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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 9001:2015 and ISO 13485:2016 certified facility in Louisville, Kentucky. 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.

Modifications for RNA or RNA/DNA Chimeric 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

Modifications for siMAXTM siRNA 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
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.
Attachment Mods
Attachment Mods Designator 5' Int 3' Structure
Amino Modifier C6 [AmC6]     link
Phosphate [PHO]   link
Non-flour labels
Non-flour labels Designator 5' Int 3' Structure
Biotin [BIO]     link
Biotin-TEG (5' or 3') [BIOTEG]     link

 

Overview

This tab includes the chemical structures for the following modification groups.

  • Attachment Mods
  • DNA Analogs
  • Fluorophores
  • Mixed Bases
  • Quenchers
  • Spacers
  • Biotins
  • Dual-labeled Probes
  • Modified Bases
  • RNA Analogs
  • TINA Mods
  • Miscellaneous

Attachment Mods

Amino, thiol, acrydite, and phosphate groups incorporated during synthesis allow post synthesis reactions for attaching a variety of labels or for coupling the oligo with other molecules.

Click here for info about TINA modifications

Modifier
[Designator]
Availability
Structure
3'-PT-Amino-Modifier C3
[AmC3-PT-Q]
3'
Am C3-PT-Q
Amino Modifier C12
[AmC12]
5'
Am C12
Amino Modifier C2 dT
[AmC2-dT]
5', Internal
Am C2-dT
Amino Modifier C3
[AmC3]
5'
Am C3
Amino Modifier C6
[AminoC6]
5'
Amino C6
Amino Modifier C6 dT
[AmC6-dT]
5', Internal
Am C6-dT
Amino Modifier C7
[AmC7-Q]
3'
Am C7-Q
AminoC6 dC
[AmC6-dC]
5', Internal
Image not available.
Phosphate
[Phos]
5'
Phos (1)
Phosphate
[Phos-Q]
3'
Phos -Q
Thiol Mod C3 S-S
[ThiSS-Q]
3'
Thi SS-Q
Thiol Modifier C6 S-S
[ThiSS]
5', Internal
Thi SS
Uni-Link AminoModifier
[Am-Uni]
5', Internal
Am -Uni

 

DNA Analogs

 

Molecules with similar structure to DNA often readily substitute in the DNA strand for a variety of experimental uses. Modifications in this category include inosine, uridine, wobbles, etc.

Click here for info about TINA modifications

 

Modifier
[Designator]
Availability
Structure
3-Nitropyrrole
[NitPyr]
5', Internal
Nitroyrrole
5-Nitroindole
[5-NitIdl-Q]
3'
5-Nitroindole
[5-NitIdl]
5', Internal
AP-dC
[AP-dC]
5', Internal
Image not available.
dK
[dK]
5', Internal
dP
[dP-Q]
3'
dP
[dP]
5', Internal
dP + dK mixture
[dPdK]
5', Internal
deoxyInosine
[I]
5', Internal
deoxyInosine
[I-Q]
3'
deoxyUridine
[U]
5', Internal
deoxyUridine
[U-Q]
3'

 

Fluorophores

Fluorescent molecules offer a wide variety of applications requiring detection of hybridization including in situ probes, sequencing, and genotyping.

