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Custom DNA Oligos Modifications

Fluorescent Dyes Labels

The most important fluorescent compounds used to label oligonucleotides are fluorescein and various fluorescein analogs. Fluorescein is a multi-ring aromatic compound that is strongly fluorescent.

* The fluorescent color was calculated with the maximum emission wavelength, for your reference only.

Label NamePurificationsPositionsExcitation
Maximum (nm)
Emission
Maximum (nm)
Price(2OD)Price(5OD)Price(10OD)Fluorescent
Color
Cy3HPLC5', 3'End549566$98.5$128.0$196.9
Cy5HPLC5', 3'End646669$98.5$128.0$196.9
FAMHPLC5', 3'End495520$30.8$40.0$61.5
HEXHPLC5’End535556$49.2$64.0$98.5
TETHPLC5’End521536$49.2$64.0$98.5
FITCHPLC5', 3'End492515$36.9$48.0$73.8
6-JOEHPLC5', 3'End529555$84.6$110.0$169.2
ROXHPLC5', 3'End586610$84.6$110.0$169.2
TAMRAHPLC5', 3'End557583$76.9$100.0$153.8
Helix Fluor555HPLC5', 3'End542558$76.9$100.0$153.8
Helix Fluor575HPLC5', 3'End546575$76.9$100.0$153.8
Texas RedHPLC5', 3'End588601$76.9$100.0$153.8
Quasar 570HPLC5', 3'End548566$76.9$100.0$153.8
Quasar 670HPLC5', 3'End647670$76.9$100.0$153.8
Cy3.5HPLC5', 3'End581596$76.9$100.0$153.8
Cy5.5NSHPLC5', 3'End678701$76.9$100.0$153.8
Cy7NSHPLC5', 3'End750780$76.9$100.0$153.8
CAL Fluor Red 590HPLC5', 3'End569591$76.9$100.0$153.8
CAL Fluor Red 610HPLC5', 3'End590610$76.9$100.0$153.8
DABCYLHPLC5', 3'End4530$76.9$100.0$153.8
AMCAHPLC5', 3'End353455$76.9$100.0$153.8
DEACHPLC5', 3'End411471$76.9$100.0$153.8
MCAHPLC5', 3'End322390$76.9$100.0$153.8
LRB RedHPLC5', 3'End568583$76.9$100.0$153.8
CR6GHPLC5', 3'End524556$76.9$100.0$153.8
Bodi Fluor R6GHPLC5', 3'End528547$76.9$100.0$153.8
NBD-XHPLC5', 3'End467539$76.9$100.0$153.8
California RedHPLC5', 3'End583603$76.9$100.0$153.8
iFluor™ 647HPLC5', 3'End649664$76.9$100.0$153.8
iFluor™ 660HPLC5', 3'End662678$76.9$100.0$153.8
iFluor™ 680HPLC5', 3'End676695$76.9$100.0$153.8
iFluor™ 700HPLC5', 3'End685710$76.9$100.0$153.8
iFluor™ 710HPLC5', 3'End712736$76.9$100.0$153.8
iFluor™ 750HPLC5', 3'End749775$76.9$100.0$153.8
iFluor™ 800HPLC5', 3'End801820$76.9$100.0$153.8
VICHPLC5’End538554$76.9$100.0$153.8
LC RED-610HPLC3’End590610$76.9$100.0$153.8
LC RED-640HPLC3’End625640$76.9$100.0$153.8
LC RED-705HPLC3’End685705$76.9$100.0$153.8
Bodipy 493/503HPLC3’End493503$76.9$100.0$153.8
Bodipy 564/570HPLC3’End564570$76.9$100.0$153.8
Bodipy 581/591HPLC3’End581591$76.9$100.0$153.8
Bodipy 630/650HPLC3’End630650$76.9$100.0$153.8
Bodipy 650/665HPLC3’End650665$76.9$100.0$153.8
BODIPY R6GHPLC3’End528547$76.9$100.0$153.8
SIMAHPLC5’End533557$76.9$100.0$153.8
Yakima Yellow EpochHPLC5', 3'End530549$46.2$46.2$76.9

Dual Labels

Dual-labeled fluorescent probes typically contain a 5' fluorophore and a 3' quencher. The probes are often designed to anneal between the upstream and the downstream primer in a PCR reaction. These are commonly used with quantitative PCR, mutation detection, allele determination, and SNP detection.

