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

Monday, 30 May 2016: 16:00
Aqua 311 A (Hilton San Diego Bayfront)
D. Bouilly, J. Hon, N. S. Daly, S. Trocchia, S. Vernick, S. Warren, K. L. Shepard, R. L. Gonzalez Jr., and C. Nuckolls (Columbia University)
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.