How Surfaces Affect Hybridization Kinetics.

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.

Whispering gallery mode single nanoparticle detection and sizing: the validity of the dipole approximation.

Interactions between whispering gallery modes (WGMs) and small nanoparticles are commonly modeled 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 Letter, 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, the 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.