Cyanine5 phosphoramidite

Product Introduction

Cyanine5 is one of the dyes that are used in qPCR. The corresponding filter set is found on many qPCR machines.,This reactive derivative is useful for the synthesis of qPCR probes having Cyanine5 at 5'-end, the most typical location of fluorophore. This is a terminating, non-nucleoside reagent.,Amidite group in this reagent is bound to a secondary oxygen. This provides extra stability against Arbuzov rearrangement-a reaction that leads to amidite deterioration in solution in oligonucleotide synthesizer. This molecular design increases stability of the reagent, maintaining efficient coupling over longer time.

Chemical Information
Purity	NMR 1H, 31P, HPLC-MS (80%)
IUPAC Name	N-[4-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxycyclohexyl]-6-[3,3-dimethyl-2-[5-(1,3,3-trimethylindol-1-ium-2-yl)penta-2,4-dienylidene]indol-1-yl]hexanamide;chloride
Canonical SMILES	CC(C)N(C(C)C)P(OCCC#N)OC1CCC(CC1)NC(=O)CCCCCN2C3=CC=CC=C3C(C2=CC=CC=CC4=[N+](C5=CC=CC=C5C4(C)C)C)(C)C.[Cl-]
InChI	InChI=1S/C47H66N5O3P.ClH/c1-35(2)52(36(3)4)56(54-34-20-32-48)55-38-30-28-37(29-31-38)49-45(53)27-14-11-19-33-51-42-24-18-16-22-40(42)47(7,8)44(51)26-13-10-12-25-43-46(5,6)39-21-15-17-23-41(39)50(43)9;/h10,12-13,15-18,21-26,35-38H,11,14,19-20,27-31,33-34H2,1-9H3;1H
InChI Key	JTFPONRIAYGAKY-UHFFFAOYSA-N
Appearance	Dark colored solid

Computed Properties
Hydrogen Bond Donor Count	1
Hydrogen Bond Acceptor Count	7
Rotatable Bond Count	18
Exact Mass	815.4670057 g/mol
Monoisotopic Mass	815.4670057 g/mol
Topological Polar Surface Area	80.8Ų
Heavy Atom Count	57
Formal Charge	0
Complexity	1460
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