Daniel Ramos

Label-free detection of DNA hybridization based on hydration-induced tension in nucleic acid films

The properties of water at the nanoscale are crucial in many areas of biology, but the confinement of water molecules in sub-nanometre channels in biological systems has received relatively little attention. Advances in nanotechnology make it possible to explore the role played by water molecules in living systems, potentially leading to the development of ultrasensitive biosensors. Here we show that the adsorption of water by a self-assembled monolayer of single-stranded DNA on a silicon microcantilever can be detected by measuring how the tension in the monolayer changes as a result of hydration. Our approach relies on the microcantilever bending by an amount that depends on the tension in the monolayer. In particular, we find that the tension changes dramatically when the monolayer interacts with either complementary or single mismatched single-stranded DNA targets. Our results suggest that the tension is mainly governed by hydration forces in the channels between the DNA molecules and could lead to the development of a label-free DNA biosensor that can detect single mutations. The technique provides sensitivity in the femtomolar range that is at least two orders of magnitude better than that obtained previously with label-free nanomechanical biosensors and with label-dependent microarrays.

Nanomechanical mass sensing and stiffness spectrometry based on two-dimensional vibrations of resonant nanowires.

One-dimensional nanomechanical resonators based on nanowires and nanotubes have emerged as promising candidates for mass sensors. When the resonator is clamped at one end and the atoms or molecules being measured land on the other end (which is free to vibrate), the resonance frequency of the device decreases by an amount that is proportional to the mass of the atoms or molecules. However, atoms and molecules can land at any position along the resonator, and many biomolecules have sizes that are comparable to the size of the resonator, so the relationship between the added mass and the frequency shift breaks down. Moreover, whereas resonators fabricated by top-down methods tend to vibrate in just one dimension because they are usually shaped like diving boards, perfectly axisymmetric one-dimensional nanoresonators can support flexural vibrations with the same amplitude and frequency in two dimensions. Here, we propose a new approach to mass sensing and stiffness spectroscopy based on the fact that the nanoresonator will enter a superposition state of two orthogonal vibrations with different frequencies when this symmetry is broken. Measuring these frequencies allows the mass, stiffness and azimuthal arrival direction of the adsorbate to be determined.

Effect of the adsorbate stiffness on the resonance response of microcantilever sensors

The authors present a theoretical model to predict the resonance frequency shift due to molecule adsorption on micro- and nanocantilevers. They calculate the frequency shift experienced by cantilevers made of either silicon or the polymer SU-8, when two adsorbates, myosin protein and an alkanethiol, are attached to the cantilever surface. They demonstrate that the effect of the adsorbate stiffness can be comparable or even larger than the mass effect, producing positive frequency shifts. The results provide methods for decoupling both opposite effects and routes for the design of resonators with high sensitivity to molecule adsorption based on either stiffness or mass effects.

Origin of the response of nanomechanical resonators to bacteria adsorption

Resonant microcantilevers are being actively investigated as sensitive mass sensors for biological detection. By performing experiments of adsorption of the bacteria Escherichia coli on singly clamped microcantilevers, we demonstrate that the effect of the added mass is not the only and may not be the main origin of the response of these sensors. The experiments show that the magnitude and sign of resonance frequency shift both depend critically on the distribution of the adsorbed bacterial cells on the cantilever. We relate this behavior to the added mass that shifts the resonance to lower frequencies and the higher effective flexural rigidity of the cantilever due to the bacteria stiffness that shifts the resonance to higher frequencies. Both effects can be uncoupled by positioning the cells where each effect dominates, near the free cantilever end for measuring the added mass or near the clamping for measuring the increase of flexural rigidity.

Photothermal excitation of microcantilevers in liquids

We report the selective excitation of the flexural modes of microcantilevers in aqueous solutions, by applying the photothermal excitation technique. The experiments show that a particular vibration mode can be efficiently excited by focusing the intensity-modulated laser beam on regions of high curvature of the vibration shape. In addition, the resulting resonant peaks in liquid appear distorted by an amplitude component that decreases with the frequency. This distortion produces a shift of the resonance to lower frequencies. A theoretical model based on the transformation of optical energy into mechanical energy via an intermediate thermal stage is proposed to interpret the experimental results. The theory shows that the driven oscillation of the cantilever depends on the curvature of the eigenmode at the excitation position and the heating induced by the excitation laser, which decreases with the frequency. The results reported here set the basis for efficient excitation of high vibration modes in liqu...

