lists many of the fluorescent dyes currently available with their excitation and emission wavelengths and their most optimal quencher option.
Dye-quencher compatibility
Dye Name
Ex.
Em.
BHQ Quenchers
Quenchers
Alexa 350
346
442
BHQ-0 l(MAX)= 495nm Range= 430-520nm
QSY-35 l(MAX)= 475nm
DABCYL l(MAX)= 479nm
Pacific Blue
416
451
Marina Blue
362
459
Eclipse l(MAX)= 522nm
Acridine
462
Edans
336
468
Coumarin
432
472
BODIPY 493/503
493
503
Cy2
489
506
BODIPY FL-X
504
510
DANSYL
335
518
Alexa 488
495
519
BHQ-1 l(MAX)= 534nm Range= 480-580nm
FAM
Oregon Green
500
520
Rhodamine Green-X
528
NBD-X
466
535
TET
521
536
Alexa 430
434
541
QSY-7&9 l(MAX)= 560nm
BODIPY R6G-X
529
547
JOE
548
Yakima Yellow
531
549
Alexa 532
532
554
VIC
538
HEX
556
R6G
524
557
BHQ-2 l(MAX)= 579nm Range= 550-650nm
Alexa 555
555
565
BODIPY 564/570
563
569
BODIPY TMR-X
544
570
Cy3
550
Alexa 546
573
TAMRA
576
Rhodamine Red-X
560
580
BODIPY 581/591
581
591
Redmond Red
579
595
Cy3.5
596
ROX
575
602
Alexa 568
578
603
Cal Red
583
Texas Red
589
610
BODIPY TR-X
588
616
Alexa 594
590
617
BODIPY 630/650-X
625
640
BHQ-3 l(MAX)= 680nm Range= 620-730nm
LC Red 640
Alexa 633
632
647
BODIPY 650/665-X
646
660
QSY-21 l(MAX)= 661nm
Alexa 647
650
665
Cy5
649
670
Alexa 660
663
690
BBQ650 l(MAX)= 650nm Range= 550-750nm
Cy5.5
675
694
Alexa 680
679
702
Alexa 700
723
Alexa 750
749
775
See dye listings, quencher pair and emission color spectrum
Pdf file contain information on how to choose reporter-quencher pairs for efficient quenching through formation of intramolecular dimers.
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