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Genetic research programs such as the human genome project have demonstrated the need for selective detection of nucleic acids at ultralow concentrations (McKusik, V. A. FASEB J. 1991, 5, 12-20. Cui, X.; et al. Proc. Natl. Acad. Sci. U.S.A. 1989, 89, 9389-9393). Current detection techniques require amplification of the genetic material by the polymerase chain reaction (PCR) and detection of the amplified product by fluorescence.A new reliable method for DNA detection has been developed based on adsorption of DNA on colloidal silver and subsequent signal detection using surface-enhanced resonance Raman scattering (SERRS). It uses specifically designed primers and can be applied directly to genetic analysis. Improved surface and aggregation chemistry, utilizing modified DNA and a novel aggregating agent, has resulted in acceptable reproducibility for biological detection. DNA was detected down to 8 × 10 -13 M, which equates to less than one molecule in the interrogation volume at any one time, and an RSD of 10% was obtained. The increased sensitivity compared to fluorescence circumvents the need for an amplification step, and much greater selectivity is obtained due to the sharp vibrational spectra observed, thus reducing the need for separation procedures. The method is potentially sensitive enough to eliminate the need for time-consuming amplification steps and provide a new dimension to labeling chemistry and multiplex analysis of DNA.

The phylogeny and taxonomy of mammalian species were originally based upon shared or derived morphological characteristics. However, genetic analyses have more recently played an increasingly important role in confirming existing or establishing often radically different mammalian groupings and phylogenies. The two most commonly used genetic loci in species identification are the cytochrome oxidase I gene (COI) and the cytochrome b gene (cyt b). For the first time this study provides a detailed comparison of the effectiveness of these two loci in reconstructing the phylogeny of mammals at different levels of the taxonomic hierarchy in order to provide a basis for standardizing methodologies in the future. Interspecific and intraspecific variation is assessed and for the first time, to our knowledge, statistical confidence is applied to sequence comparisons. Comparison of the DNA sequences of 217 mammalian species reveals that cyt b more accurately reconstructs their phylogeny and known relationships between species based on other molecular and morphological analyses at Super Order, Order, Family and generic levels. Cyt b correctly assigned 95.85% of mammal species to Super Order, 94.31% to Order and 98.16% to Family compared to 78.34%, 93.36% and 96.93% respectively for COI. Cyt b also gives better resolution when separating species based on sequence data. Using a Kimura 2-parameter p-distance (x100) threshold of 1.5–2.5, cyt b gives a better resolution for separating species with a lower false positive rate and higher positive predictive value than those of COI.

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