Click here for info about TINA modifications

Modifier
[Designator]
Availability
Structure
5-FAM
[5-fam]
5'
6-Carboxyfluorescein
[6Fl]
5', Internal
6-Carboxyrhodamine (ester)
[CR6G]
5', 3', Internal
6-FAM
[6-Fam-Q]
3'
6-FAM (standard)
[6-FAM]
5'
6-Joe, SE (ester)
[JOE]
5', 3', Internal
ATTO390 (ester)
[ATTO390]
5', 3', Internal
Image not available.
ATTO488 (ester)
[ATTO488]
5', 3', Internal
Image not available.
ATTO532 (ester)
[ATTO532]
5', 3', Internal
Image not available.
ATTO550 (ester)
[ATTO550]
5', 3', Internal
Image not available.
ATTO565 (ester)
[ATTO565]
5', 3', Internal
Image not available.
ATTO590 (ester)
[ATTO590]
5', 3', Internal
Image not available.
ATTO633 (ester)
[ATTO633]
5', 3', Internal
Image not available.
ATTO647N (ester)
[ATTO647N]
5', 3', Internal
Image not available.
ATTO655 (ester)
[ATTO655]
5', 3', Internal
Image not available.
ATTO700 (ester)
[ATTO700]
5', 3', Internal
Image not available.
ATTO740 (ester)
[ATTO740]
5', 3', Internal
Image not available.
Alexa Fluor 350 (ester)
[Alexa350]
5', 3', Internal
Alexa Fluor 488 (ester)
[Alexa488]
5', 3', Internal
Alexa Fluor 532 (ester)
[Alexa532]
5', 3', Internal
Alexa Fluor 546 (ester)
[Alexa546]
5', 3', Internal
Alexa Fluor 555 (ester)
[Alexa555]
5', 3', Internal
Image not available.
Alexa Fluor 568 (ester)
[Alexa568]
5', 3', Internal
Alexa Fluor 594 (ester)
[Alexa594]
5', 3', Internal
Alexa Fluor 633 (ester)
[Alexa633]
5', 3', Internal
Image not available.
Alexa Fluor 647 (ester)
[Alexa647]
5', 3', Internal
Image not available.
Alexa Fluor 660 (ester)
[Alexa660]
5', 3', Internal
Image not available.
Alexa Fluor 680 (ester)
[Alexa680]
5', 3', Internal
Image not available.
Alexa Fluor 700 (ester)
[Alexa700]
5', 3', Internal
Image not available.
Alexa Fluor 750 (ester)
[Alexa750]
5', 3', Internal
Image not available.
Cyanine3
[Cyanine3]
5'
Cyanine3 (ester)
[Cyanine3es]
3'
Image not available.
Cyanine3.5
[Cyanine35]
5', Internal
Cyanine3.5 (ester)
[Cyanine35es]
3'
Image not available.
Cyanine5
[Cyanine5]
5'
Cyanine5 (ester)
[Cyanine5es]
3'
Image not available.
Cyanine5.5
[Cyanine55]
5'
DY682 (replaces IRD700)
[DY682]
5', 3'
Image not available.
DY782 (replaces IRD800)
[DY782]
5'
Image not available.
Fluorescein
[Fl]
5', Internal
Fluorescein-dT
[Fl-dT]
5', Internal
HEX
[5HEX]
5'
Oregon Green 488 (ester)
[OrGre]
5', 3', Internal
ROX (ester)
[ROX]
5', 3', Internal
TAMRA (STANDARD)
[TAMRA]
5'
TAMRA (STANDARD)
[Tamra-Q]
3'
TAMRA-dT
[TAMdT]
5', Internal
TET
[5TET]
5'
Tamra (ester) - 5-isomer
[TMR-5]
5', 3', Internal
Texas Red-X (ester)
[TxRed]
5', 3', Internal
Tide Fluor 1
[TF1]
5', 3', Internal
Image not available.
Tide Fluor 2
[TF2]
5', 3', Internal
Image not available.
Tide Fluor 3
[TF3]
5', 3', Internal
Image not available.
Tide Fluor 4
[TF4]
5', 3', Internal
Image not available.
Tide Fluor 5
[TF5]
5', 3', Internal
Image not available.
Tide Quencher 2 ester
[TQ2es]
5', 3', Internal
Image not available.

 

Mixed Bases

Standard bases used in combination to create a base comprised of a mixture of 2-4 bases (e.g. A/C or A/C/G). This category includes IUB Wobbles and custom wobbles.

