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Cyanine5.5 phosphoramidite, 5'-terminal
| Catalog Number | A19-0084 |
| Category | DNA Stains |
| Molecular Formula | C55H71N5ClO3P |
| Molecular Weight | 916.61 |
* Please be kindly noted products are not for therapeutic use. We do not sell to patients.
Product Introduction
Cyanine5.5 is a fluorophore with the emission in far red range of the spectrum. This dye is useful for multiplex qPCR. Commercial six-channel qPCR instruments often have a channel for Cyanine5.5.,This phosphoramidite can be used for the synthesis of 5'-labeled oligonucleotides by direct labeling in oligonucleotide synthesizer.,The structure of phosphoramidite functional group that is attached to a secondary carbon atom provides extra stability against Arbuzov rearrangement. This helps maintaining coupling performance over a longer storage time in oligonucleotide synthesizer, compared to phosphoramidites derived of primary alcohols.
Chemical Information
Product Specification
Computed Properties
| Purity | NMR 1H, 31P, HPLC-MS (85%) |
| IUPAC Name | N-[4-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxycyclohexyl]-6-[1,1-dimethyl-2-[5-(1,1,3-trimethylbenzo[e]indol-3-ium-2-yl)penta-2,4-dienylidene]benzo[e]indol-3-yl]hexanamide;chloride |
| Canonical SMILES | CC(C)N(C(C)C)P(OCCC#N)OC1CCC(CC1)NC(=O)CCCCCN2C3=C(C4=CC=CC=C4C=C3)C(C2=CC=CC=CC5=[N+](C6=C(C5(C)C)C7=CC=CC=C7C=C6)C)(C)C.[Cl-] |
| InChI | InChI=1S/C55H70N5O3P.ClH/c1-39(2)60(40(3)4)64(62-38-20-36-56)63-44-32-30-43(31-33-44)57-51(61)27-14-11-19-37-59-48-35-29-42-22-16-18-24-46(42)53(48)55(7,8)50(59)26-13-10-12-25-49-54(5,6)52-45-23-17-15-21-41(45)28-34-47(52)58(49)9;/h10,12-13,15-18,21-26,28-29,34-35,39-40,43-44H,11,14,19-20,27,30-33,37-38H2,1-9H3;1H |
| InChIKey | GECQYBXOGKSPTM-UHFFFAOYSA-N |
| Appearance | Dark colored solid |
| CF260 | 0.07 |
| CF280 | 0.03 |
| Fluorescence Quantum Yield | 0.2 |
| Excitation | 694 |
| Emission | 710 |
| Storage | Storage: 12 months after receival at -20 °C in the Dark. Transportation: at room temperature for up to 3 weeks. Avoid prolonged exposure to light. Desiccate. |
| Hydrogen Bond Donor Count | 1 |
| Hydrogen Bond Acceptor Count | 7 |
| Rotatable Bond Count | 18 |
| Exact Mass | 915.4983058 g/mol |
| Monoisotopic Mass | 915.4983058 g/mol |
| Topological Polar Surface Area | 80.8Ų |
| Heavy Atom Count | 65 |
| Formal Charge | 0 |
| Complexity | 1720 |
| Isotope Atom Count | 0 |
| Defined Atom Stereocenter Count | 0 |
| Undefined Atom Stereocenter Count | 1 |
| Defined Bond Stereocenter Count | 0 |
| Undefined Bond Stereocenter Count | 3 |
| Covalently-Bonded Unit Count | 2 |
| Compound Is Canonicalized | Yes |
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