IRDye 680-NHS

Click here for a list of fluorophores.

This modification is a post synthesis conjugation to a primary amino group thus an additional modification with an amino group is required. A C3, C6 or C12 amino group can be placed at the 5' or for the 3' end a C3 or C7 amino and for internal positions an amino modified base is used, e.g Amino dT C6.

Yield of Post Synthesis NHS, Maleimide & Click Ligand Conjugation*

Oligo Scale of Synthesis	Yield, nmols
50 nmol	2 nmol
200 nmol	5 nmol
1 umol	16 nmol
2 umol	30 nmol
5 umol	75 nmol
10 umol	150 nmol
15 umol	225 nmol
* The yield will be lower for oligos longer than 50mer. Click here for yield table of long oligos.
* Click here for RNA Oligos scale of synthesis and yield.
NHS Ligand conjugation requires a primary amino group. Gene Link offers a wide selection of amino modifications for 5', 3' and internal sites. Click here for a list of conjugation chemistry modifications.
Maleimide Ligand conjugation requires a thiol group. Gene Link offers a wide selection of thiol modifications for 5', 3' and internal sites. Click here for a list of conjugation chemistry modifications.
Click Chemistry Ligand conjugation requires a corresponding Click modification; examples Alkyne:Azide, Azide:DBCO, BCN:Azide, BCN: TCO:Tetrazine. Gene Link offers a wide selection of click modifications for 5', 3' and internal sites. Click here for a list of click chemistry modifications.

IRDye700 is a near-IR fluorescent dye used for labeling oligonucleotides. IRDye800 has an absorbance maximum of 680 nm and an emission maximum of 694 nm. The combination of narrow absorbance/emission bands and low-background autofluorescence in the IR region results in higher S/N ratios and thus enhanced detection sensitivity compared with fluorophores with absorbance/emission maxima in the visible region (1). IRDye700 is used as a reporter moiety in real-time PCR applications. For such probes, IRDye700 is most commonly paired with the dark quencher QC-1, as the two have excellent spectral overlap (2).

IRDye700 can be used to label DNA oligos for use as hybridization probes in a variety of in vivo and in vitro research or diagnostic applications, as well as for structure-function studies of DNA, RNA, and protein-oligonucleotide complexes. Oligos labeled with IRDye700 at the 5’-end can be used as PCR and Sanger DNA sequencing primers to generate fluorescently-labeled PCR, sequencing or genetic analysis (AFLP, microsatellite) products (3-5).

Near Infrared Fluorophore Spectral Data & Quencher Selection Guide
Fluorophore Name	Excitation Max, nm +/-10	Emission Max, nm +/-10	Extinction Coefficient*	Color**	Quencher
Cy5	650	665	250,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
IRDye 650 NHS	650	665	230,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
AZ647 NHS	655	680	191,800	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
AZ680 NHS	678	701	185,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
Cy5.5	684	710	198,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
IRDye 700 NHS	684	710	288,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
AZdye700 NHS	696	719	192,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
Atto 700 NHS	699	715	120,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
Cy7 NHS	740	773	199,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
IRDye 750 NHS	756	776	260,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
cy7.5 NHS	788	808	223,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
IRDye 800 NHS	795	819	240,000	Human vision is insensitive to light beyond ~650 nm.	BBQ-650 λ (max) = 650nm Range = 550-750 nm
* Extinction coefficient at λ (max) in cm-1M-1. ** Typical emission color seen through the eyepiece of a conventional fluorescence microscope with appropriate filters. Near-IR region. Human vision is insensitive to light beyond ~650 nm; it is not possible to view near-IR fluorescent dyes. Click here for a list of fluorophores.
Click here for list of quenchers.

References
1. Middendorf, L.R., Bruce, J.C., Eckles, R.D., Grone, D.L., Roemer, S.C., Sloniker, G.D., Steffens, D.L., Sutter, S.L., Brumbaugh, J.A., et al. Continuous, on-line DNA sequencing using a versatile infrared laser scanner/electrophoresis apparatus. Electrophoresis (1992), 13: 487-494.
2. Peng X., Chen, H., Draney, D.R., Volcheck, W., Schutz-Geschwender, A., Olive, D.M. A nonfluorescent, broad-range quencher dye for Forster resonance energy transfer assays. Anal. Biochem. (2009), 388: 220-228.
3. Yomano, L.P., Scopes, R.K., Ingram, L.O. Cloning, sequencing, and expression of the Zymomonas mobilis phosphoglycerate mutase gene (pgm) in Escherichia coli. J. Bacteriol. (1993), 175: 3926-3933.
4. Oetting, W.S., Lee, H.K., Flanders, D.J., Wiesner, T.A., King, R.A. Linkage Analysis with Multiplexed Short Tandem Repeat Polymorphisms Using Infrared Fluorescence and M13 Tailed Primers. Genomics (1995), 30: 450-458.
5. Myburg, A.A., Remington, D.L, O’Malley, D.M., Sederoff, R.R., Whetton, R.W. High-Throughput AFLP Analysis Using Infrared Dye-Labeled Primers and an Automated DNA Sequencer. Biotechniques (2001), 30: 348-357.
- IRDye 680-NHS