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Oligo Modifications—Standard and Custom

We partner every day with you, our customers, to find unique solutions that match your needs and applications. The tabs here show the most commonly requested modifications. Our scientists can also include modifications sythesized by you into our oligos. Please contact our Customer Service representatives at GenomicsServices@eurofins.com for more info.

We offer a wide variety of modifications for both DNA and RNA oligos. While all the modifications listed here are permitted for oligos synthesized at 200 nmol synthesis scale and delivered in tubes, several modifications are available at other synthesis scales as well.

Independent of the intended application, some modifications require further purification before being shipped out to you. Each order editor has a dropdown list of available modifications that you can order. Alternately, you can type in the designator in the sequence to order the same; note that the designators are case sensitive. Additional information on the availabel modifications, the designator used for ordering the same, and the chemical structure can be found by following the hyperlink in the tables listing the modifications in the tabs.

The modifications have been categorized based on their features. Predefined Dye–Quencher combinations are available when you order dual-labeled or MGB probes. Furthermore, dinucleotide DNA base combinations are also listed in the siMAXTM siRNA order editor.  

Modifications Available for Custom Oligonucleotides delivered in Tubes

Fluorescent Dyes
Fluorophore Designator 5' Int 3' Max Abs (nm) Max Em (nm) Extinction coefficient (M-1cm–1) QY††
Alexa Fluor 350 [Alexa350] 346 442 19,000  
Alexa Fluor 405 [Alexa405] 401 421 34,000  
Alexa Fluor 488 [Alexa488] 496 519 71,000 0.92
Alexa Fluor 532 [Alexa532] 532 553 81,000 0.61
Alexa Fluor 546 [Alexa546] 556 573 104,000 0.79
Alexa Fluor 555 [Alexa555] 555 565 150,000 0.1
Alexa Fluor 568 [Alexa568] 578 603 91,000 0.69
Alexa Fluor 594 [Alexa594] 590 617 73,000 0.66
Alexa Fluor 633 [Alexa633] 632 647 239,000  
Alexa Fluor 647 [Alexa647] 650 665 239,000 0.33
Alexa Fluor 660 [Alexa660] 663 690 132,000 0.37
Alexa Fluor 680 [Alexa680] 679 702 184,000 0.36
Alexa Fluor 700 [Alexa700] 702 723 192,000 0.25
Alexa Fluor 750 [Alexa750] 749 775 240,000 0.12
ATTO 390 [ATTO390] 390 479 24,000  
ATTO 488 [ATTO488] 501 523 90,000 0.8
ATTO 532 [ATTO532] 532 553 115,000 0.9
ATTO 550 [ATTO550] 554 576 120,000 0.8
ATTO 565 [ATTO565] 563 592 120,000 0.9
ATTO 590 [ATTO590] 594 624 120,000 0.8
ATTO 633 [ATTO633] 629 657 130,000 0.64
ATTO 647N [ATTO647N] 644 669 150,000 0.65
ATTO 655 [ATTO655] 663 684 125,000 0.3
ATTO 700 [ATTO700] 700 719 120,000 0.25
ATTO 740 [ATTO740] 740 764 120,000 0.1
Cyanine3.5 dye [Cy35]   591 604 116,000 0.15
Cyanine5 dye [Cy5]     646 662 250,000 0.3
Cyanine5.5 dye [Cy55]     688 707 209,000 0.3
5-FAM [5FAM]     492 518    
6-FAM [FAM]   495 521 75,000 0.9
Fluorescein [FL]   495 520 83,000 0.9
Fluorescein dT [FLUdT]   494 522 75,000 0.9
HEX [HEX]     537 556 96,000 0.7
JOE [JOE] 520 548 73,000 0.7
Oregon Green 488 [OG488] 496 524 76,000  
