WARNING: This product is for research use only, not for human or veterinary use.

MedKoo CAT#: 555718

CAS#: 143413-85-8 (iodide)

Description: YOYO-1 is a green fluorescent dye used in DNA staining. It belongs to the family of monomethine cyanine dyes and is a tetracationic homodimer of Oxazole Yellow (abbreviated YO, hence the name YOYO), typically available as tetraiodide salt. In aqueous buffer, free YOYO-1 dye (absorption: λmax 458 nm, emission: λmax 564 nm) has very low fluorescence quantum yield, however the intensity of fluorescence increases 3200 times upon binding through bis-intercalation to double-stranded DNA (absorption: λmax 489 nm, emission: λmax 509 nm).

Chemical Structure

CAS# 143413-85-8 (iodide)

Theoretical Analysis

MedKoo Cat#: 555718
Name: YOYO-1
CAS#: 143413-85-8 (iodide)
Chemical Formula: C49H58I4N6O2
Exact Mass:
Molecular Weight: 1270.6609
Elemental Analysis: C, 46.32; H, 4.60; I, 39.95; N, 6.61; O, 2.52

Price and Availability

This product is not in stock, which may be available by custom synthesis. For cost-effective reason, minimum order is 1g (price is usually high, lead time is 2~3 months, depending on the technical challenge). Quote less than 1g will not be provided. To request quote, please email to sales @medkoo.com or click below button.
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Related CAS #: 143413-85-8 (iodide)   753420-24-5 (cation)    

Synonym: YOYO-1; YOYO1; YOYO 1; Thiazole orange dimer YOYO 1;

IUPAC/Chemical Name: 1-(3-((3-(dimethyl(3-(4-((E)-(3-methylbenzo[d]oxazol-2(3H)-ylidene)methyl)quinolin-1-ium-1-yl)propyl)ammonio)propyl)dimethylammonio)propyl)-4-((Z)-(3-methylbenzo[d]oxazol-2(3H)-ylidene)methyl)quinolin-1-ium iodide


InChi Code: InChI=1S/C49H58N6O2.4HI/c1-50-44-22-11-13-24-46(44)56-48(50)36-38-26-30-52(42-20-9-7-18-40(38)42)28-15-32-54(3,4)34-17-35-55(5,6)33-16-29-53-31-27-39(41-19-8-10-21-43(41)53)37-49-51(2)45-23-12-14-25-47(45)57-49;;;;/h7-14,18-27,30-31,36-37H,15-17,28-29,32-35H2,1-6H3;4*1H/q+4;;;;/p-4

SMILES Code: CN\1C2=CC=CC=C2O/C1=C/C3=CC=[N+](C4=CC=CC=C34)CCC[N+](C)(C)CCC[N+](C)(C)CCC[N+]5=CC=C(C6=CC=CC=C65)/C=C\7/N(C8=CC=CC=C8O7)C.[I-].[I-].[I-].[I-]

Appearance: Solid powder

Purity: >98% (or refer to the Certificate of Analysis)

Shipping Condition: Shipped under ambient temperature as non-hazardous chemical. This product is stable enough for a few weeks during ordinary shipping and time spent in Customs.

Storage Condition: Dry, dark and at 0 - 4 C for short term (days to weeks) or -20 C for long term (months to years).

Solubility: Soluble in DMSO

Shelf Life: >3 years if stored properly

Drug Formulation: This drug may be formulated in DMSO

Stock Solution Storage: 0 - 4 C for short term (days to weeks), or -20 C for long term (months).

HS Tariff Code: 2934.99.9001

Preparing Stock Solutions

The following data is based on the product molecular weight 1270.6609 Batch specific molecular weights may vary from batch to batch due to the degree of hydration, which will affect the solvent volumes required to prepare stock solutions.

Recalculate based on batch purity %
Concentration / Solvent Volume / Mass 1 mg 5 mg 10 mg
1 mM 1.15 mL 5.76 mL 11.51 mL
5 mM 0.23 mL 1.15 mL 2.3 mL
10 mM 0.12 mL 0.58 mL 1.15 mL
50 mM 0.02 mL 0.12 mL 0.23 mL

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1: Wang L, Pyle JR, Cimatu KA, Chen J. Ultrafast Transient Absorption Spectra of Photoexcited YOYO-1 molecules call for additional investigations of their fluorescence quenching mechanism. J Photochem Photobiol A Chem. 2018 Dec 1;367:411-419. doi: 10.1016/j.jphotochem.2018.09.012. Epub 2018 Sep 10. PubMed PMID: 30410276; PubMed Central PMCID: PMC6217845.

2: Pyle JR, Chen J. Correction: Photobleaching of YOYO-1 in super-resolution single DNA fluorescence imaging. Beilstein J Nanotechnol. 2018 Mar 6;9:809-811. doi: 10.3762/bjnano.9.74. eCollection 2018. PubMed PMID: 29601063; PubMed Central PMCID: PMC5852459.

3: Pyle JR, Chen J. Photobleaching of YOYO-1 in super-resolution single DNA fluorescence imaging. Beilstein J Nanotechnol. 2017 Nov 2;8:2296-2306. doi: 10.3762/bjnano.8.229. eCollection 2017. Erratum in: Beilstein J Nanotechnol. 2018 Mar 6;9:809-811. PubMed PMID: 29181286; PubMed Central PMCID: PMC5687005.

4: Roushan M, Azad Z, Lim SF, Wang H, Riehn R. Interference of ATP with the fluorescent probes YOYO-1 andYOYO-3 modifies the mechanical properties of intercalator-stained DNA confined in nanochannels. Mikrochim Acta. 2015 Jun 1;182(7):1561-1565. PubMed PMID: 27134313; PubMed Central PMCID: PMC4846983.

