Detection of G-quartet Structure in a DNA Aptamer Stationary Phase Using a Fluorescent Dye

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Abstract:

The fluorescent porphyrin dye N-methylmesoporphyrin IX (NMM) was used to provide direct evidence of intramolecular G-quartet formation by an oligonucleotide immobilized at the inner surface of a fused silica capillary. The oligonucleotide is the thrombin-binding DNA aptamer, which has been used in several analytical applications, including a stationary phase for open tubular capillary electrochromatography. Spectroscopic studies of the dye in batch solutions of the aptamer and of an oligonucleotide with the same base composition, but in a different, ''scrambled'' sequence that does not form an intramolecular G-quartet, provided evidence of selective fluorescence enhancement of NMM by the aptamer in the intramolecular G-quartet structure. On-column experiments compared results for injections of NMM onto an aptamer-coated capillary, a capillary coated with the scrambled sequence oligonucleotide, and a bare fused silica capillary. Results show that while NMM adsorbs to both coated capillaries, the selective fluorescence enhancement provides evidence of the intramolecular G-quartet structure on the aptamer-coated capillary.

Document Type: Research Article

DOI: http://dx.doi.org/10.1366/0003702041389364

Affiliations: Department of Chemistry, Duke University, Box 90346, Durham, North Carolina 27708

Publication date: July 1, 2004

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