Dyes available for oligonucleotide labeling

All probes are double HPLC purified*. Failure sequences are removed during the first HPLC; the second HPLC is performed to remove unlabeled oligonucleotides and excessive dye. As a result only labeled oligonucleotides of excellent quality are obtained.

*with the exception of the directly coupled dyes where no excessive dye must be eliminated

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product absorption emission e [cm-1M-1] Pyrene 340 nm 376 nm 43000 Dansyl-X 340 nm 520 nm 4200 Alexa Fluor® 350 345 nm 440 nm 19000 Eterneon™ 350/4301) 8) 350 nm 430 nm 15220 Eterneon™ 350/4551) 8) 350 nm 455 nm 27300 AMCA -X 353 nm 442 nm 19000 Eterneon™ 384/4801) 8) 384 nm 480 nm 18000 Atto 390 390 nm 479 nm 24000 Eterneon™ 393/5231) 8) 393 nm 523 nm 27680 Eterneon™ 394/5071) 8) 394 nm 507 nm 30000 Alexa Fluor® 405 400 nm 424 nm 34000 Dy 415 418 nm 467 nm 34000 Hydroxy coumarin (HYCO) 419 nm 447 nm 36000 D-AMCA 432 nm 472 nm 56000 Alexa Fluor® 4301) 434 nm 541 nm 16000 Atto 425 436 nm 484 nm 45000 Atto 465 453 nm 508 nm 75000 Dabcyl8) 453 nm none 32000 Eterneon™ 480/6351) 8) 480 nm 635 nm 29900 Dy 485 XL1) 485 nm 560 nm 50000 Fluorescein-5-EX 491 nm 515 nm 86000 BHQ-0 493 nm none 34000 FAM, 5-isomer 494 nm 520 nm 78000 Alexa Fluor® 488 494 nm 520 nm 71000 Atto 495 495 nm 527 nm 80000 Dy 495 495 nm 520 nm 70000 FAM, 6-isomer8) 496 nm 516 nm 83000 IBApy493/5035) 500 nm 509 nm 79000 Dy 480 XL1) 500 nm 630 nm 50000 Atto 4886)8) 501 nm 523 nm 90000 IBApy FL5) 502 nm 510 nm 82000 Oyster 4888) 502 nm 532 nm 85000 Dy 505 505 nm 530 nm 85000 Dy 505-X 505 nm 530 nm 85000 Rhodamine 110X 505 nm 530 nm 85000 Dy 510 XL1) 509 nm 590 nm 50000 Dy 481 XL1) 515 nm 650 nm 50000 TET 519 nm 539 nm * Dy 520 XL1) 520 nm 664 nm 50000 JOE, 6-isomer 520 nm 548 nm 71000 Dy 521 XL1) 523 nm 668 nm 50000 Carboxy-rhodamine 6G, 6-isomer 524 nm 550 nm 102000 Carboxy-rhodamine 6G, 5-isomer 524 nm 557 nm 108000 Atto 520 524 nm 557 nm 108000 Alexa Fluor® 532 525 nm 550 nm 81000 IBApy R6G5) 528 nm 547 nm 70000 Atto 5328) 532 nm 553 nm 115000 IBApy 530/5505) 534 nm 551 nm 77000 BHQ-1 534 nm none 34000 HEX 537 nm 556 nm * Atto 540Q 542 nm none 105000 IBApy TMR-X5) 544 nm 570 nm 56000 TAMRA, 5-isomer 546 nm 579 nm 91000 TAMRA, 6-isomer 547 nm 573 nm 91000 Dy 555 547 nm 572 nm 100000 Quasar 5703) 547 nm 570 nm 115000 Dy 556 548 nm 573 nm 100000 Cy3TM NHS 550 nm 570 nm 150000 Cy3TM Amidite 550 nm 570 nm 150000 Dy 554 551 nm 572 nm 100000 Oyster 550 551 nm 570 nm 150000 Oyster 5558) 552 nm 572 nm 150000 Atto 5508) 554 nm 576 nm 120000 Alexa Fluor® 546 555 nm 570 nm 104000 Alexa Fluor® 555 555 nm 565 nm 150,000 Dy 5473) 557 nm 574 nm 150000 Dy 548 558 nm 572 nm 150000 Dy 560 559 nm 578 nm 120000 Atto 5658) 566 nm 590 nm 120000 Carboxy-X-rhodamine, 5-isomer 574 nm 602 nm 78000 Alexa Fluor® 568 575 nm 560 nm 91300 