5: Lindberg DJ, Esbjörner EK. Detection of amyloid-β fibrils using the DNA-intercalating dye YOYO-1: Binding mode and fibril formation kinetics. Biochem Biophys Res Commun. 2016 Jan 8;469(2):313-8. doi: 10.1016/j.bbrc.2015.11.051. Epub 2015 Dec 2. PubMed PMID: 26612254.

6: Chen H, Zhu Z, Lu JJ, Liu S. Charging YOYO-1 on capillary wall for online DNA intercalation and integrating this approach with multiplex PCR and bare narrow capillary-hydrodynamic chromatography for online DNA analysis. Anal Chem. 2015 Feb 3;87(3):1518-22. doi: 10.1021/ac504257b. Epub 2015 Jan 15. PubMed PMID: 25555111; PubMed Central PMCID: PMC4318619.

7: Kundukad B, Yan J, Doyle PS. Effect of YOYO-1 on the mechanical properties of DNA. Soft Matter. 2014 Dec 28;10(48):9721-8. doi: 10.1039/c4sm02025a. PubMed PMID: 25366273.

8: Datta SG, Reynolds C, Goud YK, Datta B. Interaction of YOYO-1 with guanine-rich DNA. J Biomol Struct Dyn. 2014;32(7):1155-63. doi: 10.1080/07391102.2013.807752. Epub 2013 Jul 5. PubMed PMID: 23829319.

9: Gilroy EL, Hoffmann SV, Jones NC, Rodger A. Is photocleavage of DNA by YOYO-1 using a synchrotron radiation light source sequence dependent? Eur Biophys J. 2011 Oct;40(10):1121-9. doi: 10.1007/s00249-011-0739-7. Epub 2011 Sep 20. PubMed PMID: 21931957.

10: Campo JJ, Aponte JJ, Nhabomba AJ, Sacarlal J, Angulo-Barturen I, Jiménez-Díaz MB, Alonso PL, Dobaño C. Feasibility of flow cytometry for measurements of Plasmodium falciparum parasite burden in studies in areas of malaria endemicity by use of bidimensional assessment of YOYO-1 and autofluorescence. J Clin Microbiol. 2011 Mar;49(3):968-74. doi: 10.1128/JCM.01961-10. Epub 2011 Jan 12. PubMed PMID: 21227985; PubMed Central PMCID: PMC3067720.

11: Reuter M, Dryden DT. The kinetics of YOYO-1 intercalation into single molecules of double-stranded DNA. Biochem Biophys Res Commun. 2010 Dec 10;403(2):225-9. doi: 10.1016/j.bbrc.2010.11.015. Epub 2010 Nov 10. PubMed PMID: 21073861.

12: Günther K, Mertig M, Seidel R. Mechanical and structural properties of YOYO-1 complexed DNA. Nucleic Acids Res. 2010 Oct;38(19):6526-32. doi: 10.1093/nar/gkq434. Epub 2010 May 28. PubMed PMID: 20511588; PubMed Central PMCID: PMC2965214.

13: Murade CU, Subramaniam V, Otto C, Bennink ML. Force spectroscopy and fluorescence microscopy of dsDNA-YOYO-1 complexes: implications for the structure of dsDNA in the overstretching region. Nucleic Acids Res. 2010 Jun;38(10):3423-31. doi: 10.1093/nar/gkq034. Epub 2010 Feb 2. PubMed PMID: 20129944; PubMed Central PMCID: PMC2879515.

14: Xie L, Li Q, Johnson J, Zhang J, Milhous W, Kyle D. Development and validation of flow cytometric measurement for parasitaemia using autofluorescence and YOYO-1 in rodent malaria. Parasitology. 2007 Aug;134(Pt 9):1151-62. Epub 2007 Apr 20. PubMed PMID: 17445324.

15: Li Q, Gerena L, Xie L, Zhang J, Kyle D, Milhous W. Development and validation of flow cytometric measurement for parasitemia in cultures of P. falciparum vitally stained with YOYO-1. Cytometry A. 2007 May;71(5):297-307. PubMed PMID: 17279569.

16: Gichner T, Mukherjee A, Velemínský J. DNA staining with the fluorochromes EtBr, DAPI and YOYO-1 in the comet assay with tobacco plants after treatment with ethyl methanesulphonate, hyperthermia and DNase-I. Mutat Res. 2006 Jun 16;605(1-2):17-21. Epub 2006 Mar 29. PubMed PMID: 16574466.

17: Jiménez-Díaz MB, Rullas J, Mulet T, Fernández L, Bravo C, Gargallo-Viola D, Angulo-Barturen I. Improvement of detection specificity of Plasmodium-infected murine erythrocytes by flow cytometry using autofluorescence and YOYO-1. Cytometry A. 2005 Sep;67(1):27-36. PubMed PMID: 16082714.

18: Lakowicz JR, Malicka J, Gryczynski I. Increased intensities of YOYO-1-labeled DNA oligomers near silver particles. Photochem Photobiol. 2003 Jun;77(6):604-7. PubMed PMID: 12870845; PubMed Central PMCID: PMC2753835.

19: Sauvaigo S, Petec-Calin C, Caillat S, Odin F, Cadet J. Comet assay coupled to repair enzymes for the detection of oxidative damage to DNA induced by low doses of gamma-radiation: use of YOYO-1, low-background slides, and optimized electrophoresis conditions. Anal Biochem. 2002 Apr 1;303(1):107-9. PubMed PMID: 11906159.

20: Yoshinaga N, Akitaya T, Yoshikawa K. Intercalating fluorescence dye YOYO-1 prevents the folding transition in giant duplex DNA. Biochem Biophys Res Commun. 2001 Aug 17;286(2):264-7. PubMed PMID: 11500031.