This paper describes the use of plasmonics-based nanoprobes that act as molecular sentinels for DNA diagnostics. The plasmonics nanoprobe comprises a metal nanoparticle and a stem-loop DNA molecule tagged with a Raman label. The nanoprobe utilizes the specificity and selectivity of the DNA hairpin probe sequence to detect a specific target DNA sequence of interest. In the absence of target DNA, the stem-loop configuration maintains the Raman label in proximity to the metal nanoparticle, inducing an intense surface-enhanced Raman scattering (SERS) effect that produces a strong Raman signal upon laser excitation. Upon hybridization of a complementary target DNA sequence to the nanoprobe, the stem-loop configuration is disrupted, causing the Raman label to physically separate from the metal nanoparticle, thus quenching the SERS signal. The usefulness and potential application of the plasmonics nanoprobe for diagnosis is demonstrated using the gag gene sequence of the human immunodeficiency virus type 1 (HIV-1). We successfully demonstrated the specificity and selectivity of the plasmonics nanoprobes to detect PCR amplicons of the HIV gene. The potential for combining the spectral selectivity and high sensitivity of the SERS process with inherent molecular specificity of DNA hairpins to diagnose molecular target sequences in homogeneous solutions is discussed.

We present recent development and applications of a surface-enhanced Raman scattering (SERS) technology for use in medical diagnostics and biological imaging. For medical diagnostics, we use Raman-active dye-labeled DNA gene probes and nanostructured metallic substrates as SERS-active platforms. The surface-enhanced Raman gene probes can be used to detect DNA biotargets (e.g. gene sequences, bacteria and viral DNA) via hybridization to DNA sequences complementary to these probes. The SERS gene probes eliminate the need for radioactive labels and have great potential to provide both sensitivity, selectivity and label multiplexing for DNA sequencing and clinical assays. We also describe a hyperspectral surface-enhanced Raman imaging (HSERI) system that combines imaging capabilities with SERS detection to identify cellular components with high spatial and temporal resolution. The HSERI system's application to biological imaging is demonstrated using Raman dye-labeled silver nanoparticles in cellular systems.

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An advanced hyper-spectral imaging (HSI) system has been developed having obvious applications for cancer detection. This HSI system is based on state-of-the-art liquid crystal tunable filter technology coupled to an endoscope. The goal of this unique HSI technology being developed is to obtain spatially resolved images of the slight differences in luminescent properties of malignant versus non-malignant tissues. In this report, the development of the instrument is discussed and the capability of the instrument is demonstrated by observing mouse carcinomas in-vivo. It is shown that the instrument successfully distinguishes between normal and malignant mouse skin. It is hoped that the results of this study will lead to advances in the optical diagnosis of cancer in humans.

The aim of this study was to develop new strategies for analyzing molecular signatures of disease states approaching real-time using single pair fluorescence resonance energy transfer (spFRET) to rapidly detect point mutations in unamplified genomic DNA. In addition, the detection process was required to discriminate between normal and mutant (minority) DNAs in heterogeneous populations. The discrimination was carried out using allele-specific primers, which flanked the point mutation in the target gene and were ligated using a thermostable ligase enzyme only when the genomic DNA carried this mutation. The allele-specific primers also carried complementary stem structures with end-labels (donor/acceptor fluorescent dyes, Cy5/Cy5.5, respectively), which formed a molecular beacon following ligation. We coupled ligase detection reaction (LDR) with spFRET to identify a single base mutation in codon 12 of a K-ras oncogene that has high diagnostic value for colorectal cancers. A simple diode laser-based fluorescence system capable of interrogating single fluorescent molecules undergoing FRET was used to detect photon bursts generated from the molecular beacon probes formed upon ligation. LDR-spFRET provided the necessary specificity and sensitivity to detect single-point mutations in as little as 600 copies of human genomic DNA directly without PCR at a level of 1 mutant per 1000 wild type sequences using 20 LDR thermal cycles. We also demonstrate the ability to rapidly discriminate single base differences in the K-ras gene in less than 5 min at a frequency of 1 mutant DNA per 10 normals using only a single LDR thermal cycle of genomic DNA (600 copies). Real-time LDR-spFRET detection of point mutations in the K-ras gene was accomplished in PMMA microfluidic devices using sheath flows.

