6-VIC phosphoramidite

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Physical properties

Molecular weight	1023.38
Solvent	MeCN

Spectral properties

Excitation (nm)	526
Emission (nm)	543

Storage, safety and handling

H-phrase	H303, H313, H333
Hazard symbol	XN
Intended use	Research Use Only (RUO)
R-phrase	R20, R21, R22
Storage	Freeze (< -15 °C); Minimize light exposure
UNSPSC	12171501

Overview SDS Protocol

CAS

1414265-81-8

Molecular weight

1023.38

Excitation (nm)

526

Emission (nm)

543

6-VIC phosphoramidite is an asymmetrical xanthene dye widely used to prepare fluorescence-labeled oligonucleotides and design qPCR probes, such as TaqMan, Molecular Beacon, and Scorpion. Its spectral characteristics are similar to HEX and JOE, emitting fluorescence in the green-yellow range. 6-VIC phosphoramidite can efficiently label oligonucleotides at their 5'-end using standard or automated synthesis protocols. Protecting groups on the 6-VIC moiety are removed under standard conditions of cleavage and deprotection with concentrated ammonia.

Calculators

Common stock solution preparation

Table 1. Volume of MeCN needed to reconstitute specific mass of 6-VIC phosphoramidite to given concentration. Note that volume is only for preparing stock solution. Refer to sample experimental protocol for appropriate experimental/physiological buffers.

	0.1 mg	0.5 mg	1 mg	5 mg	10 mg
1 mM	97.715 µL	488.577 µL	977.154 µL	4.886 mL	9.772 mL
5 mM	19.543 µL	97.715 µL	195.431 µL	977.154 µL	1.954 mL
10 mM	9.772 µL	48.858 µL	97.715 µL	488.577 µL	977.154 µL

Molarity calculator

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Mass (Calculate)		Molecular weight		Volume (Calculate)		Concentration (Calculate)		Moles
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Spectrum

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Spectral properties

Excitation (nm)	526
Emission (nm)	543

Product Family

Name	Excitation (nm)	Emission (nm)	Extinction coefficient (cm ^-1 M ^-1)
6-FAM phosphoramidite [5'-Fluorescein phosphoramidite] CAS 204697-37-0	493	517	83000
6-Fluorescein phosphoramidite	498	517	80000¹
6-TET phosphoramidite [5'-Tetrachlorofluorescein phosphoramidite] CAS#: 877049-90-6	521	542	73000
6-HEX phosphoramidite [5'-Hexachlorofluorescein phosphoramidite]	533	559	73000
6-VIC, SE [6-VIC NHS ester]	526	543	-
6-JOE Phosphoramidite	520	545	75000¹
5-VIC phosphoramidite	526	543	-
6-VIC Azide	526	543	-
6-VIC Alkyne	526	543	-

Images

Figure 1. Chemical structure for 6-VIC phosphoramidite.

References

View all 50 references: Citation Explorer

Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing.
Authors: Zhang, Yanjun and Tang, Yin and Sun, Zhongxing and Jia, Junqi and Fang, Yuan and Wan, Xinyi and Fang, Dong
Journal: Genome research (2023): 412-426

CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing.
Authors: Carbonell-Sala, Silvia and Lagarde, Julien and Nishiyori, Hiromi and Palumbo, Emilio and Arnan, Carme and Takahashi, Hazuki and Carninci, Piero and Uszczynska-Ratajczak, Barbara and Guigó, Roderic
Journal: bioRxiv : the preprint server for biology (2023)

Targeted Virome Sequencing Enhances Unbiased Detection and Genome Assembly of Known and Emerging Viruses-The Example of SARS-CoV-2.
Authors: Pogka, Vasiliki and Papadopoulou, Gethsimani and Valiakou, Vaia and Sgouras, Dionyssios N and Mentis, Andreas F and Karamitros, Timokratis
Journal: Viruses (2022)

Targeted long-read sequencing reveals clonally expanded HBV-associated chromosomal translocations in patients with chronic hepatitis B.
Authors: van Buuren, Nicholas and Ramirez, Ricardo and Soulette, Cameron and Suri, Vithika and Han, Dong and May, Lindsey and Turner, Scott and Parvangada, P C and Martin, Ross and Chan, Henry L Y and Marcellin, Patrick and Buti, Maria and Bui, Nam and Bhardwaj, Neeru and Gaggar, Anuj and Li, Li and Mo, Hongmei and Feierbach, Becket
Journal: JHEP reports : innovation in hepatology (2022): 100449

Internal oligo(dT) priming introduces systematic bias in bulk and single-cell RNA sequencing count data.
Authors: Svoboda, Marek and Frost, H Robert and Bosco, Giovanni
Journal: NAR genomics and bioinformatics (2022): lqac035

Sequencing of Uniform Multifunctional Oligoesters via Random Chain Cleavages.
Authors: Soete, Matthieu and Du Prez, Filip E
Journal: Angewandte Chemie (International ed. in English) (2022): e202202819

Cost-Efficient Sequence-Based Nonextensible Oligonucleotide in Real-Time PCR and High-Throughput Sequencing.
Authors: Zhang, Kerou and Song, Ping and Dai, Peng and Zhang, Jinny Xuemeng and Wu, Lucia Ruojia and Cheng, Lauren Yuxuan and Pinto, Alessandro and Kwong, Lawrence and Cabrera, Karina and Wen, Ruoxin and Zhang, David Yu
Journal: ACS sensors (2022): 1165-1174

A Comparison of Bioinformatics Pipelines for Enrichment Illumina Next Generation Sequencing Systems in Detecting SARS-CoV-2 Virus Strains.
Authors: Afiahayati, and Bernard, Stefanus and Gunadi, and Wibawa, Hendra and Hakim, Mohamad Saifudin and Marcellus, and Parikesit, Arli Aditya and Dewa, Chandra Kusuma and Sakakibara, Yasubumi
Journal: Genes (2022)

Transcriptome Sequencing Reveals Tgf-β-Mediated Noncoding RNA Regulatory Mechanisms Involved in DNA Damage in the 661W Photoreceptor Cell Line.
Authors: Huang, Yuke and Chen, Xi and Jiang, Zhigao and Luo, Qian and Wan, Linxi and Hou, Xiangtao and Yu, Keming and Zhuang, Jing
Journal: Genes (2022)

Case study: Targeted RNA-sequencing of aged formalin-fixed paraffin-embedded samples for understanding chemical mode of action.
Authors: Cannizzo, Michael D and Wood, Charles E and Hester, Susan D and Wehmas, Leah C
Journal: Toxicology reports (2022): 883-894