Table of Fluorochromes

Contributor: David Chambers
E-mail: davidc@ccmi.salk.edu
Affiliation: Flow Cytometry Laboratory, The Salk Institute
URL: http://flowcyt.salk.edu/

This is a table of characteristics for fluorochromes used in flow cytometry, within groups, roughly in order of excitation wavelength.

Colors you might see with a capable browser are only a rough approximation.

Probe Ex (nm) Em (nm) MW Notes
Reactive and conjugated probes
Hydroxycoumarin 325 386 331 Succinimidyl ester
Aminocoumarin 350 445 330 Succinimidyl ester
Methoxycoumarin 360 410 317 Succinimidyl ester
Cascade Blue 375;400 423 596 Hydrazide
Lucifer yellow 425 528    
NBD 466 539 294 NBD-X
R-Phycoerythrin (PE) 480;565 578 240,000  
PE-Cy5 conjugates 480;565;650 670   aka Cychrome, R670, Tri-Color, Quantum Red
PE-Cy7 conjugates 480;565;743 767    
Red 613 480;565 613   PE-Texas Red
Fluorescein 495 519 389 FITC; pH sensitive
BODIPY-FL 503 512    
Cy3 512;552 565,615    
TRITC 547 572 444 TRITC
X-Rhodamine 570 576 548 XRITC
Lissamine Rhodamine B 570 590    
PerCP 490 675   Peridinin chlorphyll protein
Texas Red 589 615 625 Sulfonyl chloride
Cy5 625-650 670    
Cy7 743 767 1,001  
Allophycocyanin (APC) 650 660 104,000  
TruRed 490,675 695   PerCP-Cy5.5 conjugate
APC-Cy7 conjugates 650;755 767   PharRed
Nucleic acid probes
Hoechst 33342 343 483  616  AT-selective
DAPI 345 455    AT-selective
Hoechst 33258 345 478  624  AT-selective
SYTOX Blue 431 480  ~400  DNA
Chromomycin A3 445 575    CG-selective
Mithramycin 445 575    
YOYO-1 491 509   1270.65  
SYTOX Green 504 523  ~600  DNA
SYTOX Orange 547 570  ~500  DNA
Ethidium Bromide 493 620  394.31  
7-AAD 546 647    7-aminoactinomycin D, CG-selective
Acridine Orange 503 530/640   DNA/RNA
TOTO-1, TO-PRO-1 509 533   Vital stain, TOTO: Cyanine Dimer
TO-PRO: Cyanine Monomer
Thiazole Orange 510 530    
Propidium Iodide (PI) 536 617 668.4  
TOTO-3, TO-PRO-3 642 661    
LDS 751 543;590 712;607  471.98  DNA (543ex/712em), RNA (590ex/607em)
Cell function probes
Indo-1 361/330 490/405 1010 AM ester. Low/High Ca++,
Fluo-3 506 526 855 AM ester. pH > 6
DCFH 505 535 529 2'7'Dichorodihydrofluorescein, oxidized form
DHR 505 534 346 Dihydrorhodamine 123, oxidized form,
light catalyzes oxidation
SNARF 548/579 587/635   pH 6/9
Fluorescent Proteins
Y66F 360 508    
Y66H 360 442    
EBFP 380 440    (Clonetech) Quantum yield 0.18
Wild Type 396,475 508,503    
GFPuv 385 508    (Clonetech)
ECFP 434 477    (Clonetech) Quantum yield 0.40
Y66W 436 485    
S65A 471 504    
S65C 479 507    
S65L 484 510    
S65T 488 511    
EGFP 489 508    (Clonetech) Quantum yield 0.60
EYFP 514 527    (Clonetech) Quantum yield 0.61
DsRed 558 583    (Clonetech) Quantum yield 0.29
Other probes
Monochlorobimane 380 461 226 Glutathione probe
Calcein 496 517 623 pH > 5

Legend:

  • Ex: Peak excitation wavelength (nm)
  • Em: Peak emission wavelength (nm)
  • MW: Molecular weight