Modification Options

Please email us if you have a different modification from the options below.

5' Modifications

 

Modification Name Electronic Ordering Code Absorption Maximum (nm) Emission Maximum (nm) Extinction Coefficient (OD/mole) At 260 nm
Generic Modifications
Aldehyde ALD n/a n/a n/a
Alkaline Phosphatase ALP n/a n/a n/a
Amine® (Primary) AMN n/a n/a n/a
Biotin BIO n/a n/a n/a
Horse Radish Peroxidase HRP n/a n/a n/a
Phosphate PHO n/a n/a n/a
Thiol THL n/a n/a n/a
Fluorescent Dye Modifications
Fluorescein FLO 494 520 31,500
HEX HEX 535 553 31,580
ROX* ROX 576 601 22,500
TET TET 522 538 16,255
TAMRA* TAM 565 580 32,300

Molecular Probe Dyes
Dye Electronic Ordering Code Color Absorption Maximum (nm) Molar Emission Maximum (nm) Extinction Coefficient (cm-1M-1)
Alexa Fluor 488* 488 Green 490 519 71,000
Alexa Fluor 532* 532 Green 532 553 81,000
Alexa Fluor 546* 546 Yellow 556 573 104,000
Alexa Fluor 555* 555 Orange/yellow 555 565 150,000
Alexa Fluor 594* 594 orange 590 617 73,000
Alexa Fluor 647* 647 Red 650 655 239,000
Alexa Fluor 660* 660 Red 663 690 132,000
Alexa Fluor 750* 750 purple 749 755 240,000
BODIPY® FL* BDA Far red 502 510 82,000
BODIPY® 530/550* BDB – 534 551 77,000
BODIPY® 493/503* BDC – 500 509 79,000
BODIPY® 558/569* BDE – 559 568 97,000
BODIPY® 564/570* BDF – 563 569 142,000
BODIPY® 576/589* BDG – 575 588 83,000
BODIPY® 581/591* BDH – 581 591 136,000
BODIPY® FL-X* BDI – 504 510 85,000
BODIPY® TR-X* BDJ – 588 616 68,000
BODIPY® TMR* BDK – 544 570 56,000
BODIPY® R6G* BDL – 528 547 70,000
BODIPY® R6G-X* BDM – 529 547 73,000
BODIPY® 630/650* BDN – 625 640 101,000
BODIPY® 650/665* BDP – 651 660 100,000
CASCADE BLUE™ Dye* CSB Blue 400 420 28,000
MARINA BLUE™ Dye* MNB Blue 362 459 19,000
OREGON GREEN® 514* OGB Green 506 526 85,000
OREGON GREEN® 488* OGC Green 495 521 76,000
OREGON GREEN® 488-X* OGD Green 494 517 84,000
PACIFIC BLUE™ Dye* PFB Blue 416 451 36,000
RHODAMINE GREEN™ Dye* RGA Green 504 532 78,000
RHODOL GREEN™ Dye* RGB Green 496 523 63,000
RHODAMINE GREEN™-X* RGC Green 503 528 74,000
RHODAMINE RED™-X* RRA Red 560 580 129,000
TEXAS RED®* TXR Red 595 615 80,000
TEXAS RED®-X* TRX Red 583 603 136,000

*Molecular Probe Dyes are licensed from Molecular Probes, Inc.
MARINA BLUE™, OREGON GREEN®, PACIFIC BLUE™, RHODAMINE GREEN™, RHODOL GREEN™, AND TEXAS RED® are trade marks of Molecular Probes, Inc.
**Red colored dyes are HPLC purified.

Internal Modifications

 

Alternative bases Description Electronic Ordering Code
Deoxyuracil Useful with UDG for ligase-free cloning. U
Deoxyinosine Deoxyinosine has the capacity to base-pair with all four bases; however, it does so with varying affinities. The order of stabilities for the different combinations, from greatest to least stable, reported by Martin et al. are as follows: I:C, I:A, I:T, and I:G. I:C pairs were found to be slightly less stable than A:T pairs (Martin, F.H., Castro, M.M., Aboul-ela, F., and Tinoco, I. Jr. (1985) Nucleic Acids Res.13, 8927.) I
Phosphothiates A sulfur is substituted for one of the oxygens in the phosphodiester bonds between the nucleotides. This linkage is to the 3’ side of the designated base. (see below)
A-Phosphorothioate   F
C-Phosphorothioate   O
G-Phosphorothioate   E
T-Phosphorothioate   Z
Mixed Bases* Degenerate bases. Equal amounts of the designated bases are delivered by the synthesizer.  
A+C+G+T   N
A+C+G   V
A+T+G   D
T+C+G   B
A+T+C   H
A+T   W
C+G   S
T+G   K
A+C   M
C+T   Y
A+G   R

*Mixed bases may be designated at any position for the 50 nmole scale and above. For the 25 nmole scale, mixed bases may be designated for any except the 3’-most base. Mixed bases are achieved by having the synthesizer deliver an equal amount of each base at the given base addition. Differences in coupling efficiency may result in the end product being slightly skewed toward the base that couples with the highest efficiency.

3' Modifications


Dye Name Absorption Maximum (nm) Emission Maximum (nm) Extinction Coefficient (OD/mole) At 260 nm Electronic Ordering Code
Biotin n/a n/a n/a BIO
Phosphate n/a n/a n/a PHO

Note: Not all modifications are available at all scales and purifications. Modifications other than internal mixed bases are not available for oligos ordered for Next-Day delivery. Please contact technical support for more information.