Carboxy-X-rhodamine, 6-isomer 575 nm 602 nm 82000 BHQ-2 579 nm none 38000 Dy 590 580 nm 599 nm 120000 Cy3.5TM NHS 581 nm 596 nm 150000 Cy3.5TM Amidite 581 nm 596 nm 150000 Sulforhodamine 101 583 nm 603 nm 116000 Atto 580Q 586 nm none 110000 Alexa Fluor® 594 590 nm 615 nm 73,000 Atto 5908) 598 nm 634 nm 120000 Atto 594 601 nm 627 nm 120000 Dy 610 610 nm 630 nm 80000 Alexa Fluor® 610 612 nm 628 nm 138000 Atto 6102) 616 nm 646 nm 150000 Atto 612Q 615 nm none 114000 Atto 620 619 nm 643 nm 120000 Dy 615 621 nm 641 nm 200000 Atto 6338) 629 nm 657 nm 130000 EVOblueTM30 630 nm 670 nm 100000 Alexa Fluor® 633 632 nm 647 nm 100000 Atto 6372) 633 nm 658 nm 120000 Dy 634 635 nm 658 nm 200000 Dy 630 630 nm 655 nm 120000 Dy 631 637 nm 658 nm 200000 Dy 632 637 nm 657 nm 200000 Dy 633 637 nm 657 nm 200000 Atto 647-N4)8) 644 nm 669 nm 150000 Quasar 6704) 644 nm 670 nm 187000 Oyster 645 645 nm 666 nm 240000 Dy 635 647 nm 671 nm 200000 Dy 636 647 nm 671 nm 200000 Cy5TM NHS 649 nm 670 nm 250000 Cy5TMAmidite 649 nm 670 nm 250000 Alexa Fluor® 647 650 nm 670 nm 239000 BBQ 650 598 nm none 40667 Oyster 6478) 651 nm 671 nm 240000 Oyster 650 651 nm 671 nm 240000 Dy 6474) 653 nm 672 nm 250000 Dy 648 653 nm 674 nm 250000 Dy 650 653 nm 674 nm 220000 Dy 652 654 nm 675 nm 220000 Dy 651 656 nm 678 nm 220000 Alexa Fluor® 660 660 nm 690 nm 132000 DyQ 660 660 nm none 140000 DyQ 661 662 nm none 140000 Atto 6558) 663 nm 684 nm 125000 Methylene Blue (on request) 665 nm 690 nm 93000 BHQ-3 672 nm none 42700 Dy 677 673 nm 694 nm 180000 Dy 676 674 nm 699 nm 180000 Oyster 680 674 nm 693 nm 250000 Cy5.5TM NHS 675 nm 694 nm 250000 Cy5.5TM Amidite 675 nm 694 nm 250000 Atto 680 680 nm 700 nm 125000 Alexa Fluor® 680 680 nm 700 nm 184000 Dy 680 690 nm 709 nm 140000 Dy 682 690 nm 709 nm 140000 Dy 681 691 nm 708 nm 140000 Atto 700 700 nm 718 nm 120000 Alexa Fluor® 700 702 nm 723 nm 192000 Dy 701 706 nm 731 nm 140000 Dy 700 707 nm 730 nm 140000 Atto 7252) 725 nm 752 nm 120000 Dy 730 732 nm 758 nm 240000 Dy 734 734 nm 766 nm 240000 Dy 731 736 nm 760 nm 240000 Dy 732 736 nm 759 nm 240000 Atto 7402) 740 nm 764 nm 120000 Dy 750 747 nm 776 nm 270000 Dy 752 748 nm 772 nm 270000 Cy7TM NHS 748 nm 767 nm 250000 Alexa Fluor® 750 749 nm 775 nm 240000 Dy 751 751 nm 779 nm 270000 Dy 7497) 752 nm 778 nm 250000 Dy 776 771 nm 801 nm 240000 Oyster 800 778 nm 796 nm 260000 Dy 780 782 nm 800 nm 170000 Dy 782 (infrared!) 782 nm 800 nm 102000 Dy 781 783 nm 800 nm 170000 Dy 831 844 nm none 220000

1) dyes with large Stokes shift 2) very base-sensitive, additional purification strongly recommended 3) very good alternative for Cy 3 4) very good alternative for Cy 5 5) not available in the US 6) almost identical spectrophysical properties as Alexa Fluor® 488 7) very good alternative for Cy7 8) also available for Click-Chemistry

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