Click here for info about TINA modifications

Modifier
[Designator]
Availability
Structure
3' B Wobble (C+G+T)
[B-Q]
3'
3' D Wobble (A+G+T)
[D-Q]
3'
3' H Wobble (A+C+T)
[H-Q]
3'
3' K Wobble (G+T)
[K-Q]
3'
3' M Wobble (A+C)
[M-Q]
3'
3' N Wobble (A+C+G+T)
[N-Q]
3'
3' R Wobble (A+G)
[R-Q]
3'
3' S Wobble (C+G)
[S-Q]
3'
3' V Wobble (A+C+G)
[V-Q]
3'
3' W Wobble (A+T)
[W-Q]
3'
3' Y Wobble (C+T)
[Y-Q]
3'
B Wobble (C+G+T)
[B]
5', Internal
D Wobble (A+G+T)
[D]
5', Internal
H Wobble (A+C+T)
[H]
5', Internal
K Wobble (G+T)
[K]
5', Internal
M Wobble (A+C)
[M]
5', Internal
Mix-1 MG
[Mix-1]
5', Internal
Image not available.
N Wobble (A+C+G+T)
[N]
5', Internal
R Wobble (A+G)
[R]
5', Internal
S Wobble (C+G)
[S]
5', Internal
V Wobble (A+C+G)
[V]
5', Internal
W Wobble (A+T)
[W]
5', Internal
Wobble 10%A 20%G 70%T
[10-00-20-70]
5', 3', Internal
Wobble 20%A 20%C 60%G
[20-20-60-00]
5', 3', Internal
Wobble 20%A 20%C 60%T
[20-20-00-60]
5', 3', Internal
Wobble 20%A 40%C 40%T
[20-40-00-40]
5', 3', Internal
Wobble 20%A 80%G
[20-0-80-0]
5', 3', Internal
Wobble 30%A 30%C 40%T
[30-30-00-40]
5', 3', Internal
Wobble 30%A 70%G
[30-0-70-0]
5', 3', Internal
Wobble 40%A 30%G 30%T
[40-00-30-30]
5', 3', Internal
Wobble 40%A 40%G 20%T
[40-00-40-20]
5', 3', Internal
Wobble 60%A 20%C 20%G
[60-20-20-00]
5', 3', Internal
Wobble 60%A 20%G 20%T
[60-00-20-20]
5', 3', Internal
Wobble 60%C 20%G 20%T
[00-60-20-20]
5', 3', Internal
Wobble 70%A 20%C 10%T
[70-20-00-10]
5', 3', Internal
Wobble 70%C 30%T
[0-70-0-30]
5', 3', Internal
Wobble 80%A 20%C
[80-20-00-00]
5', 3', Internal
Wobble 80%C 20%G
[00-80-20-00]
5', 3', Internal
Wobble 80%C 20%T
[00-80-00-20]
5', 3', Internal
Wobble 90%C 10%T
[00-90-00-10]
5', 3', Internal
Y Wobble (C+T)
[Y]
5', Internal

Quenchers

Quenchers are most commonly paired with specific fluorophores and are chosen based on their ability to absorb energy at the emission wavelength of the fluorophore.

Click here for info about TINA modifications

Modifier
[Designator]
Availability
Structure
5-Dabcyl
[5-Dabcyl]
5'
BHQ1-dT
[BHQ1-dT]
5', Internal
BHQ2-dT
[BHQ2-dT]
5', Internal
Black Hole Quencher 1
[BHQ1]
5', Internal
Black Hole Quencher 1
[BHQ1a-Q]
3'
Black Hole Quencher 2
[BHQ2]
5', Internal
Black Hole Quencher 2
[BHQ2a-Q]
3'
Dabcyl (STANDARD)
[Dabcyl-Q]
3'
Dabsyl-dT
[Dab-dT]
5', Internal
QSY 7 (ester)
[QSY7]
5', 3', Internal
Tide Quencher 1
[TQ1-Q]
3'
Image not available.
Tide Quencher 2
[TQ2-Q]
3'
Image not available.
Tide Quencher 3
[TQ3-Q]
3'
Image not available.
Tide Quencher 4
[TQ4-Q]
3'
Image not available.

 

Spacers

Spacers form a non-binding bridge between areas of an oligo. Among our offerings are C3 spacer which can substitute for an unknown base and Spacer 18 which introduces a hydrophobic area in an oligo.

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Modifier
[Designator]
Availability
Structure
Spacer 18
[Sp-C18]
5', Internal
Spacer 9
[Sp-9]
5', Internal
Spacer C3
[Sp-3-Q]
3'
Spacer C3
[Sp-3]
5', Internal
dSpacer
[Sp-d]
5', Internal

 

Biotins

Biotin offers a variety of uses in research including assays in drug discovery, histological, and cytological applications and capture methods are based on the high affinity of biotin for avidin and streptavidin.

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Modifier
[Designator]
Availability
Structure
3'-Biotin
[Biotin-Q]
3'
Image not available.
5'-Biotin
[Biotin-5]
5'
Biotin PC (Photocleavable)
[Bio-PC]
5'
Biotin-ON
[Bio-ON]
5', Internal
Biotin-TEG (STANDARD)
[BioTEG-Q]
3'
Biotin-TEG (STANDARD)
[BioTEG]
5'
Biotin-TEG (internal)
[BioTEGi]
Internal
Biotin-dT
[Bio-dT]
5', Internal

 

Dual-labeled Probes

A selected grouping of highly popular Fluorophore/Quencher pairings for real-time/qPCR applications.

