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The BODIPY® dyes, based on the 4,4-Difluoro-4-bora-3a,4a-diaza-s-indacene (or DIPYrrometheneBOron difluoride) core (Figure 1), are among the few fluorescent dyes to contain a boron atom as part of the core structure.
Figure 1 | Structure of the BODIPY® (dipyrrometheneboron difluoride) core
BODIPY® dyes are stable in physiological conditions, are relatively insensitive to variations in pH, and generally have high quantum yields and sharp emission peaks. Few of the BODIPY® are soluble in water, which limits the usefulness of the BODIPY® dyes in some applications (e.g. protein labelling); however, this is not generally a problem in DNA labelling because synthesis and labelling is done under non-aqueous conditions, and the labelled oligonucleotides are soluble in water. For a review on the synthesis and spectroscopic properties of BODIPY® dyes see Loudet and Burgess, Chem. Rev. 107 (1), 4891-4932, 2007.
The Invitrogen BODIPY® dyes were developed by Molecular Probes, Inc., now part of Life Technologies, and are now sold by Life Technologies.
Table 1 ⎪ Invitrogen BODIPY® dyes
| Name | λmax / nm (absorption) | λmax / nm (emission) | Colour | E at emission λmax | Φ | τ / ns |
|---|---|---|---|---|---|---|
| BODIPY® 493/503 | 500 | 506 | Green | 79 000 | - | - |
| BODIPY® FL-X | 504 | 510 | Green | 85 000 | - | - |
| BODIPY® FL | 505 | 513 | Green | 80 000 | - | - |
| BODIPY® R6G | 528 | 550 | Green/Yellow | 70 000 | - | - |
| BODIPY® 530/550 | 534 | 554 | Green/Yellow | 77 000 | - | - |
| BODIPY® TMR-X | 542 | 574 | Yellow | 60 000 | - | - |
| BODIPY® 558/568 | 558 | 569 | Yellow | 97 000 | - | - |
| BODIPY® 564/570 | 565 | 571 | Yellow | 142 000 | - | - |
| BODIPY® 576/589 | 576 | 590 | Orange | 83 000 | - | - |
| BODIPY® 581/591 | 584 | 592 | Orange | 136 000 | - | - |
| BODIPY® TR-X | 589 | 617 | Orange/Red | 68 000 | - | - |
| BODIPY® 630/650-X | 625 | 640 | Red | 101 000 | - | - |
| BODIPY® 650/665-X | 646 | 660 | Red | 102 000 | - | - |
The BODIPY® "-X" dyes have an aminohexanoyl spacer between the BODIPY® dye core and point of attachment to DNA.
Figure 2 | BODIPY® dyes
The CHROMIS dyes, available from Cyanagen S.r.l., also contain the dipyrrometheneboron difluoride moiety.
Table 2 ⎪ Selected CHROMIS dyes
| Name | λmax / nm (absorption) | λmax / nm (emission) | Colour | E at emission λmax | Φ | τ / ns |
|---|---|---|---|---|---|---|
| Chromis 500N | 496 | 506 | Green | 88 000 | - | - |
Figure 3 | Selected CHROMIS dyes
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