Agbavwe, C. et al. Efficiency, error and yield in light-directed maskless synthesis of DNA microarrays. J. Nanobiotechnol. 9 (2011). Sanborn, M. E., Connolly, B. K., Gurunathan, K. & Levitus, M. Fluorescence properties and photophysics of the sulfoindocyanine Cy3 linked covalently to DNA. J. Phys. Chem. B 111, 11064–11074 (2007). The pH value of protein solution shall be 8.5±0.5. If the pH is lower than 8.0, 1 M sodium bicarbonate shall be used for adjustment. Chemically, cyanines are a conjugated system between two nitrogen atoms; in each resonance structure, exactly one nitrogen atom is oxidized to an iminium. Typically, they form part of a nitrogenous heterocyclic system. [2] Cy3B: This product is manufactured under an exclusive license from Carnegie Mellon University and is covered by US patent number 6,133,445 and equivalent patents and patent applications in other countries.

Pershina, A. G.; Demin, A. M.; Perekucha, N. A.; Brikunova, O. Y.; Efimova, L. V.; Nevskaya, K. V.; Vakhrushev, A. V.; Zgoda, V. G.; Uimin, M. A.; Minin, A. S.; Malkeyeva, D.; Kiseleva, E.; Zima, A. P.; Krasnov, V. P.; Ogorodova, L. M. Peptide Ligands on the PEGylated Nanoparticle Surface and Human Serum Composition Are Key Factors for the Interaction between Immune Cells and Nanoparticles. Colloids and Surfaces B: Biointerfaces, 2023, 221, 112981. doi: 10.1016/j.colsurfb.2022.112981 The following protocol is an example of dye-protein conjugate purification by using a SepHadex G-25 column. Mujumdar, R. B., Ernst, L. A., Mujumdar, S. R., Lewis, C. J. & Waggoner, A. S. Cyanine dye labeling reagents—sulfoindocyanine Succinimidyl Esters. Bioconjugate Chem. 4, 105–111 (1993). are provided for Customer as the end-user and solely for research and development uses. Any use of Product for diagnostic,

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For applications to biotechnology, special cyanine dyes are synthesized from 2, 3, 5 or 7-methine structures with reactive groups on either one or both of the nitrogen ends so that they can be chemically linked to either nucleic acids or protein molecules. Labeling is done for visualization and quantification purposes. Biological applications include comparative genomic hybridization and gene chips, which are used in transcriptomics, and various studies in proteomics such as RNA localization, [7] molecular interaction studies by fluorescence resonance energy transfer ( FRET) and fluorescent immunoassays. a b Ernst LA, Gupta RK, Mujumdar RB, Waggoner AS (Jan 1989). "Cyanine dye labeling reagents for sulfhydryl groups". Cytometry. 10 (1): 3–10. doi: 10.1002/cyto.990100103. PMID 2917472. Zhu, H.L., Fohlerova, Z., Pekarek, J., Basova, E. & Neuzil, P. Recent advances in lab-on-a-chip technologies for viral diagnosis. Biosens. Bioelectron. 153 (2020).

CytoCy5S: The use of this product in an NTR gene reporter assay is the subject of US patent number 7,579,140 in the name of Cytiva. a b Berneth, Horst (2008). "Methine Dyes and Pigments". Ullmann's Encyclopedia of Industrial Chemistry. Weinheim: Wiley-VCH. doi: 10.1002/14356007.a16_487.pub2. Nie, Q.; Li, C.; Wang, Y.; Hu, Y.; Pu, W.; Zhang, Q.; Cai, J.; Lin, Y.; Li, G.; Wang, C.; Li, L.; Dou, Y.; Zhang, J. Pathologically Triggered in Situ Aggregation of Nanoparticles for Inflammation-Targeting Amplification and Therapeutic Potentiation. Acta Pharmaceutica Sinica B, 2023, 13(1), 390–409. doi: 10.1016/j.apsb.2022.07.013 Example: assuming the required marker protein is 500 μL 2 mg/mL IgG (MW=150,000), use 100 μL DMSO dissolve 1 mg Cy5.5, the required Cy5.5 volume is 5.05 μL, and the detailed calculation process is as follows: Sale, lease, license or other grant of rights to use this material or any material derived or produced from it.

