Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair
Abstract
1. Introduction
2. Results
2.1. Optical Spectra
2.2. Surface Plasmon Resonance (SPR) Measurements
2.3. Single-Molecule Measurements
3. Discussion
4. Materials and Methods
4.1. Optical Measurements
4.2. Surface Plasmon Resonance Measurements
4.3. Single-Molecule Measurements
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sample | λmax (abs) | λmax (fl) |
---|---|---|
CY3-26 | 550 | 566 |
TLG | 549 | 564 |
TLoG | 549 | 565 |
TLA | 550 | 565 |
TLI | 549 | 566 |
ON34 | 550 | 565 |
Probe | Analyte | KD/nM | KD Ratio | ∆G/kJ/mol |
---|---|---|---|---|
TLG | 7m | 2230(90) | ||
3CY3-7m | 107(3) | 20.8 | 7.4 | |
5CY3-7m | 77.4(23) | 28.8 | 8.2 | |
TLoG | 7m | 4401(229) | ||
3CY3-7m | 253(6) | 17.4 | 7.0 | |
5CY3-7m | 155(3) | 28.4 | 8.2 | |
TLA | 7m | 9475(1832) | 27.3 | 8.0 |
3CY3-7m | 347(12) | |||
TLI | 7m | 8832(866) | 28.8 | 8.0 |
3CY3-7m | 307(5) | |||
TLG | 8mG | 320(16) | 12.2 | 6.1 |
3CY3-8mG | 26.2(20) | |||
TLoG | 8mG | 230(13) | 10.6 | 5.8 |
3CY3-8mG | 21.6(24) |
Probe | Analyte | Dye Class | Dye Charge | KD/nM | KD Ratio | ∆G/kJ/mol |
---|---|---|---|---|---|---|
Bio34G | 7n | - | - | 978(25) | - | - |
5CY3-7n | sym. cyanine | +1 | 32.8(41) | 29.8 | 8.3 | |
3CY3-7n | sym. cyanine | +1 | 46.4(15) | 21.1 | 7.5 | |
CY3-7nPEG | sym. cyanine | +1 | 84.6(56) | 11.6 | 6.0 | |
CY3B-7n | sym. cyanine | 0 | 92.9(42) | 10.5 | 5.8 | |
DY547-7n | sym. cyanine | −1 | 206(6) | 4.5 | 3.7 | |
DY530-7n | rhodamine | −1 | 217(9) | 4.5 | 3.7 | |
TAMRA-7n | rhodamine | 0 | 278(5) | 3.5 | 3.1 | |
TexasRed-7n | rhodamine | 0 | 94.0(51) | 10.4 | 5.7 | |
ATTO532-7n | rhodamine | −1 | 200(8) | 4.9 | 3.9 | |
ATTO550-7n | rhodamine | +1 | 39.1(44) | 25.0 | 7.9 | |
CY5-7n | sym. cyanine | +1 | 28.8(17) | 34.0 | 8.6 | |
DY630-7n | asym. cyanine | 0 | 84.4(27) | 11.6 | 6.0 | |
ATTO647N-7n | carbopyronine | 0 | 32.2(41) | 30.3 | 8.4 | |
MB-7n | phenothiazine | +1 | 29.6(18) | 33.0 | 8.6 | |
FAM-7n | fluorescein | −2 | 881(69) | 1.1 | 0.3 | |
Bio34r | 7r | - | - | 506(210) | - | - |
DY548-7r | sym. cyanine | −2 | 423(49) | 1.2 | 0.4 | |
DY549-7r | sym. cyanine | −3 | 534(68) | 0.95 | −0.1 |
Probe | Analyte | KD/nM | KD Ratio | ∆G/kJ/mol |
---|---|---|---|---|
Bio34G | 7T | 3025(68) | 19.7 | 7.3 |
CY3-7T | 153(3) | |||
Bio34I | 7n | 7419(61) | 28.8 | 8.2 |
CY3-7n | 257(10) | |||
Bio34U | 7n | 14,830(494) | 7.4 | 4.9 |
CY3-7n | 1987(42) | |||
Bio34ap | 7n | 45,111(24,127) | ||
CY3-7n | 15,015(6605) | 3.0 | 2.7 | |
3CY3-7n | 1744(124) | 25.9 | 8.0 |
Oligonucleotide | Sequence |
---|---|
TLG | |
TLoG | |
TLA | |
TLI | |
7m | 5′CACGGTC |
5CY3-7m | 5′CY3–CACGGTC |
3CY3-7m | 5′CACGGTC–CY3 |
8mG | 5′GGCACGGTG |
3CY3-8mG | 5′GCACGGTG–CY3 |
Bio25LNA | 5′AGTACAGATCATGCGTCGGGTTTTT-Biotin |
CY3-26 | 5′CY3–CGATCAAGTACAGATCATGCGTCGGG |
CY3-27 | 5′CY3–TCGATCAAGTACAGATCATGCGTCGGG |
ON34 | TTTTTGGAAACTGTATTGGCACTGAGTAGACTCC |
Bio34G | 5′Biotin-TTTTTGGAAACTGTATTGGCACTGAGTAGACTCC |
Bio34I | 5′Biotin-TTTTTGGAAACTGTATTGGCACTIAGTAGACTCC |
Bio34U | 5′Biotin-TTTTTGGAAACTGTATTGGCACTUAGTAGACTCC |
Bio34ap | 5′Biotin-TTTTTGGAAACTGTATTGGCACTapAGTAGACTCC |
7n | CAGTGCC |
5CY3-7n | 5′CY3-CAGTGCC |
3CY3-7n | 5′CAGTGCC-CY3 |
DYE-7n | 5′DYE-CAGTGCC |
7T | 5′CY3-TCAGTGC |
CY3-7T | 5′CY3-TCAGTGC |
Bio34r | 5′Biotin-TTTTTGGAAACTGTATTGTCACGGAGTAGACTTT |
7r | 5′CCGTGAC |
DY548-7r | 5′DY548-CCGTGAC |
DY549-7r | 5′DY549-CCGTGAC |
Sample Availability: Samples of the compounds are not available from the authors. |
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Sobek, J.; Schlapbach, R. Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair. Molecules 2020, 25, 5369. https://doi.org/10.3390/molecules25225369
Sobek J, Schlapbach R. Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair. Molecules. 2020; 25(22):5369. https://doi.org/10.3390/molecules25225369
Chicago/Turabian StyleSobek, Jens, and Ralph Schlapbach. 2020. "Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair" Molecules 25, no. 22: 5369. https://doi.org/10.3390/molecules25225369
APA StyleSobek, J., & Schlapbach, R. (2020). Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair. Molecules, 25(22), 5369. https://doi.org/10.3390/molecules25225369