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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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)

Low-input Nucleus Isolation and Multiplexing with Barcoded Antibodies of Mouse Sympathetic Ganglia for Single-nucleus RNA Sequencing.
Authors: Ge, Yang and van Roon, Lieke and Chen, H Sophia and Methorst, Ruben and Paton, Martin and DeRuiter, Marco C and Kielbasa, Szymon M and Jongbloed, Monique R M
Journal: Journal of visualized experiments : JoVE (2022)

Multiplexed Single-Nucleus RNA Sequencing Using Lipid-Oligo Barcodes.
Authors: Zhang, Qi and Kim, Seong Won and Gorham, Joshua M and DeLaughter, Daniel M and Ward, Tarsha and Seidman, Christine E and Seidman, Jonathan G
Journal: Current protocols (2022): e579

High-Throughput Activity Profiling of RNA-Cleaving DNA Catalysts by Deoxyribozyme Sequencing (DZ-seq).
Authors: Sednev, Maksim V and Liaqat, Anam and Höbartner, Claudia
Journal: Journal of the American Chemical Society (2022): 2090-2094

ProbeTools: designing hybridization probes for targeted genomic sequencing of diverse and hypervariable viral taxa.
Authors: Kuchinski, Kevin S and Duan, Jun and Himsworth, Chelsea and Hsiao, William and Prystajecky, Natalie A
Journal: BMC genomics (2022): 579

Improved nanopore direct RNA sequencing of cardiac myocyte samples by selective mt-RNA depletion.
Authors: Naarmann-de Vries, Isabel S and Eschenbach, Jessica and Dieterich, Christoph
Journal: Journal of molecular and cellular cardiology (2022): 175-186

Generation of Centered Log-Ratio Normalized Antibody-Derived Tag Counts from Large Single-Cell Sequencing Datasets.
Authors: Lacar, Benjamin
Journal: Methods in molecular biology (Clifton, N.J.) (2022): 203-217

Nondestructive Sequencing of Enantiopure Oligoesters by Nuclear Magnetic Resonance Spectroscopy.
Authors: Lee, Jeong Min and Jang, Heejeong and Lee, Seul Woo and Kim, Kyoung Taek
Journal: JACS Au (2022): 2108-2118

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