Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
10771897 | Biochemical and Biophysical Research Communications | 2005 | 12 Pages |
Abstract
Single and dual-labeled fluorescent oligodeoxynucleotides are used in many molecular biology applications. We investigated the effects of commonly used fluorescent dyes and quenchers on the thermodynamic stability of a model probe-target DNA duplex. We demonstrate that those effects can be significant. Fluorescent dyes and quenchers were attached to the probe ends. In certain combinations, these groups stabilized the duplex up to 1.8 kcal/mol and increased Tm up to 4.3 °C. None of the groups tested significantly destabilized the duplex. Rank order of potency was, starting with the most stabilizing group: Iowa Black RQ â¼Â Black Hole 2 > Cy5 â¼Â Cy3 > Black Hole 1 > QSY7 â¼Â Iowa Black FQ > Texas Red â¼Â TAMRA > FAM â¼Â HEX â¼Â Dabcyl > TET. Longer linkers decreased stabilizing effects. Hybridizations to targets with various dangling ends were also studied and were found to have only minor effects on thermodynamic stability. Depending on the dye/quencher combination employed, it can be important to include thermodynamic contributions from fluorophore and quencher when designing oligonucleotide probe assays.
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Authors
Bernardo G. Moreira, Yong You, Mark A. Behlke, Richard Owczarzy,