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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 nmole 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.  

Do not see a modification you want? Contact us. We may be able to accommodate non-standard modifications.

Modifications Available for Custom Oligonucleotides delivered in Tubes

Do not see a modification you want? Contact us. We may be able to accommodate non-standard modifications.

Fluorescent Dyes
 

Fluorophore

Designator

5'

Int

3'

Max Abs (nm)

Max Em (nm)

Extinction coefficient (M-1cm–1)

QY††

Alexa Fluor 405

[Alexa405]

401

421

34,000

 

Alexa Fluor 350

[Alexa350]

346

424

19,000

 

Tide Fluor 1

[TF1]

341

447

 

0.95

ATTO 390

[ATTO390]

390

479

24,000

 

5-FAM

[5FAM]

   

492

518

   

Alexa Fluor 488

[Alexa488]

496

519

71,000

0.92

Fluorescein

[FL]

 

495

520

83,000

0.9

6-FAM

[FAM]

 

495

521

75,000

0.9

Fluorescein dT

[FLUdT]

 

494

522

75,000

0.9

Tide Fluor 2

[TF2]

499

522

 

0.9

ATTO 488

[ATTO488]

501

523

90,000

0.8

Oregon Green 488

[OG488]

496

524

76,000

 

TET

[TET]

   

519

539

86,000

0.9

JOE

[JOE]

520

548

73,000

0.7

Alexa Fluor 532

[Alexa532]

532

553

81,000

0.61

ATTO 532

[ATTO532]

532

553

115,000

0.9

HEX

[HEX]

   

537

556

96,000

0.7

Alexa Fluor 555

[Alexa555]

555

565

150,000

0.1

Alexa Fluor 546

[Alexa546]

556

573

104,000

0.79

ATTO 550

[ATTO550]

554

576

120,000

0.8

TAMRA dT

[TAMdT]

 

544

576

90,000

 

Tide Fluor 3

[TF3]

554

578

 

0.86

TAMRA

[TAM]

   

556

580

89,000

0.7

5-Tamra (ester)

[TMR5]

   

557

583

   

ATTO 565

[ATTO565]

563

592

120,000

0.9

ROX

[ROX]

575

602

82,000

 

Alexa Fluor 568

[Alexa568]

578

603

91,000

0.69

Texas Red

[TxRed]

583

603

116,000

 

Cyanine3.5 dye

[Cy35]

 

591

604

116,000

0.15

CAL Fluor Red 610

[CalFluor610]

   

590

610

108,000

 

Tide Fluor 4

[TF4]

588

610

 

0.7

Alexa Fluor 594

[Alexa594]

590

617

73,000

0.66

ATTO 590

[ATTO590]

594

624

120,000

0.8

CAL Fluor 590

[CalFluor590]

   

544

637

   

Alexa Fluor 633

[Alexa633]

632

647

239,000

 

ATTO 633

[ATTO633]

629

657

130,000

0.64

Cyanine5 dye

[Cy5]

   

646

662

250,000

0.3

Alexa Fluor 647

[Alexa647]

650

665

239,000

0.33

ATTO 647N

[ATTO647N]

644

669

150,000

0.65

Tide Fluor 5

[TF5]

656

670

 

0.27

ATTO 655

[ATTO655]

663

684

125,000

0.3

Alexa Fluor 660

[Alexa660]

663

690

132,000

0.37

Alexa Fluor 680

[Alexa680]

679

702

184,000

0.36

Tide Fluor 6

[TF6]

686

702

 

0.23

Cyanine5.5 dye

[Cy55]

   

688

707

209,000

0.3

ATTO 700

[ATTO700]

700

719

120,000

0.25

Alexa Fluor 700

[Alexa700]

702

723

192,000

0.25

ATTO 740

[ATTO740]

740

764

120,000

0.1

Alexa Fluor 750

[Alexa750]

749

775

240,000

0.12

Tide Fluor 7

[TF7]

756

775

 

0.12

Tide Fluor 8

[TF8]

787

808

   
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 [ThiolC6]   link
Thiol Mod C3 S-S [ThiolC3]     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
Acridite [5Acrd]     link
5' Dabcyl-dT [5DabsyldT] or [5DabcyldT]   link
I [I]   link
U [U]   link
dP + dK mixture [dPdK]   link
Phosphorothioation (PTO Bond)A 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)
BBQ650 [BBQ650] 550-720   650 33,000
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%)
Hand Mixed Wobbles [%-%-%-%] % defines the mixture of bases
Modified Bases, Spacers, Misc
Modified Bases, Spacers, Misc Code 5' Int 3' Structure
I [I]  ✓ link
U [U]  ✓ link
Spacer C3 [SpC3] link
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 [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.

 

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'
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
[ThiolC3]
3'
Thi SS-Q
Thiol Modifier C6 S-S
[ThiolC6]
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.
Cal Fluor Red 610
5' 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.

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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'
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

Order TINA

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.