Saoji Maithili, Zhang Daoning, Paukstelis Paul J
Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742.
Biomolecular NMR Facility, College Park, MD, 20742.
Biopolymers. 2015 Nov;103(11):618-26. doi: 10.1002/bip.22688.
DNA is a widely used biopolymer for the construction of nanometer-scale objects due to its programmability and structural predictability. One long-standing goal of the DNA nanotechnology field has been the construction of three-dimensional DNA crystals. We previously determined the X-ray crystal structure of a DNA 13-mer that forms a continuously hydrogen bonded three-dimensional lattice through Watson-Crick and non-canonical base pairs. Our current study sets out to understand how the sequence of the Watson-Crick duplex region influences crystallization of this 13-mer. We screened all possible self-complementary sequences in the hexameric duplex region and found 21 oligonucleotides that crystallized. Sequence analysis showed that one specific Watson-Crick pair influenced the crystallization propensity and the speed of crystal self-assembly. We determined X-ray crystal structures for 13 of these oligonucleotides and found sequence-specific structural changes that suggests that this base pair may serve as a structural anchor during crystal assembly. Finally, we explored the crystal self-assembly and nucleation process. Solution studies indicated that these oligonucleotides do not form base pairs in the absence of cations, but that the addition of divalent cations leads to rapid self-assembly to higher molecular weight complexes. We further demonstrate that crystals grown from mixtures of two different oligonucleotide sequences contain both oligonucleotides. These results suggest that crystal self-assembly is nucleated by the formation of the Watson-Crick duplexes initiated by a simple chemical trigger. This study provides new insight into the role of sequence for the assembly of periodic DNA structures.
由于其可编程性和结构可预测性，DNA是一种广泛用于构建纳米级物体的生物聚合物。DNA纳米技术领域一个长期的目标是构建三维DNA晶体。我们之前确定了一种DNA 13聚体的X射线晶体结构，该13聚体通过沃森-克里克碱基对和非经典碱基对形成连续氢键连接的三维晶格。我们目前的研究旨在了解沃森-克里克双链区域的序列如何影响这种13聚体的结晶。我们筛选了六聚体双链区域中所有可能的自互补序列，发现了21种结晶的寡核苷酸。序列分析表明，一个特定的沃森-克里克碱基对影响结晶倾向和晶体自组装速度。我们确定了其中13种寡核苷酸的X射线晶体结构，发现了序列特异性的结构变化，这表明该碱基对可能在晶体组装过程中作为结构锚。最后，我们探索了晶体自组装和成核过程。溶液研究表明，这些寡核苷酸在没有阳离子的情况下不会形成碱基对，但添加二价阳离子会导致快速自组装成更高分子量的复合物。我们进一步证明，由两种不同寡核苷酸序列的混合物生长的晶体同时包含这两种寡核苷酸。这些结果表明，晶体自组装是由一个简单化学触发引发的沃森-克里克双链体的形成而成核的。这项研究为序列在周期性DNA结构组装中的作用提供了新的见解。
