Monitoring the hydration of DNA self-assembled monolayers using an extensional nanomechanical resonator

Abstract

We have fabricated an ultrasensitive nanomechanical resonator based on the extensional vibration mode to weigh the adsorbed water on self-assembled monolayers of DNA as a function of the relative humidity. The water adsorption isotherms provide the number of adsorbed water molecules per nucleotide for monolayers of single stranded (ss) DNA and after hybridization with the complementary DNA strand. Our results differ from previous data obtained with bulk samples, showing the genuine behavior of these self-assembled monolayers. The hybridization cannot be inferred from the water adsorption isotherms due to the low hybridization efficiency of these highly packed monolayers. Strikingly, we efficiently detect the hybridization by measuring the thermal desorption of water at constant relativity humidity. This finding adds a new nanomechanical tool for developing a label-free nucleic acid sensor based on the interaction between water and self-assembled monolayers of nucleic acids.

Biosensors based on nanomechanical systems

“…Unfortunately, miniaturization of the resonators to the nanoscale does not help, and may worsen the quality factors [91][92] . Researchers are trying to "catch" the concept of quartz crystal microbalances in which the viscous dissipation is largely minimized when the surface oscillates parallel to the liquid/solid interface instead of transversally as it occurs in singly and doubly clamped beams when they oscillate in flexural modes [93][94][95] . Recently, advances in micro-and nanofabrication have provided micromechanical resonators based on the extensional vibration modes for a variety of mechanical geometries with frequencies of tens of MHz and quality factors in liquids of 1000-2000 93 .…”

“…In addition, the measurement of the resonant frequency of these devices in liquid is scientifically and The device mass and the detected mass levels are plotted as empty and filled symbols, respectively. The data split into measurements in vacuum [115][116][117] (red), air 94,[118][119][120] (green) and liquid 107,[121][122] (blue). In air and vacuum, the measurements are usually performed ex-situ before and after the biological assay to attain the highest sensitivity in the resonance frequency due to the high quality factor.…”

Hydration Induced Stress on DNA Monolayers Grafted on Microcantilevers

“…5,6 We have also previously demonstrated exsitu hybridization detection in air after incubation with the sample solutions by harnessing the hydration-induced tension in nucleic acid films 7 or water desorption. 8 Surface stress biosensors have proven high sensitivity that adds to the advantages of a label-free technology. However, their application to clinical diagnosis will also demand for a method capable of providing hundreds of measurements in a short time, as well as manageable preparation steps for the microcantilever sensors that can still provide reproducible mechanical patterns.…”

Ultrasensitive thermometer for atmospheric pressure operation based on a micromechanical resonator

“…Directly integrated thermometers that can work in air with very high resolution are demanding in many applications such as: monitoring cell activity via calorimetry , investigation of DNA-water interaction [16], photothermal analysis of airborne nanoparticles [16] infrared detection [17][18][19][20]. Moreover, in microfabricated gas analysis systems the control of the temperature of several elements is fundamental:…”

“…The device reaches a temperature resolution of 3 mK at 5% relative humidity (RH) as well as being able to monitor the desorption of water molecule with a resolution of 0.007 water molecules per nm 2 from the resonator surface (at constant temperature), thanks to its extreme distributed mass sensitivity of 14.8 kHz m 2 /fg (to be compared to values in Table 1 in reference 22). Considering that one monolayer corresponds to ~1 water molecules per nm 2 the device is able to precisely monitor adsorption and desorption processes happening on the surface [16].…”