvasive method that provides a fast dynamic and structural analysis and allows the characterization of the different synthetic DNA nanoconstructs in solution. A validation of the LS results is obtained through Monte Carlo (MC) simulations and atomic force microscopy (AFM). In particular, a mesoscale molecular model for DNA, developed by Knotts et al., is exploited to perform MC simulations and to obtain information about the conformations as well as the conformational flexibilities of these nanostructures, while AFM provides a very detailed particle analysis that yields an estimation of the particle size and size distribution. The structural features obtained by MC and AFM are in good agreement with DLS, showing that DLS is a fast and reliable tool for characterization of DNA nanostructures in solution.
通过使用六种独特的42聚体DNA寡核苷酸在溶液中获得DNA纳米结构，这些寡核苷酸的序列被设计成形成一种准六边形结构。通过在每个序列中间插入两个非碱基配对的胸腺嘧啶来提供所需的灵活性，这两个胸腺嘧啶充当柔性铰链，并在形成纳米结构时构成其角。我们表明，通过特定设计的线性寡核苷酸的自组装形成了直径约7纳米的六边形纳米结构及其相应的线性开放结构。首次通过使用动态光散射（DLS）对纳米结构进行原位结构和动力学表征，DLS是一种非侵入性方法，可提供快速的动态和结构分析，并能够表征溶液中不同的合成DNA纳米结构。通过蒙特卡罗（MC）模拟和原子力显微镜（AFM）对动态光散射结果进行了验证。特别是，利用Knotts等人开发的DNA中尺度分子模型进行MC模拟，并获得有关这些纳米结构的构象以及构象灵活性的信息，而AFM提供了非常详细的颗粒分析，可估算颗粒大小和大小分布。通过MC和AFM获得的结构特征与DLS结果高度一致，表明DLS是表征溶液中DNA纳米结构的快速可靠工具。
