Complete Mapping of DNA‐Protein Interactions at the Single‐Molecule Level

Abstract

DNA-protein interaction plays an essential role in the storage, expression, and regulation of genetic information. A 1D/3D facilitated diffusion mechanism has been proposed to explain the extraordinarily rapid rate of DNA-binding protein (DBP) searching for cognate sequence along DNA and further studied by single-molecule experiments. However, direct observation of the detailed chronological protein searching image is still a formidable challenge. Here, for the first time, a single-molecule electrical monitoring technique is utilized to realize label-free detection of the DBP-DNA interaction process based on high-gain silicon nanowire field-effect transistors (SiNW FETs). The whole binding process of WRKY domain and DNA has been visualized with high sensitivity and single-base resolution. Impressively, the swinging of hydrogen bonds between amino acid residues and bases in DNA induce the dynamic collective motion of DBP-DNA. This in situ, label-free electrical detection platform provides a practical experimental methodology for dynamic studies of various biomolecules.

Single-exonuclease nanocircuits reveal the RNA degradation dynamics of PNPase and demonstrate potential for RNA sequencing

“…To realize the successful immobilization of PNPase at the single-molecule level, the hydrosilylation of Si‒H bonds was chosen as the initial treatment. In order to improve the yield of alkyne hydrosilylation, we used high-purity undecynic acid as the grafted reagent 17 . The freshly etched device was placed inside the Schlenk bottle and then 3 mg powders of undecynic acid were covered on the device.…”

“…In comparison with optical technologies, the electrical detection approach can directly record the single-event behavior without fluorescent labeling requirements and bleaching problems; it also possesses higher temporal resolution. These advances in single-molecule electrical measurements have enabled in vitro investigations of single-molecule enzyme dynamics, such as adenosine triphosphatase hydrolysis kinetics 14 , the binding mechanism of the DNA polymerase I with deoxyribonucleoside triphosphate analogs 15 , peptidoglycan hydrolysis kinetics 16 , and DNA binding kinetics of WRKY peptides 17 .…”

DNA-mediated dynamic plasmonic nanostructures: assembly, actuation, optical properties, and biological applications

“…Dynamic plasmonic nanoassemblies are booming, and DNA-based self-assembly provides adequate opportunities for reconfigurable systems that can operate automatically and respond to physical or chemical stimuli. Because DNA structures can respond to biological processes such as strand displacement reactions, 219,220 DNA aptamer-target and DNA-protein interactions, 221–223 dynamic plasmonic nanostructures are promising candidates for many biosensing and bioimaging applications with remarkable target modularity and specificity that facilitate exploration of molecular binding and interaction mechanisms. However, DNA-mediated dynamic plasmonic assemblies operate in solutions and are prone to disassembly at high temperature ( i.e.…”

Unraveling the impact of nano-scaling on silicon field-effect transistors for the detection of single-molecules

“…The group reports on the observation of discrete random telegraph signals in micron length bottom-up silicon nanowire FETs with diameters ranging from 20-40 nm. [33][34][35][36][37] The work ascribes these signals to single DNA hairpins, 34 binding of single protein complexes 35 as well as the real-time conformation changes of single protein complexes. 36,37 Random telegraph noise (RTN) due to interface traps can result in similar discrete signals.…”

“…[33][34][35][36][37] The work ascribes these signals to single DNA hairpins, 34 binding of single protein complexes 35 as well as the real-time conformation changes of single protein complexes. 36,37 Random telegraph noise (RTN) due to interface traps can result in similar discrete signals. A thorough analysis of RTN with sufficient device statistics has not been reported in this work to unequivocally exclude traps as a cause of the signal.…”