Multiplexed detection of oligonucleotide targets has been performed with gold nanoparticle probes labeled with oligonucleotides and Raman-active dyes. The gold nanoparticles facilitate the formation of a silver coating that acts as a surface-enhanced Raman scattering promoter for the dye-labeled particles that have been captured by target molecules and an underlying chip in microarray format. The strategy provides the high-sensitivity and high-selectivity attributes of gray-scale scanometric detection but adds multiplexing and ratioing capabilities because a very large number of probes can be designed based on the concept of using a Raman tag as a narrow-band spectroscopic fingerprint. Six dissimilar DNA targets with six Raman-labeled nanoparticle probes were distinguished, as well as two RNA targets with single nucleotide polymorphisms. The current unoptimized detection limit of this method is 20 femtomolar.

Crystal balls: Colloidal crystal microbeads with a three‐dimensional photonic crystal structure can be fabricated with a droplet generator and their reflection spectra used as encoding elements. A multiplex bioassay demonstrates their reliability as encoded carriers (see picture: red, green, and blue beads are immobilized with human, mouse, and rabbit immunoglobulin, respectively).

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Helicase-dependent amplification (HDA) is a novel method for the isothermal in vitro amplification of nucleic acids. The HDA reaction selectively amplifies a target sequence by extension of two oligonucleotide primers. Unlike the polymerase chain reaction (PCR), HDA uses a helicase enzyme to separate the deoxyribonucleic acid (DNA) strands, rather than heat denaturation. This allows DNA amplification without the need for thermal cycling. The helicase used in HDA is a helicase super family II protein obtained from a thermophilic organism, Thermoanaerobacter tengcongensis (TteUvrD). This thermostable helicase is capable of unwinding blunt-end nucleic acid substrates at elevated temperatures (60° to 65°C). The HDA reaction can also be coupled with reverse transcription for ribonucleic acid (RNA) amplification. The products of this reaction can be detected during the reaction using fluorescent probes when incubations are conducted in a fluorimeter. Alternatively, products can be detected after amplification using a disposable amplicon containment device that contains an embedded lateral flow strip.

We combine scanning tunneling spectroscopy and photoluminescence excitation spectroscopy (PLE) to study the electronic level structure and single electron charging effects of InAs and novel InAs/ZnSe core/shell nanocrystal quantum dots. The two techniques provide complementary information on the electronic structure of these systems. In the tunneling spectra of core InAs nanocrystals grown by colloidal chemistry, 2-7 nm in diameter, we directly identify atomic-like electronic quantum dot states with s and p character as two-and sixfold charging multiplets. These measurements are correlated with the low temperature PLE data and, surprisingly, excellent agreement was observed between spacings of levels detected by the two techniques, yielding new information on the quantum dot level structure. The combined tunneling and optical spectroscopy approach was also applied to the study of InAs/ZnSe core/shell nanocrystals, which have a high fluorescence quantum yield in the near IR range. The tunneling spectroscopy shows changes in their electronic structure compared to the cores with the s-p gap closing in thicker shells. This observation is supported by PLE spectroscopy, establishing the effectiveness of the combined optical-tunneling spectroscopy approach in the study of quantum dots.