Mass Sensing Based on Deterministic and Stochastic Responses of Elastically Coupled Nanocantilevers

Coupled nanomechanical systems and their entangled eigenstates offer unique opportunities for the detection of ultrasmall masses. In this paper we show theoretically and experimentally that the stochastic and deterministic responses of a pair of coupled nanocantilevers provide different and complementary information about the added mass of an analyte and its location. This method allows the sensitive detection of minute quantities of mass even in the presence of large initial differences in the active masses of the two cantilevers. Finally, we show the fundamental limits in mass detection of this sensing paradigm.

Detection of bacteria based on the thermomechanical noise of a nanomechanical resonator: origin of the response and detection limits

We have measured the effect of bacteria adsorption on the resonant frequency of microcantilevers as a function of the adsorption position and vibration mode. The resonant frequencies were measured from the Brownian fluctuations of the cantilever tip. We found that the sign and amount of the resonant frequency change is determined by the position and extent of the adsorption on the cantilever with regard to the shape of the vibration mode. To explain these results, a theoretical one-dimensional model is proposed. We obtain analytical expressions for the resonant frequency that accurately fit the data obtained by the finite element method. More importantly, the theory data shows a good agreement with the experiments. Our results indicate that there exist two opposite mechanisms that can produce a significant resonant frequency shift: the stiffness and the mass of the bacterial cells. Based on the thermomechanical noise, we analyse the regions of the cantilever of lowest and highest sensitivity to the attachment of bacteria. The combination of high vibration modes and the confinement of the adsorption to defined regions of the cantilever allows the detection of single bacterial cells by only measuring the Brownian fluctuations. This study can be extended to smaller cantilevers and other biological systems such as proteins and nucleic acids.

Arrays of dual nanomechanical resonators for selective biological detection.

Arrays of small nanomechanical resonators with dual geometry have been fabricated for sensitive biological detection. The arrays consist of silicon nitride resonating 100 nm thick cantilevers with sensing gold areas alternately placed on the free and fixed cantilever ends. The Au areas act as sensing regions as can be functionalized by means of thiol chemistry. The nanomechanical arrays provide a double flavor of the adsorbed molecules: the added mass reported by the cantilevers with the Au area at the tip and the nanoscale elasticity reported by the cantilevers with the Au area at the clamp. The devices were applied for DNA detection based on Watson-Crick pairing rules. The proposed design for nanomechanical resonators provides higher specificity for DNA sensing in comparison with conventional single cantilevers. The nanoscale elasticity induced by the DNA hybridization arises from the intermolecular interactions between the adsorbates bound to the cantilever and the surface stress.

Study of the Origin of Bending Induced by Bimetallic Effect on Microcantilever

An analytical model for predicting the deflection and force of a bimaterial cantilever is presented. We introduce the clamping effect characterised by an axial load upon temperature changes. This new approach predicts a non linear thermal dependence of cantilever strain. A profilometry technique was used to measure the thermal strain. Comparison with experimental results is used to verify the model. The concordance of the analytical model presented with experimental measurements is better than 10%..

Phototermal self-excitation of nanomechanical resonators in liquids

We report the use of the photothermal actuation for the self-excitation of a selected vibration mode of a microcantilever in liquid. The gain of the positive feedback loop is adjusted in order to obtain a negative effective damping. In this regime, the amplitude noise is squeezed due to the nonlinear saturation of the system and the phase noise is largely reduced. The microcantilever vibration achieved a frequency stability of the order of 1ppm for a bandwidth of 1Hz. This is at least two orders of magnitude better than previous measurements in liquids. The obtained sensitivity is applied for detecting in real time the change of the fluid properties when glycerol is added to water at a concentration of 1% (m∕m).