Table 23.1 Spectral characteristics of Molecular Probes dyes.

DyeExcitation Maximum (nm)*Emission Maximum (nm)*
Acridine orange500 (+DNA)
460 (+RNA)
526 (+DNA)
650 (+RNA)
Alexa Fluor 350 dye, 7-amino-4-methylcoumarin (AMC)346442
Alexa Fluor 405 dye402421
Alexa Fluor 430 dye434539
Alexa Fluor 488 dye495519
Alexa Fluor 514 dye518540
Alexa Fluor 532 dye531554
Alexa Fluor 546 dye556573
Alexa Fluor 555 dye555565
Alexa Fluor 568 dye578603
Alexa Fluor 594 dye590617
Alexa Fluor 610 dye612628
Alexa Fluor 633 dye632647
Alexa Fluor 635 dye633647
Alexa Fluor 647 dye650668
Alexa Fluor 660 dye663690
Alexa Fluor 680 dye679702
Alexa Fluor 700 dye702723
Alexa Fluor 750 dye749775
Alexa Fluor 790 dye782805
Allophycocyanin650660
7-Aminoactinomycin D (7-AAD) †546647
BCECF indicator482 (low pH)
503 (high pH)
520 (low pH)
528 (high pH)
Bimane380458
BOBO-1, BO-PRO-1462481
BODIPY 630/650 dye630650
BODIPY 650/665 dye650665
BODIPY FL dye505513
BODIPY TMR-X dye542574
BODIPY TR-X dye589617
Calcein494517
Calcium Crimson indicator590615
Calcium Green indicators506533
Calcium Orange indicator549576
Carboxy SNARF indicators548 (low pH)
576 (high pH)
587 (low pH)
635 (high pH)
6-Carboxyrhodamine 6G525555
Cascade Blue dye400420
Cascade Yellow dye402545
DAPI †358461
Di-8-ANEPPS, Di-4-ANEPPS ‡468635
DiA ‡456590
DiD (DiIC18(5))644665
DiI (DiIC18(3))549565
DiO (DiOC18(3))484501
DiR (DiIC18(7))750779
ELF 97 alcohol345530
Eosin524544
ER Tracker Blue-White DPX ‡372556
EthD-1 †528617
Ethidium bromide †518605
Fluo-3 indicator506526
Fluo-4 indicator494516
Fluorescein, FITC494518
FM 1-43, FM 1-43FX ‡479598
FM 4-64, FM 4-64FX ‡506750
Fura-2 indicator363 (low [Ca2+])
335 (high [Ca2+])
512 (low [Ca2+])
505 (high [Ca2+])
Fura Red indicator472 (low [Ca2+])
436 (high [Ca2+])
657 (low [Ca2+])
637 (high [Ca2+])
Hoechst 33258, Hoechst 33342 †352461
7-Hydroxy-4-methylcoumarin360455
Indo-1 indicator346 (low [Ca2+])
330 (high [Ca2+])
475 (low [Ca2+])
401 (high [Ca2+])
JC-1498 (monomer)
593 (aggregate)
525 (monomer)
595 (aggregate)
JC-9506525 (monomer)
635 (aggregate)
JOE dye525555
Lissamine rhodamine B570590
Lucifer yellow CH428536
LysoSensor Blue DND-167374425
LysoSensor Green DND-153, DND-189442505
LysoSensor Yellow/Blue DND-160 (PDMPO)384 (low pH)
329 (high pH)
540 (low pH)
440 (high pH)
LysoTracker Green504511
LysoTracker Red577592
Magnesium Green indicator506531
Marina Blue dye365460
MitoTracker Green FM490516
MitoTracker Orange CMTMRos551576
MitoTracker Red CMXRos578599
Monobromobimane §394490
NBD amines465535
NeuroTrace 500/525 green-fluorescent Nissl stain †500525
Nile red ‡549628
Oregon Green 488 dye and Oregon Green 488 BAPTA indicators496524
Oregon Green 514 dye511530
Pacific Blue dye410455
Pacific Orange dye400551
POPO-1, PO-PRO-1 †434456
Propidium iodide †536617
Rhodamine 110496520
Rhodamine Red dye570590
R-phycoerythrin565575
Resorufin571585
RH 414 ‡500635
Rhod-2 indicator552578
Rhodamine Green dye502527
Rhodamine 123507529
ROX dye580605
Sodium Green indicator507535
SYTO blue-fluorescent nucleic acid stains 40, 41, 42, 43 †428 ± 6454 ± 13
SYTO blue-fluorescent nucleic acid stains 44, 45 †450 ± 5478 ± 7
SYTO green-fluorescent nucleic acid stains 12, 13, 16, 21, 23, 24 †494 ± 6515 ± 7
SYTO green-fluorescent nucleic acid stains 11, 14, 15, 20, 22, 25 †515 ± 7543 ± 13
SYTO orange-fluorescent nucleic acid stains 80, 81, 82, 83 †537 ± 7552 ± 8
SYTO orange-fluorescent nucleic acid stains 84, 85 †567583
SYTO red-fluorescent nucleic acid stains 17, 59, 61, 64 †615 ± 15632 ± 13
SYTO red-fluorescent nucleic acid stains 60, 62, 63 †655 ± 3675 ± 3
SYTOX Blue nucleic acid stain †445470
SYTOX Green nucleic acid stain †504523
SYTOX Orange nucleic acid stain †547570
Tetramethylrhodamine, Rhodamine B555580
Texas Red and Texas Red-X dye595615
TOTO-1, TO-PRO-1 †514533
TOTO-3, TO-PRO-3 †642660
X-rhod-1 indicator580602
YOYO-1, YO-PRO-1 †491509
YOYO-3, YO-PRO-3 †612631
* Fluorescence excitation and emission maxima in nm are listed here, and fluorescence spectra are available at (thermofisher.com/spectraviewer). Transmittance curves and other specific microscopy filter information can be found through microscope manufacturers or at filter manufacturer websites, including Chroma Technology Corp. (www.chroma.com), Omega Optical, Inc. (www.omegafilters.com) and  Semrock, Inc. (www.semrock.com). † Excitation and emission peaks listed for dye/nucleic acid complex. ‡ Excitation and emission peaks listed for lipid-bound dye. § Excitation and emission peaks listed for glutathione-conjugated dye.