A DNA-Micropatterned Surface for Propagating Biomolecular Signals by Positional on-off Assembly of Catalytic Nanocompartments

Data underlying the figures in the publication: Maffeis, V. <em>et al.</em> “A DNA-Micropatterned Surface for Propagating Biomolecular Signals by Positional on-off Assembly of Catalytic Nanocompartments” <em>Small</em> <strong>2022</strong>, 2202818, https://doi.org/10.1002/smll.202202818 Concept figures, Unicode origin graph (opj), TEM pictures, AFM pictures, LSM pictures TOC <strong>Figure 1</strong> Concept figure representing the 3D view of micropatterned CNC immobilization promoting a cascade reaction between two distinct CNCs that ultimately results in a bioluminescent surface. <strong>Figure 2</strong> Schematic reactions involved in the biomolecular signal propagation. <strong>Figure 3</strong> Design and characterization of CNC-1 and CNC-2 (SLS and TEM). <strong>Figure 4</strong> Schematic rapresentation of DNA synthesis inside Klenow-CNCs by SYBR green I. <strong>Figure 5</strong> <em>a)</em> FCS autocorrelation curves of free Atto-488-template DNA (red) and Atto-488-template DNA CNC (blue); <em>b)</em> Activity of free Klenow polymerase, Klenow polymerase CNC with melittin, Klenow polymerase CNC without melittin at 25 °C; <em>c)</em> Enzyme activity of melittin-permeabilized Klenow CNCs and free Klenow fragment treated for 1 h at 55 °C; <em>d)</em> Enzyme activity of melittin-permeabilized Klenow CNCs and free Klenow fragment treated for 1 h at 75 °C. <strong>Figure 6</strong> <em>a)</em> Chemical functionalization of the micro-printed glass surface with the amino-functionalized ssDNA; <em>b)</em> AFM height image of the DNA-functionalized glass slide recorded in 10 mm Tris-HCl buffer at pH 7.2 at the resolution of 128 lines; <em>c)</em> CLSM image of glass surface microprinted with Cy5-labeled NH2-modified 31-mer. <strong>Figure 7</strong> <em>a)</em> left, AFM height image, middle, phase type image, and right, height profile (corresponding to dashed white line) of tandem CNCs attached via DNA hybridization on the microprinted glass surface recorded in 10 mm Tris-HCl buffer at pH 7.2; <em>b)</em> left, AFM height image, middle, phase type image and right, corresponding height profile of a single CNC; <em>c)</em> CLSM micrographs of polymersomes labeled with either cholesterol functionalized Atto-488 (green) or Dylight-633 (red)-DNA and immobilized by hybridization on a microprinted glass surface. Left panel, 488-channel, middle panel, 633-channel, right panel, merged image. Scale bars: 5 µm; <em>d)</em> Bioluminescence generation by permeable Klenow-CNCs and permeable ATP sulfurylase-CNCs (blue), by nonpermeable Klenow-CNCs and nonpermeable ATP sulfurylase-CNCs (pink), by the substrate mix alone (black), and by D-Luciferin and luciferase (red). Error bands represent ±SD, n = 3 replicates; <em>e)</em> QCM-D measurement of immobilized CNCs following repeated loading-removal cycles. Frequency (blue) and dissipation (brown) were recorded at three overtones (n = 3, 5, 7) as a function of time. (i, iv, vii) Addition of adaptor DNA, (ii, v, viii) immobilization of 22-mer polymersomes, and (iii, vi, ix) separation of DNA strands with 1 m NaOH.本数据集对应发表论文的配图：Maffeis V. 等人《用于通过催化纳米区室（catalytic Nanocompartments）的位置型通断组装传播生物分子信号的DNA微图案化表面》，发表于*Small* 2022, 2202818，DOI链接：https://doi.org/10.1002/smll.202202818。本数据集包含概念图、Unicode源图（opj格式）、透射电子显微镜（Transmission Electron Microscopy, TEM）图像、原子力显微镜（Atomic Force Microscopy, AFM）图像、激光扫描共聚焦显微镜（Laser Scanning Microscopy, LSM）图像以及目录图（TOC）。 **图1**：展示微图案化催化纳米区室（CNC）固定化的三维视图，其可促进两种不同CNC间的级联反应，最终得到具有生物发光特性的表面。 **图2**：生物分子信号传播所涉及的示意性反应过程。 **图3**：CNC-1与CNC-2的设计与表征（静态光散射SLS与TEM）。 **图4**：通过SYBR Green I染色观测Klenow酶包埋纳米区室（Klenow-CNCs）内DNA合成的示意图。 **图5**： a) 游离Atto-488标记模板DNA（红色曲线）与Atto-488标记模板DNA包埋纳米区室（蓝色曲线）的荧光相关光谱（Fluorescence Correlation Spectroscopy, FCS）自相关曲线； b) 25℃下游离Klenow聚合酶、添加蜂毒肽（melittin）的Klenow聚合酶纳米区室，以及未添加蜂毒肽的Klenow聚合酶纳米区室的酶活性； c) 经蜂毒肽透化处理的Klenow纳米区室，与55℃处理1小时的游离Klenow片段的酶活性； d) 经蜂毒肽透化处理的Klenow纳米区室，与75℃处理1小时的游离Klenow片段的酶活性。 **图6**： a) 氨基修饰单链DNA（single-stranded DNA, ssDNA）对微印刷玻璃表面的化学功能化修饰； b) 在pH 7.2的10 mmol/L Tris-HCl缓冲液中，以128线分辨率采集的DNA功能化玻璃片的AFM高度图像； c) 经Cy5标记的氨基修饰31-mer寡核苷酸微印刷的玻璃表面的共聚焦激光扫描显微镜（Confocal Laser Scanning Microscopy, CLSM）图像。 **图7**： a) 在pH 7.2的10 mmol/L Tris-HCl缓冲液中采集的、通过DNA杂交锚定在微印刷玻璃表面的串联CNC的图像：左为AFM高度图像，中为相型图像，右为对应白色虚线的高度轮廓图； b) 单个CNC的相关图像：左为AFM高度图像，中为相型图像，右为对应高度轮廓图； c) 分别经胆固醇修饰Atto-488（绿色通道）或Dylight-633（红色通道）标记DNA的聚合物囊泡，通过杂交锚定在微印刷玻璃表面的CLSM显微图像：左为488通道成像，中为633通道成像，右为合并图像。标尺：5 μm； d) 透化处理的Klenow-CNC与ATP硫酸化酶-CNC组合（蓝色组）、非透化处理的Klenow-CNC与ATP硫酸化酶-CNC组合（粉色组）、仅底物混合液（黑色组），以及D-荧光素（D-Luciferin）与荧光素酶组合（红色组）产生的生物发光信号。误差带表示±标准偏差（Standard Deviation, SD），重复次数n=3； e) 重复加载-洗脱循环后锚定CNC的石英晶体微天平耗散型（Quartz Crystal Microbalance with Dissipation monitoring, QCM-D）检测结果：以三个泛音（n=3、5、7）的频率（蓝色曲线）与耗散值（棕色曲线）随时间的变化为观测指标。(i, iv, vii) 为添加衔接DNA步骤；(ii, v, viii) 为22-mer聚合物囊泡的锚定步骤；(iii, vi, ix) 为用1 mol/L NaOH解离DNA链步骤。