Detection of G-quartet structure in a DNA aptamer stationary phase using a fluorescent dye.
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.
Department of Chemistry, Duke University, Box 90346, Durham, NC 27708, USA.
Michelle Viglietta
MV
Joyce
Linda B
LB
McGown
D001483:Base Sequence; D002845:Chromatography; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes; D008652:Mesoporphyrins; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D012822:Silicon Dioxide; D013050:Spectrometry, Fluorescence; D013056:Spectrophotometry, Ultraviolet
D005456:Fluorescent Dyes; D008652:Mesoporphyrins; D009838:Oligodeoxyribonucleotides; C065420:N-methylmesoporphyrin IX; D012822:Silicon Dioxide; D004247:DNA