Hybridization between nucleic acid strands immobilized on a solid support with partners in solution is widely practiced in bioanalytical technologies and materials science. An important fundamental aspect of understanding these reactions is the role played by immobilization in the dynamics of duplex formation and disassembly. This report reviews and analyzes literature kinetic data to identify commonly observed trends and to correlate them with probable molecular mechanisms. The analysis reveals that while under certain conditions impacts from immobilization are minimal so that surface and solution hybridization kinetics are comparable, it is more typical to observe pronounced offsets between the two scenarios. In the forward (hybridization) direction, rates at the surface commonly decrease by one to two decades relative to solution, while in the reverse direction rates of strand separation at the surface can exceed those in solution by tens of decades. By recasting the deviations in terms of activation barriers, a consensus of how immobilization impacts nucleation, zipping, and strand separation can be conceived within the classical mechanism in which duplex formation is rate limited by preassembly of a nucleus a few base pairs in length, while dehybridization requires the cumulative breakup of base pairs along the length of a duplex. Evidence is considered for how excess interactions encountered on solid supports impact these processes.
Interactions between whispering gallery modes (WGMs) and small nanoparticles are commonly modelled by treating the particle as a point dipole scatterer. This approach is assumed to be accurate as long as the nanoparticle radius, a, is small compared to the WGM wavelength λ. In this article, however, we show that the large field gradients associated with the evanescent decay of a WGM causes the dipole theory to significantly underestimate the interaction strength, and hence induced WGM resonance shift, even for particles as small as a ∼ λ/10. To mitigate this issue we employ a renormalized Born approximation to more accurately determine nanoparticle induced resonance shifts and hence enable improved particle sizing. The domain of validity of this approximation is investigated and supporting experimental results are presented.Nanoparticles, such as viruses, only exist in small concentrations in biological fluids. This has compelled researchers to develop measurement techniques that can detect viruses and other particles at the ultimate sensitivity, i.e., one at a time. One such technique, utilising whispering gallery mode (WGM) micro-cavity transducers has proven to be a particularly sensitive and versatile platform for particle sensing and for studying the interaction of nanoparticles with surface anchored antibodies [1][2][3][4]. WGM microcavities however also enable nanoparticle size to be measured through observation of the frequency shift [5,6] or mode splitting [7,8] that is induced when a nanoparticle binds to the resonator surface. With sufficient accuracy such size information can be used as a particle discriminant.Frequently, the WGM transduction mechanism is treated as an interaction between the WGM's evanescent near field and a point dipole induced in the nanoparticle, a model which is considered accurate so long as the particle radius, a, is small compared with the wavelength λ. In this article we show that even for small particles, dipole theory can underestimate the interaction strength resulting in potential sizing errors. This discrepancy arises from an inadequate description of the field within the nanoparticle, which varies on the scale of the characteristic WGM decay length as opposed to the wavelength. Using a renormalized Born approximation for the internal field we present analytic formulae which enable accurate particle sizing from WGM resonance shifts and hence overcome these limitations. Experimental results are presented to support our theory.To get a feeling for the origin of the mode shift we start by describing the mechanism heuristically. As a nanoparticle enters the evanescent field of an unperturbed WGM generated by N trapped photons of frequency f , the field does reactive work ∆W to polarize the particle. The * matthew.foreman@imperial.ac.uk † sarnold935@aol.com photons pay for this interaction by reducing their energy, E = N hf , generating a corresponding frequency shift ∆f in accordance with the polarization energy,. The resulting fractional change in frequency is found by div...
Charge influences the binding of virus and other nano-particles to microcavity bio-sensors, although surprisingly there have been no reports of the determination of either cavity charge density σw or nanoparticle charge qp using these sensors. In this letter, we experimentally demonstrate an approach for the determination of both. We use an opto-mechanical Whispering Gallery Mode (WGM) Carousel trap to extract the electrostatic interaction energy versus separation s between the cavity surface and a nanoparticle from WGM frequency fluctuations induced by the orbiting particle. Next, we fit this interaction energy to linearized wall-colloid theory (Debye-Hückel theory) for a particle whose charge is known and determine σw. With this microcavity charge density in hand, a larger particle having unknown charge and orbiting the same microcavity has its charge measured from its associated electrostatic interaction energy. This charge is found to be smaller by 10% when compared to results from independent zeta potential measurements and outside of one standard deviation. However, non-linear Gouy-Chapman theory when applied to our measured data arrives at a charge that overlaps zeta potential measurements. Our method is non-destructive, enabling the same particle to be passed on for further characterization.
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