Materials

Table 1 is a listing of reporter dyes that are commonly used to label oligos. The dyes that are available as an amidite are shown in bold. Some of the dyes

Table 1

Common Reporter Dyes for Oligos

Common Reporter Dyes for Oligos

Table 1

Dye name

Absorption max (nm)

Emission max (nm)

Dye type

BODIPY FL

502

510

O

FAM

495

520

F

Oregon Green 488

494

517

F

Rhodamine Green

503

528

R

Oregon Green 514

506

526

F

TET

521

536

F

Cal Gold

522

544

F

BODIPY R6G

528

547

O

Yakima Yellow

526

548

F

JOE

520

548

F

HEX

535

556

F

Cal Orange

540

561

R

BODIPY TMR-X

544

570

O

Quasar-570 /Cy3

550

570

C

TAMRA

555

576

R

Rhodamine Red-X

560

580

R

Redmond Red

554

590

O

BODIPY 581/591

581

591

O

Cy3.5

581

596

C

ROX

575

602

R

Cal Red/Texas Red

593

613

R

BODIPY TR-X

588

616

O

BODIPY 630/665-X

647

665

O

Pulsar-650

460

650

O

Quasar-670/Cy5

649

670

C

Cy5.5

675

694

C

Dyes in bold are available as amidites and/or CPGs. F, fluorescein; R, rhodamine; C, cyanine; O, other (see Fig. 2).

Dyes in bold are available as amidites and/or CPGs. F, fluorescein; R, rhodamine; C, cyanine; O, other (see Fig. 2).

in Table 1 are proprietary and others, such as FAM, are ubiquitous. There are many commercial sources for fluorescent dye labels and for oligonucleotide probes. The core structures of the fluorescein, rhodamine, and cyanane dyes are shown in Fig. 2.

Table 2 lists dark quenchers that are commonly used in fluorogenic oligo probes. The quenchers that are available as an amidite as well as a CPG are shown in bold; these quenchers can easily be incorporated as 5', 3', or internal modifications. Many of the quenchers listed in Table 2 are proprietary, yet, they may be licensed and sold by several different companies. Figure 2 shows the core structures of dabcyl and Black Hole Quencher™ (BHQ).

Fluorescein Rhodamine Cyanine

Fig. 2. Core structures for fluorescein, rhodamine and cyanine dyes, dabcyl, and Black Hole Quenchers™.

Table 2

Dark Quenchers for Oligonucleotide Reporters

Dye name

Absorption max (nm)

Dabcyl

453

QSY 35

475

BHQ-0

495

Eclipse

530

BHQ-1

534

QSY 7

560

QSY 9

562

BHQ-2

579

ElleQuencher

630

Iowa Black

651

QSY 21

661

BHQ-3

672

Quenchers in bold are available in both CPG and amidite forms.

Quenchers in bold are available in both CPG and amidite forms.

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