The dilution calculator equation

Iris Dyes | Cyanine Technologies". Archived from the original on 2015-01-26 . Retrieved 2015-01-26. Levitus, M. & Ranjit, S. Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments. Q Rev. Biophys. 44, 123–151 (2011). For protein labeling, Cy3 and Cy5 dyes sometimes bear a succinimidyl group to react with amines, or a maleimide group to react with a sulfhydryl group of cysteine residues. Alexa Fluor dyes, Dylight, FluoProbes dyes, Sulfo Cy dyes, [13] Seta dyes, [14] IRIS dyes from Cyanine Technologies [15] and others can be used interchangeably with Cy dyes in most biochemical applications, with claimed improvements in solubility, fluorescence, or photostability. [16] [17] The design of DNA oligonucleotides is based on a permutation scheme allowing for all possible combinations of 5 consecutive nucleotides immediately adjacent to a fluorescent dye to be synthesized in parallel as microarrays (P 1–P 5 in Fig. 1). The total amount of unique pentanucleotides is 4 5, or 1024 oligonucleotides to be synthesized. To account for potential variability in synthesis efficiency which would produce lower fluorescence signals for poorly-synthesized sequences, the nucleotide content in all DNA sequences is kept constant by adding a subsection composed of five “N” trinucleotides (N 1 to N 5) where each N x corresponds to AGCT minus the nucleotide in P x. Between the P and N sections, a T 15 spacer is introduced and the entire oligonucleotide sequence is then synthesized over a T 5 linker separating the DNA from the surface of the array. At the 3′ end of the oligonucleotide, immediately after the pentanucleotide, a Cy3 or Cy5 dye is attached. Schematically, all 1024 combinations are represented in the form 3′Cy3/Cy5—P 1P 2P 3P 4P 5—T 15—(ACGT-P 1)—(ACGT-P 2)—(ACGT-P 3)—(ACGT-P 4)—(ACGT-P 5)—T 5—glass. Microarray synthesis

Kretschy, N., Holik, A. K., Somoza, V., Stengele, K. P. & Somoza, M. M. Next-generation o-nitrobenzyl photolabile groups for light-directed chemistry and microarray synthesis. Angew. Chem. Int. Ed. 54, 8555–8559 (2015). Among currently available fluorescent dyes, the cyanine dyes are better able to withstand the harsh dehydration and embedding conditions required for mounting sections in non-polar plastic media, such as DPX and Permount™. The cyanine dyes are brighter in the non-polar environment than in an aqueous medium, resulting in less acquisition time in the confocal microscope than that required for DyLight and Alexa Fluor® dyes (Figure 1), even though those dyes are brighter in aqueous mounting media. Sulfo–Cyanine dyes bear one or two sulfo groups, rendering the Cy dye water-soluble, but tri- and quadri-sulfonated forms are available for even higher water solubility. [8] PEGylation is another modification that confers hydrophilicity, not only to the dye but also to the labeled conjugate. Except as otherwise expressly agreed in a writing signed by a legally authorized representative of CST, the following termsThe amount of Cy5.5 required for reaction depends on the amount of protein to be labeled, and the optimal molar ratio of Cy5.5 to protein is about 10.

Sale, lease, license or other transfer of the material or any material derived or produced from it. Holz, K. et al. High-efficiency reverse (5’–>3’) synthesis of complex DNA microarrays. Sci. Rep. 8, 15099 (2018). Holz, K., Schaudy, E., Lietard, J. & Somoza, M. M. Multi-level patterning nucleic acid photolithography. Nat. Commun. 10, 3805 (2019).

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Add more PBS (pH 7.2-7.4) to the desired sample to complete the column purification. Combine the fractions that contain the desired dye-protein conjugate. Fuller, C. W. et al. The challenges of sequencing by synthesis. Nat. Biotechnol. 27, 1013–1023 (2009). Products are labeled with For Research Use Only or a similar labeling statement and have not been approved, cleared, or licensed Kaur, G., Lewis, J.S. & van Oijen, A.M. Shining a Spotlight on DNA: Single-Molecule Methods to Visualise DNA. Molecules 24 (2019). The additive effect of multiple Gs or Cs in a row is not immediately apparent, with GGGGG ranking #31 and #21 (0.71 and 0.64 relative intensity) and CCCCC ranking #1009 and #1021 (0.37 and 0.25 relative intensity) for Cy3 and Cy5, respectively. The top-ranking GAAAA motif identified in 5ʹ-Cy3 oligonucleotides here ranks #334 (0.58 relative fluorescence), further illustrating the significant differences between 5ʹ and 3ʹ labeling.