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Modifier
[Designator]
Availability
Structure
3' BHQ 1 + 5' 6-FAM
[BHQ1a-6FAM]
5', 3'
Image not available.
3' BHQ 1 + 5' HEX
[BHQ1a-5HEX]
5', 3'
Image not available.
3' BHQ 1 + 5' JOE
[BHQ1a-JOE]
5', 3'
Image not available.
3' BHQ 1 + 5' Oregon Green
[BHQ1a-OrGre]
5', 3'
Image not available.
3' BHQ 1 + 5' TET
[BHQ1a-5TET]
5', 3'
Image not available.
3' BHQ 2 + 5' Cyanine3
[BHQ2a-Cyanine3]
5', 3'
Image not available.
3' BHQ 2 + 5' Cyanine3.5
[BHQ2a-Cyanine35]
5', 3'
Image not available.
3' BHQ 2 + 5' Cyanine5
[BHQ2a-Cyanine5]
5', 3'
Image not available.
3' BHQ 2 + 5' Cyanine5.5
[BHQ2a-Cyanine55]
5', 3'
Image not available.
3' BHQ 2 + 5' HEX
[BHQ2a-5HEX]
5', 3'
Image not available.
3' BHQ 2 + 5' ROX
[BHQ2a-ROX]
5', 3'
Image not available.
3' BHQ 2 + 5' TAMRA
[BHQ2a-TAMRA]
5', 3'
Image not available.
3' BHQ 2 + 5' Texas Red
[BHQ2a-TxRed]
5', 3'
Image not available.
3' TQ1 + 5' TF1
[TQ1-TF1]
5', 3'
Image not available.
3' TQ2 + 5' TF2
[TQ2-TF2]
5', 3'
Image not available.
3' TQ3 + 5' TF3
[TQ3-TF3]
5', 3'
Image not available.
3' TQ4 + 5' TF4
[TQ4-TF4]
5', 3'
Image not available.
3' TQ5 + 5' TF5
[TQ5-TF5]
5', 3'
Image not available.
3' Tamra + 5' 6-FAM
[TAMRA-6-FAM]
5', 3'
Image not available.
3' Tamra + 5' HEX
[TAMRA-5HEX]
5', 3'
Image not available.
3' Tamra + 5' TET
[TAMRA-5TET]
5', 3'
Image not available.
Mol. Beacon, 3' Dabcyl + 5' 6-FAM
[MB-6-FAM]
5', 3'
Image not available.
Mol. Beacon, 3' Dabcyl + 5' CR6G
[MB-56CR6G]
5', 3'
Image not available.
Mol. Beacon, 3' Dabcyl + 5' Cyanine3
[MB-Cyanine3]
5', 3'
Image not available.
Mol. Beacon, 3' Dabcyl + 5' Cyanine5
[MB-Cyanine5]
5', 3'
Image not available.
Mol. Beacon, 3' Dabcyl + 5' HEX
[MB-5HEX]
5', 3'
Image not available.
Mol. Beacon, 3' Dabcyl + 5' Oregon Green
[MB-OrGre]
5', 3'
Image not available.
Mol. Beacon, 3' Dabcyl + 5' ROX
[MB-ROX]
5', 3'
Image not available.
Mol. Beacon, 3' Dabcyl + 5' TAMRA
[MB-TAMRA]
5', 3'
Image not available.
Mol. Beacon, 3' Dabcyl + 5' TET
[MB-5TET]
5', 3'
Image not available.
Mol. Beacon, 3' Dabcyl + 5' Texas Red
[MB-TxRed]
5', 3'
Image not available.

 

Modified Bases

Chemically modified bases can be used for structural studies and enhanced binding. This category includes Br-dU, 5-methyl dC, 5-iodo dU, 2-aminopurine, etc.

