The optical properties and significant surface area of CdSe/ZnS QDs make such nanoparticles an interesting platform for
the preparation of nucleic acid biosensors based on fluorescence resonance energy transfer (FRET). Interactions between
QDs and oligonucleotides affect biosensor performance and are not fully understood. Ensemble data obtained via FRET
experiments indicated that, on average, 4-5 added oligonucleotides saturated the surface of green emitting QDs. An
increase in the number of oligonucleotides per QD appeared to cause the oligonucleotides to transition from collapsed to
upright conformations. Since bulk averaging hides details of such processes, methods must be developed and materials
identified for studying QD-oligonucleotide conjugates at the single molecule level. Single QDs have been immobilized
and fluorescence intensity trajectories measured. High count rates and good photostability were achieved using carboxyl
polymer-coated QDs. Modeling of FRET efficiency based on the dimensions of QDs and oligonucleotides indicated that
transitions between collapsed and upright conformations can be accurately measured based on changes in QD
fluorescence lifetime. The ultimate goal of this work is to elucidate QD-oligonucleotide dynamics for better design and
optimization of nucleic acid biosensors based on QDs.
Interest in porous silicon (PS) has increased dramatically over the past two decades due to aspects such as
photoluminescence due to quantum confinement, large surface area, and micro/nanoscale architecture. In this work,
<111> p-type silicon wafers have been electrochemically etched with ethanolic solutions of hydrofluoric acid. Discrete
surface domains showing luminescence were observed. The domains were typically many tens of micrometers in size
and had a height of about 6-8 μm. Interestingly, central round wells of 10-30 μm diameter were observed to form within
domains. Investigation of luminescence in depth profile of the wells was done using confocal fluorescence microscopy,
and the results indicated that the domains were fully porous and luminescent throughout the entire depth. Spectrally, the
peak fluorescence emission was in the range of 550-750 nm and the spectra had an average FWHM equal to about 150
nm. Covalent attachment of organic monolayers to the porous silicon surfaces was done to try and passivate against
oxidation, and also to explore the possibilities of bioconjugation and tuning of the photoluminescence wavelength. A
reaction of hydrogen terminated silicon with ω-undecylenyl alcohol was done using irradiation by a UV source, and
successful derivatization was confirmed with IR spectroscopy. Bulk electrochemical etching of silicon provided a
method to generate distributed luminescent structures suitable for compartmentalization of reactions within wells of
micrometer dimensions without the use of spatially resolved fabrication methodologies such as epitaxial deposition,
lithography, or ion beam technologies.
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