ROX [ROX] 575 602 82,000  
TAMRA [TAM]     556 580 89,000 0.7
TAMRA dT [TAMdT]   544 576 90,000  
5-Tamra (ester) [TMR5]            
TET [TET]     519 539 86,000 0.9
Texas Red [TxRed] 583 603 116,000  
Tide Fluor 1 [TF1] 341 447   0.95
Tide Fluor 2 [TF2] 499 522   0.9
Tide Fluor 3 [TF3] 554 578   0.86
Tide Fluor 4 [TF4] 588 610   0.7
Tide Fluor 5 [TF5] 656 670   0.27
Tide Fluor 6 [TF6] 686 702   0.23
Tide Fluor 7 [TF7] 756 775   0.12
Tide Fluor 8 [TF8] 787 808    
†† QY (quantum yield) is a calculated ratio between the number of photons emitted and the number of photons absorbed. The most desireable QY for DLP purposes approaches 1.
Mixed/Degenerate Bases
MIXED BASES Designator 5' Int 3' Composition
N (any base) [N] N = (A, 25%; C, 25%; G, 25%; T, 25%)
B (not A) [B] B = (C, 33.3%; G, 33.3%; T, 33.3%)
D (not C) [D] D = (A-33.3%, G-33.3%, T-33.3%)
H (not G bases) [H] H = (A, 33.3%; C, 33.3%; T, 33.3%)
V (not T) [V] V = (A, 33.3%; C, 33.3%; G, 33.3%)
K (G and T) [K] K = (G, 50%; T, 50%)
M (A and C) [M] M = (A, 50%; C, 50%)
R (purines) [R] R = (A, 50%; G, 50%)
S (strong bonds) [S] S = (C, 50%; G, 50%)
W (weak bonds) [W] W = (A, 50%; T, 50%)
Y (pyrimidines) [Y] Y = (C, 50%; T, 50%)
Attachment Mods
Attachment Mods Designator 5' Int 3' Structure
Amino Modifier C12 [AmC12]     link
Amino Modifier C3 [AmC3]   link
Amino Modifier C6 [AmC6]     link
Amino Modifier C6-dT [AmC6dT]   link
Amino Modifier C7 [AmC7]     link
Uni-Link AminoModifier [AmUni]   link
Thiol Modifier C6 S-S [ThiSS]   link
Thiol Mod C3 S-S [ThiSS-Q]     link
Phosphate [PHO]   link
Non-fluor labels
Non-flour labels Code 5' Int 3' Structure
Biotin [BIO]     link
Biotin-dT [BIOdT]   link
Biotin-ON [BioON]   link
Biotin-TEG (5' or 3') [BIOTEG]   link
Biotin-TEG (internal) [BIOTEGi]     link
Digoxigenin (ester) [DIG] link
DNP (2,4-dinitrophenyl) [DNP]   link
Modified Bases, Spacers, Misc
Modified Bases, Spacers, Misc Code 5' Int 3' Structure
5-Methyl dC [5MedC] link
3-Nitropyrrole [NitPyr]   link
Acridite [5Acrd]     link
Dabsyl-dT [DabsyldT]   link
I [I]   link
U [U]   link
dP + dK mixture [dPdK]   link
Phosphorothioation (DNA backbone modification) *     link
dSpacer [Spd]   link
Spacer C18 [SP18]   link
Spacer C3 [SpC3] link
Spacer C9 [SpC9]   link
TINA [TINA]      
Quenchers
Quencher Code Quenching range (nm) 5' Int 3' Max Abs (nm) Extinction Coefficient (M-1cm–1)
BHQ1 [BHQ1] 480–580   534 34,000
BHQ1 dT [BHQ1dT] 480–580   534 34,000
BHQ2 [BHQ2] 550–650   579 91,000
BHQ2 dT [BHQ2dT] 550–650   579 91,000
Dabcyl dT [DABdT] 400–550   478 32,000
TAMRA [TAM] 500–600   557 91,000
Tide Quencher 1 [TQ1] 420–530     510 20,000
Tide Quencher 2 [TQ2] 440–580     531 21,000
Tide Quencher 3 [TQ3] 510–620     598 22,000
Tide Quencher 5 [TQ5] 600–730     680 24,000

Modifications available for custom oligonucleotides delivered in 96-well plates

Oligos delivered in plates, even those mixed or pooled, can contain a variety of widely-employed modifications. That list is below for your convenience. If your modification is not on the list, please contact Customer Service. We want to ensure that your research is enabled through whatever modification you may require.

