Yakima Yellow^® Phosphoramidite | CAS 502485-39-4

Name: Yakima Yellow® Phosphoramidite
Brand: BOC Sciences
Rating: 5 (1 reviews)

Catalog Number	A01-0020
Category	Fluorescent Proteins & Nucleotides
Molecular Formula	C49H60Cl4N3O10P
Molecular Weight	1023.81

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Product Introduction

Yakima Yellow® Phosphoramidite is a fluorescent phosphoramidite dye for 5’-end DNA labeling. It emits bright yellow fluorescence with excellent signal-to-noise performance.

Chemical Information
Product Specification
Application

Chemical Information

Synonyms	Y-Yellow Phosphoramidite; Yakima Yellow; 3-(5,6,4',7'-tetrachloro-5'-methyl-3',6'-dipivaloylfluorescein-2-yl)-propanamidohexyl-1-O-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidite; 1,1'-[2'-[12-[Bis(1-methylethyl)amino]-15-cyano-3-oxo-11,13-dioxa-4-aza-12-phosphapentadec-1-yl]-4',5,6,7'-tetrachloro-5'-methyl-3-oxospiro[isobenzofuran-1(3H),9'-[9H]xanthene]-3',6'-diyl] bis(2,2-dimethylpropanoate); Propanoic acid, 2,2-dimethyl-, 2'-[3-[[6-[[[bis(1-methylethyl)amino](2-cyanoethoxy)phosphino]oxy]hexyl]amino]-3-oxopropyl]-4',5,6,7'-tetrachloro-5'-methyl-3-oxospiro[isobenzofuran-1(3H),9'-[9H]xanthene]-3',6'-diyl ester; Epoch Yakima Yellow Phosphoramidite; Yakima Yellow Amidite; Yakima Yellow Phosphoramidite
IUPAC Name	[2',5,5',6-tetrachloro-7'-[3-[6-[2-cyanoethoxy-[di(propan-2-yl)amino]phosphanyl]oxyhexylamino]-3-oxopropyl]-6'-(2,2-dimethylpropanoyloxy)-4'-methyl-3-oxospiro[2-benzofuran-1,9'-xanthene]-3'-yl] 2,2-dimethylpropanoate
SMILES	CC1=C2C(=CC(=C1OC(=O)C(C)(C)C)Cl)C3(C4=CC(=C(C=C4C(=O)O3)Cl)Cl)C5=C(O2)C(=C(C(=C5)CCC(=O)NCCCCCCOP(N(C(C)C)C(C)C)OCCC#N)OC(=O)C(C)(C)C)Cl
InChI	InChI=1S/C49H60Cl4N3O10P/c1-27(2)56(28(3)4)67(62-22-16-19-54)61-21-15-13-12-14-20-55-38(57)18-17-30-23-33-43(39(53)42(30)65-46(60)48(9,10)11)63-40-29(5)41(64-45(59)47(6,7)8)37(52)26-34(40)49(33)32-25-36(51)35(50)24-31(32)44(58)66-49/h23-28H,12-18,20-22H2,1-11H3,(H,55,57)
InChIKey	POEPDWFKAYRZJK-UHFFFAOYSA-N
Appearance	Off-white solid

Product Specification

Storage

Store at -20°C

Application

Yakima Yellow® Phosphoramidite is a fluorescent nucleic-acid building block designed for dye incorporation during oligonucleotide synthesis. Its phosphoramidite functionality enables straightforward placement of the Yakima Yellow® fluorophore into DNA or RNA strands, which is why it is widely used in fluorescence-based nucleic acid assays and molecular imaging workflows that rely on labeled oligonucleotides.

1. Oligonucleotide Fluorescent Labeling

Yakima Yellow® Phosphoramidite is used by oligonucleotide chemists and assay developers to introduce a fluorescent tag directly into DNA or RNA constructs during automated synthesis. Researchers employ Yakima Yellow®-labeled oligos for tracking hybridization events, monitoring nucleic-acid interactions, and building fluorescence standards for assay development. Because the dye is installed as part of the oligonucleotide backbone workflow, it supports consistent probe positioning and facilitates downstream use in hybridization formats where the fluorophore location relative to the binding region is important.

2. Molecular Beacon Probes

Yakima Yellow® Phosphoramidite is commonly incorporated into molecular beacon designs where a fluorophore-bearing oligonucleotide undergoes target-dependent fluorescence change upon hybridization. In these systems, the labeled strand provides the optical readout used to visualize or quantify nucleic-acid recognition in solution. Molecular beacon workflows are frequently used in nucleic-acid detection method development, including format screening for probe architecture and signal behavior in fluorescence instrumentation.

3. Hybridization and Genotyping Assays

Yakima Yellow® Phosphoramidite supports fluorescence readouts in hybridization-based assays by enabling the preparation of fluorescently labeled capture or detection oligonucleotides. Lab teams use these probes to study sequence-dependent binding, optimize assay conditions, and generate fluorescence signals compatible with standard plate readers and fluorescence imaging setups. The phosphoramidite format helps streamline probe construction for multiplexing strategies where multiple sequence-specific oligos are labeled and interrogated in parallel.

4. FRET Probe Construction

Yakima Yellow® Phosphoramidite is also used in FRET-based nucleic-acid probe development, where a fluorophore-labeled oligonucleotide serves as a donor or acceptor component in distance-dependent energy transfer designs. Fluorescent probe developers incorporate Yakima Yellow® into oligos to build reporter pairs for monitoring hybridization, conformational changes, or nucleic-acid assembly states. This enables fluorescence readouts that can be tuned by probe geometry and labeling pattern, supporting assay engineering for nucleic acid analysis workflows.