Understanding DNA-encoded carbon nanotube sorting and sensing via sub-nm-resolution structural determination
Yinong Li, Yawei Wen, Leticia C. Beltrán, Li Zhu, Shishan Tian, Jialong Liu, Xuan Zhou, Piaoyi Chen, Edward H. Egelman, Ming Zheng, Zhiwei Lin
Abstract
DNA has demonstrated the abilities to differentiate single-wall carbon nanotubes (SWCNTs) with various chiralities and manipulate their analyte sensing properties. However, the fundamental mechanisms underlying these remarkable abilities remain unclear due to the lack of high-resolution determination of DNA structures on SWCNTs. Here, we combine atomic force microscopy and single-particle cryo-electron microscopy to determine DNA structures on five different types of single-chirality SWCNTs, achieving unprecedented subnanometer resolution. This resolution enables the direct observation of left-handed helical DNA structures with pitches ranging from 1.59 to 2.20 nm, depending on the DNA sequence and nanotube chirality. These findings provide structural insights into the mechanisms by which DNA differentiates the chirality of SWCNTs, and governs the sensitivity, dynamic response range, and analyte differentiability of SWCNT sensors. We propose a non-Watson-Crick hydrogen-bonding network model, which not only accounts for the observed ordered DNA structures but also facilitates the design of DNA sequences for targeted SWCNT purification and desired SWCNT sensor performance.