Direct Measurement of Single‐Molecule DNA Hybridization Dynamics with Single‐Base Resolution

Abstract

Herein, we report label-free detection of single-molecule DNA hybridization dynamics with single-base resolution. By using an electronic circuit based on point-decorated silicon nanowires as electrical probes, we directly record the folding/unfolding process of individual hairpin DNAs with sufficiently high signal-to-noise ratio and bandwidth. These measurements reveal two-level current oscillations with strong temperature dependence, enabling us to determine the thermodynamic and kinetic properties of hairpin DNA hybridization. More importantly, successive, stepwise increases and decreases in device conductance at low temperature on a microsecond timescale are successfully observed, indicating a base-by-base unfolding/folding process. The process demonstrates a kinetic zipper model for DNA hybridization/dehybridization at the single base-pair level. This measurement capability promises a label-free single-molecule approach to probe biomolecular interactions with fast dynamics.

Single‐Molecule Electrical Detection with Real‐Time Label‐Free Capability and Ultrasensitivity

“…Copyright 2012, Nature Publishing Group. c–f) Reproduced with permission . Copyright 2016, Wiley‐VCH.…”

“…During device fabrication, a lithographical gap exposes a micro‐region on a CVD‐grown silicon nanowire. After annealing the nanowire under an octadecyltrichlorosilane vapor to reduce nonspecific absorption, aminophilic functional groups such as carboxyls, aldehydes, or isothiocyanates are attached to the sidewalls of the nanowire to bind target molecules with amino groups. For example, the folding/unfolding of hairpin DNA with single‐base resolution can be monitored in real time .…”

“…After annealing the nanowire under an octadecyltrichlorosilane vapor to reduce nonspecific absorption, aminophilic functional groups such as carboxyls, aldehydes, or isothiocyanates are attached to the sidewalls of the nanowire to bind target molecules with amino groups. For example, the folding/unfolding of hairpin DNA with single‐base resolution can be monitored in real time . A hairpin‐DNA molecule with amino termination at the 5'‐end and with five base pairs in the stem and fifteen bases in the loop can be attached to the sidewalls of a silicon nanowire in an aqueous solution at pH = 7.4 (Figure c).…”

“…Information hidden in ensemble averages can be derived from a series of single‐events. For example, the randomness statistical indicator is widely used to reveal hidden intermediate steps of reactions . Randomness r is defined as a normalized variance: where r = 1 in a single‐step Poisson process, and is 1/ n in an identical n ‐step Poisson process …”

Osmolyte Effects on the Conformational Dynamics of a DNA Hairpin at Ambient and Extreme Environmental Conditions

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The structural dynamics of aDNA hairpin (Hp) are studied in the absence and presence of the two natural osmolytes trimethylamine-N-oxide (TMAO) and urea at ambient and extreme environmental conditions,i ncluding high pressures and high temperatures,byusing single-molecule Fçrster resonance energy transfer and fluorescence correlation spectroscopy. [3][4][5][6][7][8] Here,w e report on the effect of the important natural osmolytes TMAOa nd urea on the conformational dynamics of aw ellknown DNAH p [4] at both ambient and extreme environmental (i.e., high pressure and temperature) conditions by using diffusion-based single-molecule Fçrster resonance energy transfer (smFRET) and fluorescence correlation spectroscopy (FCS). [3][4][5][6][7][8] Here,w e report on the effect of the important natural osmolytes TMAOa nd urea on the conformational dynamics of aw ellknown DNAH p [4] at both ambient and extreme environmental (i.e., high pressure and temperature) conditions by using diffusion-based single-molecule Fçrster resonance energy transfer (smFRET) and fluorescence correlation spectroscopy (FCS).

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