Design Guidelines

Labels and modifications

Dyes

Freedom dyes 5'-end Int 3'-end Excit Emit Alternative 
6-FAM (Fluorescein) +   + 495 520  
MAX 550 +   + 531 560

JOE 555

VIC 554
TYE 563 +   + 549 563 Cy3
TEX 615 +   + 596 613 Texas Red-X 617
TYE 665 +     645 665 Cy5
TYE 705 +     686 705  
TET +     522 539  
HEX +     538 555  
Fluorescein dT + +   495 520  
Rhodamine dyes
 5'-end
 Int
 3'-end
 Excit
 Emit
 Alternative
TAMRA
     +
 559
 583
  
TAMRA NHS Ester
 +
 +
 +
 559
 583
  
ROX NHS Ester
 +
   +
 588
 608  

Other
 5'-end
 Int
 3'-end
 Excit
 Emit
 Alternative
Dy 750 NHS Ester
 +
     747
 776  

Attachment chemistry/linkers

Amino modifiers 5'-end Int 3'-end
Amino Modifier C6 +   +
Amino Modifier C12 +    
Amino Modifier C6 dT + +  
Amino Modifier     +
Uni-Link Amino Modifier + +  
Labels/Antibodies 5'-end Int 3'-end
Biotin +   +
Biotin dT + +  
Biotin TEG +   +
Biotin Dual +    
PC Biotin +    
Thiol modifications 5'-end Int 3'-end
Thiol Modifier C3 S-S     +
Thiol modifier C6 S-S +    
Spacers and Linkers 5'-end Int 3'-end
C3 + + +
PC Spacer + +  
Hexanediol + +  
Spacer 9 + +  
Spacer 18 + +  
1’,2’-Dideoxyribose (dSc) + +  
I-Linker +    
Other 5'-end Int 3'-end
Digoxigenin NHS Ester (DIG) +   +
Cholesteryl-TEG     +

Quenchers

  5'-end Int 3'-end
Dabcyl     +

Modified bases

  5'-end Int 3'-end
LNA (Locked Nucleic Acid) + + +
2-Aminopurine + +  
Trimer-20 + +  
Fluoro Bases + +  
2,6-Diaminopurine (2-Amino-dA) + +  
5-Bromo dU + +  
Deoxyuridine + +  
Inverted dT     +
Dideoxy-C     +
5-Methyl dC + + +
Deoxyinosine + + +
5-Nitroindole + +  
Ribo A     +
Ribo C     +
Ribo G     +
Ribo U     +
2'-O-Methyl RNA Bases + + +

Phosphorylation

  5'-end Int 3'-end
Phosphorylation +   +

Backbone modification

  5'-end Int 3'-end
Phosphorylation + + +

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