Probing DNA Conformational Changes in Real Time Using Single-Molecule Electronic Sensors Based on Carbon Nanotube Field-Effect Transistors

Abstract

In humans and other vertebrates, the ends of chromosomes are protected by a buffer region of single-stranded DNA (ssDNA) called the telomere. Telomeric ssDNA is made of multiple repeats of the nucleotide sequence GGGTTA and can form three-dimensional folded structures called G-quadruplexes, which are stabilized by monovalent cations like K+ or Na+. The formation of G-quadruplexes has been shown to disrupt the activity of enzymes necessary for telomere maintenance, enzymes that are also upregulated in many types of cancer cells and play a significant role in regulating cellular senescence. As such, G-quadruplexes are considered a potential therapeutic target for inhibiting the proliferation of cancerous cells and for treating aging-associated diseases. In this work, we use single-molecule field-effect transistors (smFETs) made from carbon nanotube devices to characterize the folding and unfolding dynamics of short stretches of telomeric ssDNA, and investigate the stability of G-quadruplex structures. First, we demonstrate a method for reliably functionalizing a carbon nanotube device with an individual ssDNA, using a combination of nano-confined covalent chemistry and bioconjugation reactions. The resulting smFET devices are then used to detect changes in the conformation of the ssDNA, in real-time and over a broad range of time scales. In the presence of K+ or Na+, we observe quantized fluctuations between high and low states in the conductance, which we are able to assign to the unfolded and G-quadruplex conformations, respectively. We discuss the effect of the identity and concentration of these two cations on the folding dynamics of G-quadruplex-forming ssDNA. In particular, we find that the folded G-quadruplex structure is 10 times more stable in K+ than Na+. This approach paves the way for investigations of the folding dynamics of various biomolecules at the single-molecule scale.