 

Standard Modifications for Plate Oligos

Fluorescent labels

Fluorophore Designator 5' Int 3' Max Abs (nm) Max Em (nm) Extinction coefficient (M-1cm–1 QY††
6-FAM [FAM]     495 521 75,000 0.9
HEX [HEX]     537 556 96,000 0.7
TAMRA [TAM]     556 580 89,000 0.7
TET [TET]     519 539 86,000 0.9
†† QY (quantum yield) is a calculated ratio between the number of photons emitted and the number of photons absorbed. The most desireable QY for DLP purposes approaches 1.
Mixed Bases
MIXED BASES Designator 5' Int 3' Composition
N (any base) [N] N = (A, 25%; C, 25%; G, 25%; T, 25%)
B (not A) [B] B = (C, 33.3%; G, 33.3%; T, 33.3%)
D (not C) [D] D = (A, 33.3%; G, 33.3%; T, 33.3%)
H (not G) [H] H = (A, 33.3%; C, 33.3%; T, 33.3%)
V (not T) [V] V = (A, 33.3%; C, 33.3%; G, 33.3%)
K (G and T) [K] K = (G, 50%; T, 50%)
M (A and C) [M] M = (A, 50%; C, 50%)
R (purines) [R] R = (A, 50%; G, 50%)
S (strong bonds) [S] S = (C, 50%; G, 50%)
W (weak bonds) [W] W = (A, 50%; T, 50%)
Y (pyrimidines) [Y] Y = (C, 50%; T, 50%)
Attachment Mods
Attachment Mods Designator 5' Int 3' Structure
Amino Modifier C12 [AmC12]     link
Amino Modifier C6 [AmC6]     link
Amino Modifier C6-dT [AmC6dT]     link
Amino Modifier C7 [AmC7]     link
Uni-Link AminoModifier [AmUni]     link
Phosphate [PHO]     link
Non-flourescent labels
Non-flour labels Designator 5' Int 3' Structure
Biotin [BIO]   link
Biotin-dT [BIOdT]     link
Biotin-TEG (5') [BIOTEG]     link

Regulated Environments

Our oligos are manufactured in our ISO 9001:2008 and ISO 13485:2003 certified facility in Louisville, Alabama. Eurofins Genomics quality management system is assurance that our oligos and other products and services are suitable for use in your cGMP, ASR, or QS regulation projects. Contact us at 1-800-688-2248 to discuss high throughput modified oligos for your FDA or CLIA regulated projects.

Available modifications for ssRNA or RNA/DNA Chimeric oligonucleotides delivered in tubes

Fluors
Fluorophore Designator 5' Int 3' Max Abs (nm) Max Em (nm) Extinction coefficient (M–1cm–1) QY††
Cyanine5 dye [Cy5]     646 662 250,000 0.3
5-FAM [5FAM]     492 518    
6-FAM [FAM]     495 521 75,000 0.9
HEX [HEX]     537 556 96,000 0.7
TET [TET]     519 539 86,000 0.9
†† QY (quantum yield) is a calculated ratio between the number of photons emitted and the number of photons absorbed. The most desireable QY for DLP purposes approaches 1.
Mixed Bases
MIXED BASES Designator 5' Int 3' Composition
N (any base) [N] N = (A, 25%; C, 25%; G, 25%; T, 25%)
B (not A) [B] B = (C, 33.3%; G, 33.3%; T, 33.3%)
D (not C) [D] D = (A, 33.3%; G, 33.3%; T, 33.3%)
H (not G) [H] H = (A, 33.3%; C, 33.3%; T, 33.3%)
V (not T) [V] V = (A, 33.3%; C, 33.3%; G, 33.3%)
K (G and T) [K] K = (G, 50%; T, 50%)
M (A and C) [M] M = (A, 50%; C, 50%)
R (purines) [R] R = (A, 50%; G, 50%)
S (strong bonds) [S] S = (C, 50%; G, 50%)
W (weak bonds) [W] W = (A, 50%; T, 50%)
Y (pyrimidines) [Y] Y = (C, 50%; T, 50%)
Attachment Mods
Attachment Mods Designator 5' Int 3' Structure
Amino Modifier C6 [AmC6]     link
Amino Modifier C6-dT [AmC6dT]     link
Amino Modifier C7 [AmC7]     link
Phosphate [PHO]   link
Non-flour labels
Non-flour labels Designator 5' Int 3' Structure
Biotin-ON [BioON]   link
Biotin-TEG (5' or 3') [BIOTEG]   link
Biotin-TEG (internal) [BIOTEGi]     link
Cholesteryl-TEG (5' or Int)nternal) [CholTEG]   link
Modified Bases, Spacers, Misc
Modified Bases, Spacers, Misc Designator 5' Int 3' Structure
2'-O-Methyl-A [2OMeA] link
2'-O-Methyl-C [2OMeC] link
2'-O-Methyl-G [2OMeG] link
2'-O-Methyl-U [2OMeU] link
2'-Fluoro-G [2FlG]   link
I [I]   link
U [U]   link