Tripathi Shailesh, Zhang Daoning, Paukstelis Paul J
Department of Chemistry & Biochemistry, Center for Biomolecular Structure & Organization, Maryland Nanocenter, University of Maryland, College Park, MD 20742, USA.
Department of Chemistry & Biochemistry, Center for Biomolecular Structure & Organization, Maryland Nanocenter, University of Maryland, College Park, MD 20742, USA
Nucleic Acids Res. 2015 Feb 18;43(3):1937-44. doi: 10.1093/nar/gkv033. Epub 2015 Jan 27.
DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson-Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC(Br)UCGGA(Br)UGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A-A base pairs between adjacent G-G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. (1)H-(1)H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.
DNA已被证明是用于纳米级构建的优异材料，因为互补DNA双链体具有可编程性且结构可预测。然而，在不存在沃森-克里克配对的情况下，DNA在结构上可能更加多样。在此，我们描述了d(ACTCGGATGAT)及其溴化衍生物d(AC(Br)UCGGA(Br)UGAT)的晶体结构。这些寡核苷酸与一条晶体学等价链形成平行链双链体，从而产生了包含四种不同对称同型碱基对的DNA晶体结构的首个实例。其中两条平行链双链体以相反方向同轴堆积，并通过在互补双链体中相邻G-G对之间插入最5'端的A-A碱基对而锁定在一起形成四链体。插入区域是一种新型的DNA三级结构基序，与i-基序相似。氢-氢核磁共振和天然凝胶电泳证实了溶液中平行链双链体的形成。最后，我们对寡核苷酸的特定核苷酸位置进行修饰并添加了d(GAY)基序，并且很容易获得了类似的晶体。这表明这种平行链DNA结构可能有助于DNA晶体和纳米结构的合理设计。
