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