Understanding Oligonucleotide Hybridization and the Role of Anchoring on the Single-Walled Carbon Nanotube Corona Phase for Viral Sensing Applications
Understanding Oligonucleotide Hybridization and the Role of Anchoring on the Single-Walled Carbon Nanotube Corona Phase for Viral Sensing Applications
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DOI：
10.1021/acs.jpcc.2c06434
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发表时间：
2022-12-27
影响因子：
3.7
通讯作者：
Strano, Michael S.
中科院分区：
文献类型：
--
作者：
Cui, Jianqiao;Gong, Xun;Strano, Michael S.
具有定制电晕相 (CP) 或表面吸附分子的半导体单壁碳纳米管 (SWCNT) 已成为传感应用的有前途的界面。分析物的吸附可以特异性地转换为其带隙近红外 (nIR) 光致发光 (PL) 的调制。最适合此目的的 CP 之一是单链 DNA (ssDNA)，其中后续的序列依赖性杂交可导致 PL 发射波长偏移。由于单链DNA吸附在单壁碳纳米管表面，由此产生的非规范杂交及其对单壁碳纳米管光物理性质的影响尚不清楚。在这项工作中，我们在 SARS-CoV-2 序列作为模型分析物的核酸传感背景下，研究了互补 ssDNA-SWCNT CP 上的 20 聚体和 21 聚体 DNA 和 RNA 杂交。我们发现SWCNT CP上杂化的范特霍夫转变焓为-11.9 kJ mol-1，远低于溶液中杂化的范特霍夫转变焓（-707 kJ mol-1）。我们使用单壁碳纳米管溶剂变色法来计算溶剂暴露表面积以表明杂交成功。我们发现，除了互补区域之外，还具有 30 聚体锚定区域可显着提高 PL 响应灵敏度和选择性，其中 (GT)15 锚定区域首选 RNA 靶标。 ssDNA-SWCNT 与分析物在 37 摄氏度下共孵育可在不牺牲特异性的情况下实现更快的杂交动力学。其他旨在改善 CP 重排动力学的方法（例如超声浴和添加表面活性剂）无效。我们还确定靶序列的选择很重要，因为靶中二级结构的形成与杂交呈负相关。性能最佳的 CP 对 DNA 和 RNA 目标的检测限分别为 11 和 13 nM。最后，我们使用唾液环境模拟传感条件，显示传感器在生物流体中的兼容性。总的来说，这项工作阐明了关键的设计特征和处理，以实现 ssDNA-SWCNT CP 上的序列特异性杂交。
Semiconducting single-walled carbon nanotubes (SWCNTs) with tailored corona phases (CPs), or surface adsorbed molecules, have emerged as a promising interface for sensing applications. The adsorption of an analyte can be specifically transduced as a modulation of their band-gap near infrared (nIR) photoluminescence (PL). One such CP ideal for this purpose is single-stranded DNA (ssDNA), where subsequent sequence-dependent hybridization can result in PL emission wavelength shifts. Due to ssDNA adsorption to the SWCNT surface, the resultant noncanonical hybridization and its effect on SWCNT photophysical properties are not well understood. In this work, we study 20-and 21-mer DNA and RNA hybridization on the complementary ssDNA-SWCNT CP in the context of nucleic acid sensing for SARS-CoV-2 sequences as model analytes. We found that the van't Hoff transition enthalpy of hybridization on SWCNT CP was -11.9 kJ mol-1, much lower than that of hybridization in solution (-707 kJ mol-1). We used SWCNT solvatochromism to calculate the solvent-exposed surface area to indicate successful hybridization. We found that having a 30-mer anchor region in addition to the complementary region significantly improved PL response sensitivity and selectivity, with a (GT)15 anchor preferred for RNA targets. Coincubation of ssDNA-SWCNTs with an analyte at 37 degrees C resulted in faster hybridization kinetics without sacrificing specificity. Other methods aimed to improve CP rearrangement kinetics such as bath sonication and surfactant additions were ineffective. We also determined that the target sequence choice is important as secondary structure formation in the target is negatively correlated with hybridization. Best performing CPs showed detection limits of 11 and 13 nM for DNA and RNA targets, respectively. Finally, we simulated sensing conditions using the saliva environment, showing sensor compatibility in biofluids. In total, this work elucidates key design features and processing to enable sequence-specific hybridization on ssDNA-SWCNT CPs.