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Modifier
[Designator]
Availability
Structure
2-Aminopurine
[2AmPur]
5', Internal
5-Bromo dU
[5Br-dU-Q]
3'
5-Bromo-dC
[5Br-dC]
5', Internal
5-Bromo-dU
[5Br-dU]
5', Internal
5-Iodo-dU
[5I-dU]
5', Internal
5-Methyl dC
[5Me-dC]
5', Internal
5-Methyl-dC
[5Me-dC-Q]
3'
8-Oxo-dG
[8Ox-dG]
5', Internal
O6-phenyl-dI
[6phnl-dI]
5', Internal
Pyrrolo-dC
[Pyrlo-dC]
5', Internal

RNA Analogs

RNA analogs are useful for creating the chimeric DNA/RNA oligos commonly used in anti-sense studies.

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Modifier
[Designator]
Availability
Structure
2'-Fluoro-A
[2F-A]
5', Internal
Image not available.
2'-Fluoro-C
[2F-C]
5', Internal
Image not available.
2'-Fluoro-G
[2F-G]
5', Internal
Image not available.
2'-Fluoro-U
[2F-U]
5', Internal
Image not available.
2'-O Methyl-A
[2OMeA-Q]
3'
2'-O Methyl-C
[2OMeC-Q]
3'
2'-O Methyl-G
[2OMeG-Q]
3'
2'-O Methyl-U
[2OMeU-Q]
3'
2'-O-Methyl-A
[2OMeA]
5', Internal
2'-O-Methyl-C
[2OMeC]
5', Internal
2'-O-Methyl-G
[2OMeG]
5', Internal
2'-O-Methyl-U
[2OMeU]
5', Internal
5'OH-Methyl-C
[5HOMedC]
5', Internal
Image not available.
Pyrrolo-RNA-C
[Pyrrolo-rC]
5', Internal
Image not available.
Ribo A
[rA]
5', Internal
Image not available.
Ribo A
[rA-Q]
3'
Image not available.
Ribo C
[rC-Q]
3'
Image not available.
Ribo C
[rC]
5', Internal
Image not available.
Ribo G
[rG-Q]
3'
Image not available.
Ribo G
[rG]
5', Internal
Image not available.
Ribo U
[rU]
5', Internal
Image not available.
Ribo U
[rU-Q]
3'
Image not available.
Ribo-8OxrG
[8Ox-rG]
5', Internal
Image not available.

 

TINA Mods

TINA – Twisted Intercalating Nucleic Acid

Higher efficiency for RT-PCR and traditional PCR with TINA labeled PCR primers

TINA molecule enhances the thermal stability of oligo duplexes while maintaining sequence specificity.

Positive effects for RT and PCR reactions

High degrees of multiplexing become feasible with TINA
TINA decreases optimal primer concentration to improve PCR efficiency
Primers remain highly discriminating in the presence of contaminating DNA
Improved sensitivity for low-abundance products
Eliminates or reduces non-specific product bands

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Publication – Improved efficiency and robustness…

Publication – Increasing analytical sensitivity…

Application Note – Improved PCR Assays…

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TINA decreases cycle of quantification (Cq) and increases annealing temperature (Ta)

Improved kinetics
Improved sensitivity
Improved specificity
TINA primers ensure reproducible inter-batch RT-PCR performance

No primer redesign needed

Specificity not affected by addition of TINA
TINA modification is attached to the 5' end for PCR applications
HPLC purification is required
TINA can be combined with other modifications


The TINA modification does not restrict or limit further modifications of the oligonucleotide

Miscellaneous

Miscellaneous modifications include phosphorothioate backbone modification, digoxigenin labeling, modified bases to prevent extension of the 3' terminus, cholesterol for cell delivery, puromycin (a tRNA mimc), etc.

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Modifier
[Designator]
Availability
Structure
2'3'-ddC
[23-ddC-Q]
3'
3'-dA (chain terminator)
[3-dA-Q]
3'
3'-dC (chain terminator)
[3-dC-Q]
3'
3'-dG (chain terminator)
[3-dG-Q]
3'
3'-dT (chain terminator)
[3-dT-Q]
3'
5-Pyrine Cap
[5-PyrCAP]
5'
Image not available.
Acrydite
[5Acrd]
5'
Cholesteryl-TEG
[Chols-Q]
3'
Cholesteryl-TEG
[Chol-TEG]
5', Internal
DNP-TEG
[DNP]
5', Internal
Digoxigenin (ester)
[Dig]
5', 3', Internal
Phosphorothioation
[*]
Internal
Puromycin
[Pmycn-Q]
3'
TINA
[TINA]
5'
Image not available.