Jan T. Liphardt
005 Shriram Center
443 Via Ortega
Stanford, CA 94305
2006 Searle Scholar
Plasmonics: Development of new ways for measuring molecular distances
A key problem in biophysics is the measurement of nm scale distances. In collaboration with the lab of Paul Alivisatos, we have been using characterizing the distance dependence of the plasmon resonance between two gold (or silver) nanoparticles. Unlike conventional dyes, noble metal nanoparticles do not blink or bleach, making it possible to track them, or use them to measure distances, for arbitrary durations. For an overview of our ongoing plasmon resonance work, please see the meeting report in Science 308 (2005).
Color effect on directed assembly of DNA-functionalized gold and silver nanoparticles. (a) The basic principle: nanoparticles functionalized with streptavidin are attached to the glass surface coated with BSA-biotin (left). Then, a second particle is attached to the first particle (center), again via biotin-streptavidin binding (right). The biotin on the second particle is covalently linked to the 3' end of a 33 base pair long ssDNA strand bound to the particle via a thiol group at the 5' end. Inset: principle of transmission darkfield microscopy. (b) Single silver particles appear blue (left) and particle pairs blue-green (right). The orange dot in the bottom comes from an aggregate of more than two particles. (c) Single gold particles appear green (left), gold particle pairs, orange (right). Inset: representative transmission electron microscopy image of a particle pair to show that each colored dot comes from light scatted from two closely lying particles, which cannot be separated optically. (d) Representative scattering spectra of single particles and particle pairs for silver (top) and gold (bottom). Silver particles show a larger spectral shift (102 nm) than gold particles (23 nm), stronger light scattering and a smaller plasmon line width. Gold, however, is chemically more stable and is more easily conjugated to biomolecules via -SH, -NH2 or -CN functional groups.
Kinetics of RNA folding; Mechanical properties of RNA
Single-ion channel and single RNA hairpin unfolding kinetics. The opening and closing of an ion channel by an electric field is a highly cooperative event, leading to all-or-none fluctuations between the closed and open states (upper panel). The equation in the inset relates the opening rate constant a to the energy required to open the channel, where ΔG is the height of the activation energy barrier at zero voltage, e is the elementary charge, and z is the number of gating charges that move in the electric field. The trace on the right illustrates a typical recording of the activity of a single ion channel. The all-or-none unfolding of an RNA hairpin (lower panel) can be triggered by a mechanical stretching force, F, applied to the 3' and 5' ends. A mechanical force increases the probability of unfolding by exponentially speeding up the rate of unfolding a and decreasing the refolding rate b, much as predicted by G. I. Bell in 1978. The trace on the right shows a recording of the all-or-none changes in length from a single RNA hairpin [The beautiful illustration is not mine, but was taken from Fernandez et al., and shows data from Liphardt et al.].
Nonequilibrium Statistical Mechanics
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