Surface-enhanced Raman scattering (SERS) was investigated for applications in the analysis of anthraquinone dyes used in works of art. Two SERS procedures were developed and evaluated with three frequently used anthraquinone dyes, alizarin, carminic acid and lac dye. The first procedure involves coating a layer of silver nanoparticles directly on pieces of filter paper stained with the dyes of interest by thermal evaporation to induce SERS effect. In the second procedure, a SERS-active Ag-Al 2 O 3 substrate was prepared by spin-coating an alumina-nanoparticle layer onto a glass slide to provide the nanostructure of the substrate, followed by thermally evaporating a layer of silver nanoparticles on top of the alumina layer. Aliquots of dye solutions were delivered onto this substrate to be analyzed. Intense SERS spectra characteristic of alizarin, carminic acid and lac dye were obtained using both SERS procedures. The effects of two parameters, the concentration of the alumina suspension and the thickness of the silver nanoparticle layer on the performance of the Ag-Al 2 O 3 substrate were examined with alizarin as the model compound. Comparative studies were conducted between the Ag-Al 2 O 3 substrate and the SERS substrate prepared using Tollens reaction. The Ag-Al 2 O 3 substrate was shown to offer larger enhancement and improved reproducibility than the Tollens substrates. Finally, the potential applicability of the Ag-Al 2 O 3 substrate for the analysis of real artifact objects was illustrated by the identification of alizarin extracted from a small piece of textile dyed using traditional methods and materials. The limit of detection for alizarin was estimated to be 7 × 10 −15 g from tests performed on solutions of known concentration.

This paper presents a novel method for DNA thermal amplification using the polymerase chain reaction (PCR) in an electrokinetically driven synchronized continuous flow PCR (EDS-CF-PCR) configuration carried out in a microfabricated polycarbonate (PC) chip. The synchronized format allowed patterning a shorter length microchannel for the PCR compared to nonsynchronized continuous flow formats, permitting the use of smaller applied voltages when the flow is driven electrically and also allowed flexibility in selecting the cycle number without having to change the microchip architecture. A home-built temperature control system was developed to precisely configure three isothermal zones on the chip for denaturing (95 degrees C), annealing (55 degrees C), and extension (72 degrees C) within a single-loop channel. DNA templates were introduced into the PCR reactor, which was filled with the PCR cocktail, by electrokinetic injection. The PCR cocktail consisted of low salt concentrations (KCl) to reduce the current in the EDS-CF-PCR device during cycling. To control the EOF in the PC microchannel to minimize dilution effects as the DNA "plug" was shuttled through the temperature zones, Polybrene was used as a dynamic coating, which resulted in reversal of the EOF. The products generated from 15, 27, 35, and 40 EDS-CF-PCR amplification cycles were collected and analyzed using microchip electrophoresis with LIF detection for fragment sizing. The results showed that the EDS-CF-PCR format produced results similar to that of a conventional block thermal cycler with leveling effects observed for amplicon generation after approximately 25 cycles. To the best of our knowledge, this is the first report of electrokinetically driven synchronized PCR performed on chip.

Single photon burst techniques were used to detect double-stranded DNA molecules in poly(methylmethacrylate) (PM MA) and polycarbonate (PC) microfluidic devices. A confocal epi-illumination detection system was constructed to monitor the fluorescence signature from single DNA molecules that were multiply labeled with the mono-intercalating dye, TOPRO-5, which possessed an absorption maximum at 765 nm allowing excitation with a solid-state diode laser and fluorescence monitoring in the near-infrared (IR). Near-IR excitation minimized autofluorescence produced from the polymer substrate, which was found to be significantly greater when excitation was provided in the visible range (488 nm). A solution containing lambda-DNA (48.5 kbp) was electrokinetically transported through the microfluidic devices at different applied voltages and solution pH values to investigate the effects of polymer substrate on the transport rate and detection efficiency of single molecular events. By applying an autocorrelation analysis to the data, we were able to obtain the molecular transit time of the individual molecules as they passed through the 7 microm laser beam. It was observed that the applied voltage for both devices affected the transport rate. However, solution pH did not alter the transit time for PM MA-based devices since the electroosmotic flow of PMMA was independent of solution pH. In addition, efforts were directed toward optimizing the sampling efficiency (number of molecules passing through the probe volume) by using either hydrodynamically focused flows from a sheath generated by electrokinetic pumping from side channels or reducing the channel width of the microfluidic device. Due to the low electroosmotic flows generated by both PMMA and PC, tight focusing of the sample stream was not possible. However, in PMMA devices, flow gating was observed by applying field strengths > -120 V/cm to the sheath flow channels. By narrowing the microchannel width, the number of molecular events detected per unit time was found to be four times higher in channels with 10 microm widths compared to those of 50 microm, indicating improved sampling efficiency for the narrower channels without significantly deteriorating detection efficiency. Attempts were made to do single molecule sizing of lambda-DNA, M13 (7.2 kbp) and pUC19 (2.7 kbp) using photon burst detection. While the average number of photons for each DNA type were different, the standard deviations were large due to the Gaussian intensity profile of the excitation beam. To demonstrate the sensitivity of single molecule analysis in the near-IR using polymer microfluidic devices, the near-IR chromophore, NN382, wasanalyzed using ourconfocal imager. A detection efficiency of 94% for single NN382 molecules was observed in the PC devices.