| Abstract
| - When fluorescently tagged oligonucleotides are located near metal surfaces, their emissionintensity is impacted by both electromagnetic effects (i.e., quenching and/or enhancement of emission)and the structure of the nucleic acids (e.g., random coil, hairpin, or duplex). We present experiments exploringthe effect of label position and secondary structure in oligonucleotide probes as a function of hybridizationbuffer, which impacts the percentage of double-stranded probes on the surface after exposure tocomplementary DNA. Nanowires containing identifiable patterns of Au and Ag segments were used as themetal substrates in this work, which enabled us to directly compare different dye positions in a singlemultiplexed experiment and differences in emission for probes attached to the two metals. The observedmetal−dye separation dependence for unstructured surface-bound oligonucleotides is highly sensitive tohybridization efficiency, due to substantial changes in DNA extension from the surface upon hybridization.In contrast, fluorophore labeled oligonucleotides designed to form hairpin secondary structures analogousto solution-phase molecular beacon probes are relatively insensitive to hybridization efficiency, since thefolded form is quenched and therefore does not appreciably impact the observed distance-dependence ofthe response. Differences in fluorescence patterning on Au and Ag were noted as a function of not onlychromophore identity but also metal−dye separation. For example, emission intensity for TAMRA-labeledoligonucleotides changed from brighter on Ag for 24-base probes to brighter on Au for 48-base probes.We also observed fluorescence enhancement at the ends of nanowires and at surface defects whereheightened electromagnetic fields affect the fluorescence.
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