Label NamePurificationsPositionsPrice(2OD)Price(5OD)Price(10OD)
5'FAM-3'TAMRAHPLC5', 3'End$138.5$180.0$276.9
5'HEX-3'TAMRAHPLC5', 3'End$169.2$220.0$338.5
5'TET-3'TAMRAHPLC5', 3'End$169.2$220.0$338.5
5'JOE-3'TAMRAHPLC5', 3'End$184.6$240.0$369.2
5'VIC-3'TAMRAHPLC5', 3'End$184.6$240.0$369.2
5'FAM-3'BHQ1HPLC5', 3'End$123.1$160.0$246.2
5'VIC-3'BHQ1HPLC5', 3'End$169.2$220.0$338.5
5'HEX-3'BHQ1HPLC5', 3'End$147.7$192.0$295.4
5'JOE-3'BHQ1HPLC5', 3'End$147.7$192.0$295.4
5'TET-3'BHQ-1HPLC5', 3'End$147.7$192.0$295.4
5'Cy5-3'BHQ2HPLC5', 3'End$147.7$192.0$295.4
5'Cy3-3'BHQ2HPLC5', 3'End$147.7$192.0$295.4
5'ROX-3'BHQ2HPLC5', 3'End$147.7$192.0$295.4
5'TET-3'BHQ2HPLC5', 3'End$147.7$192.0$295.4
5'JOE-3'BHQ2HPLC5', 3'End$147.7$192.0$295.4
5'HEX-3'BHQ2HPLC5', 3'End$147.7$192.0$295.4
5'TAMRA-3'BHQ2HPLC5', 3'End$147.7$192.0$295.4
5'Texas Red-3'BHQ2HPLC5', 3'End$147.7$192.0$295.4
5'Quasar 670-3'BHQ2HPLC5', 3'End$147.7$192.0$295.4
5'-FAM and 3'-BHQ2HPLC5', 3'End$147.7$192.0$295.4
5'Quasar 670-3'BHQ3HPLC5', 3'End$147.7$192.0$295.4
5'CY5-3'BHQ3HPLC5', 3'End$147.7$192.0$295.4
5'FAM-3'ECLIPSHPLC5', 3'End$147.7$192.0$295.4
5'HEX-3' ECLIPSHPLC5', 3'End$147.7$192.0$295.4
5'TAMRA-3'EclipseHPLC5', 3'End$147.7$192.0$295.4
5'ROX-3'EclipseHPLC5', 3'End$147.7$192.0$295.4
5'TET-3'EclipseHPLC5', 3'End$147.7$192.0$295.4
5'JOE-3'EclipseHPLC5', 3'End$147.7$192.0$295.4
5'FAM-3'MGBHPLC5', 3'End$184.6$240.0$369.2
5'HEX-3'MGBHPLC5', 3'End$184.6$240.0$369.2
5'TET-3'MGBHPLC5', 3'End$184.6$240.0$369.2
5'JOE-3'MGBHPLC5', 3'End$184.6$240.0$369.2
5'ROX-3'MGBHPLC5', 3'End$184.6$240.0$369.2
5'Texas Red-3'MGBHPLC5', 3'End$184.6$240.0$369.2
5'Quasar 670-3'MGBHPLC5', 3'End$184.6$240.0$369.2
5'VIC-3'MGBHPLC5', 3'End$307.7$400.0$615.4
5'FAM-3'DABCYLHPLC5', 3'End$147.7$192.0$295.4
5'HEX-3'DABCYLHPLC5', 3'End$147.7$192.0$295.4
5'TET-3'DABCYLHPLC5', 3'End$147.7$192.0$295.4
5'JOE-3'DABCYLHPLC5', 3'End$147.7$192.0$295.4
5'TAMRA-3'DABCYLHPLC5', 3'End$147.7$192.0$295.4
5'Texas Red-3'DabcylHPLC5', 3'End$147.7$192.0$295.4
5'ROX-3'DabcylHPLC5', 3'End$147.7$192.0$295.4
5'CY3-3'DABCYLHPLC5', 3'End$147.7$192.0$295.4
5'Cy5-3'DABCYLHPLC5', 3'End$147.7$192.0$295.4
5'Phos and 3'FAMHPLC5', 3'End$61.5$61.5$76.9
5'TAMRA and 3'PhosHPLC5', 3'End$61.5$61.5$76.9
5'C6-Biotin,3'BiotinHPLC5', 3'End$61.5$61.5$76.9
5'C6-Biotin,3'Cy5HPLC5', 3'End$76.9$76.9$107.7
5'C6-NH2,3'C3-FamHPLC5', 3'End$61.5$61.5$76.9
5'C6-NH2,3'Cy3HPLC5', 3'End$107.7$107.7$138.5
5'Cy5,SS,HPLC5', 3'End$107.7$107.7$138.5
5'Cy5,3'C7-NH2HPLC5', 3'End$107.7$107.7$138.5
5'Cy5,3'SHHPLC5', 3'End$107.7$107.7$138.5
5'Dabcyl,3'C3-FamHPLC5', 3'End$107.7$107.7$138.5
5'DlG,3'DigoxinHPLC5', 3'End$107.7$107.7$138.5
5'SH,3'Cy3HPLC5', 3'End$107.7$107.7$138.5
5'Fam,3'C3-FamHPLC5', 3'End$61.5$61.5$76.9
5'TAMRA,3'C3-FamHPLC5', 3'End$76.9$76.9$107.7

