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Oligonucleotide conjugates of Nile Red
Igor A Prokhorenko1, Natalia N Dioubankova, Vladimir A Korshun
1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
Nucleosides, Nucleotides & Nucleic Acids
|March 27, 2004
Summary
Modified oligonucleotides with Nile Red dye show quenched fluorescence. Thermal studies reveal significant interactions between the dye and DNA duplexes, impacting their stability.
Area of Science:
- Biochemistry
- Molecular Biology
- Organic Chemistry
Background:
- Oligonucleotides are crucial in molecular biology and therapeutics.
- Fluorescent dyes are used to study nucleic acid interactions.
- Nile Red is a hydrophobic fluorescent dye with applications in imaging.
Purpose of the Study:
- To covalently modify oligonucleotides with Nile Red.
- To investigate the effect of Nile Red modification on oligonucleotide fluorescence.
- To explore the interaction between modified oligonucleotides and DNA duplexes.
Main Methods:
- Covalent modification of uridine-2'-carbamate in oligonucleotides with Nile Red.
- Spectroscopic analysis of fluorescence quenching in modified oligonucleotides.
- Thermal denaturation (Tm) studies to assess DNA-DNA duplex interactions.
Main Results:
- Oligonucleotide conjugates with Nile Red exhibited quenched fluorescence.
- Nile Red modification did not prevent duplex formation.
- Thermal denaturation studies indicated significant interactions between Nile Red and DNA-DNA duplexes.
Conclusions:
- Nile Red can be covalently attached to oligonucleotides.
- The presence of Nile Red affects oligonucleotide fluorescence properties.
- Nile Red interacts with DNA duplexes, influencing their thermal stability.