Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications
Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications
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DOI：
10.1021/acsnano.9b02430
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发表时间：
2019-07-01
期刊：
影响因子：
17.1
通讯作者：
Seeman, Nadrian C.
中科院分区：
文献类型：
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作者：
Ohayon, Yoel P.;Hernandez, Carina;Seeman, Nadrian C.
DNA张拉整体三角形通过粘端粘合自组装成菱面体三维晶体。含有两个核苷酸(NT)粘性末端(GA：TC)的晶体已被报道，这些晶体在光束线NSLS-I-X25处衍射角为4.9埃。在这里，我们分析了不同的粘端长度和序列的影响，以及5‘和3’-磷酸对晶体形成和分辨率的影响。具有1-、2-、3-和4-nT粘性末端的张拉整体三角形图案都形成晶体。同一光束线的X射线衍射数据表明，1-nT粘性端(G：C)和3-nT粘性端(GAT：ATC)的晶体分辨率分别为3.4埃和4.2埃。在每种情况下，分辨率都是从完整的数据集确定的。我们还进行了试验，检查了1-核苷酸和2-核苷酸粘端磷酸化链的每一种可能的组合，并成功地结晶了所有16种可能的链组合。我们观察到5‘-磷酸在交叉链(1)、螺旋链(2)或中心链(3)上的位置对2转单体(1-2P-3P为3.0埃)和2转二聚体粘端(1-2-3P为4.1埃)体系自组装晶体的分辨率有影响。我们还研究了粘性末端两侧碱基的特性以及3‘-磷酸的使用的影响。我们得出结论，晶体分辨率不是该体系中参与分子凝聚力的直接核苷酸配对相互作用热力学的简单结果。
DNA tensegrity triangles self-assemble into rhombohedral three-dimensional crystals via sticky ended cohesion. Crystals containing two-nucleotide (nt) sticky ends (GA:TC) have been reported previously, and those crystals diffracted to 4.9 angstrom at beamline NSLS-I-X25. Here, we analyze the effect of varying sticky end lengths and sequences as well as the impact of 5'- and 3'-phosphates on crystal formation and resolution. Tensegrity triangle motifs having 1-, 2-, 3-, and 4-nt sticky ends all form crystals. X-ray diffraction data from the same beamline reveal that the crystal resolution for a 1-nt sticky end (G:C) and a 3-nt sticky end (GAT:ATC) were 3.4 and 4.2 angstrom, respectively. Resolutions were determined from complete data sets in each case. We also conducted trials that examined every possible combination of 1-nucleotide and 2-nucleotide sticky-ended phosphorylated strands and successfully crystallized all 16 possible combinations of strands. We observed the position of the 5'-phosphate on either the crossover (1), helical (2), or central strand (3) affected the resolution of the self-assembled crystals for the 2-turn monomer (3.0 angstrom for 1-2P-3P) and 2-turn dimer sticky ended (4.1 angstrom for 1-2-3P) systems. We have also examined the impact of the identity of the base flanking the sticky ends as well as the use of 3'-phosphate. We conclude that crystal resolution is not a simple consequence of the thermodynamics of the direct nucleotide pairing interactions involved in molecular cohesion in this system.