Quenchers

FRET quenching depends on the ability of the fluorophore to transfer energy to the quencher. In order for this to happen, the emission spectrum of the fluorophore must overlap with the absorption spectrum of the quencher. In order for a quencher to quench fluorescence from several different fluorophores, it must therefore have a wide absorption spectrum and a high extinction coefficient.

Label NamePurificationsPositionsPrice(2OD)Price(5OD)Price(10OD)
DABCYLHPLC3'End$61.5$80.0$123.1
TAMRAHPLC3'End$61.5$80.0$123.1
BHQ 1HPLC3'End$55.4$72.0$110.8
BHQ 2HPLC3'End$84.6$110.0$169.2
BHQ 3HPLC3'End$61.5$80.0$123.1
MGBHPLC3'End$100.0$130.0$200.0
BBQ-650HPLC3'End$61.5$80.0$123.1
TQ1HPLC3'End$61.5$80.0$123.1
TQ2HPLC3'End$61.5$80.0$123.1
TQ3HPLC3'End$61.5$80.0$123.1
TQ4HPLC3'End$61.5$80.0$123.1
TQ5HPLC3'End$61.5$80.0$123.1
TQ6HPLC3'End$61.5$80.0$123.1
QSY 7 carboxylic acidHPLC3'End$100.0$130.0$200.0
TQ7HPLC3'End$61.5$80.0$123.1

Affinity Ligands

Oligonucletides can be labeled with biotin or digoxigenin or directly labeled with alkaline phosphatase. A variety of linker arms are available as spacers to minimize steric hindrance.

Label NamePurificationsPositionsPrice(2OD)Price(5OD)Price(10OD)
Biotin dTHPLC5', 3'End,Internal$123.1$123.1$153.8
BiotinHPLC5', 3'End,Internal$24.6$32.0$49.2
Biotin-TEGHPLC5', 3'End,Internal$36.9$48.0$73.8
DIGHPLC5', 3'End$92.3$120.0$184.6

Spacers

Spacer modifcations C3, 9, C12 and 18 are used to insert a spacer arm in an oligonucleotide. These modifications can be added in multiple additions when a longer spacer is required.

Label NamePurificationsPositionsPrice(2OD)Price(5OD)Price(10OD)
Spacer C6HPLC5', 3'End,Internal$61.5$61.5$115.4
Spacer 9HPLC5', 3'End,Internal$61.5$61.5$115.4
Spacer C12HPLC5', 3'End,Internal$61.5$61.5$115.4
Spacer C3HPLC5', 3'End,Internal$46.2$46.2$76.9
Spacer C18HPLC5', 3'End,Internal$46.2$46.2$76.9
dSpacerHPLC5', 3'End,Internal$46.2$46.2$76.9

Attachment moieties

A primary amino group or a thiol group can be used to attach a variety of modifiers (such as fluorescent dyes) to an oligonucleotide or used to attach an oligonucleotide to a solid surface.

Label NamePurificationsPositionsPrice(2OD)Price(5OD)Price(10OD)
5’-Amino-Modifier-C6HPLC5'End$27.7$36.0$55.4
3’-Amino-Modifier-C7HPLC3'End$27.7$36.0$55.4
5’-Amino-Modifier-C12HPLC5'End$80.0$104.0$160.0
Thiol-Modifier C6 S-SHPLC5', 3'End,Internal$49.2$64.0$98.5
Thiol-Modifier-C3 S-SHPLC5', 3'End,Internal$49.2$64.0$98.5

TM increase

The stability of the DNA double helix depends on a fine balance of interactions including hydrogen bonds between bases, hydrogen bonds between bases and surrounding water molecules, and base-stacking interactions between adjacent bases. Slight variations in the DNA sequence can have profound implications on the stability of the DNA duplex.

Label NamePurificationsPositionsPrice(2OD)Price(5OD)Price(10OD)
2’ OMe-rAPAGE5', 3'End,Internal$46.2$46.2$76.9
2’ OMe-rCPAGE5', 3'End,Internal$46.2$46.2$76.9
2’ OMe-rGPAGE5', 3'End,Internal$46.2$46.2$76.9
2’ OMe-rUPAGE5', 3'End,Internal$46.2$46.2$76.9