Cyanine5.5 phosphoramidite, 5'-terminal

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
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
InChI Key	GECQYBXOGKSPTM-UHFFFAOYSA-N
Appearance	Dark colored solid

Computed Properties
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