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MedKoo Cat#: 145422 | Name: Wybutosine

Description:

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

Wybutosine is a tricyclic nucleoside with a large side chain found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. Wybutosine is a hyper modified guanosine. Wybutosine supports reading frame maintenance by stabilizing codon-anticodon interactions during decoding on the ribosome. Five different enzymes are needed to form a final product of Wybutosine.

Chemical Structure

Wybutosine
Wybutosine
CAS#55196-46-8

Theoretical Analysis

MedKoo Cat#: 145422

Name: Wybutosine

CAS#: 55196-46-8

Chemical Formula: C21H28N6O9

Exact Mass: 508.1918

Molecular Weight: 508.49

Elemental Analysis: C, 49.60; H, 5.55; N, 16.53; O, 28.32

Price and Availability

This product is currently not in stock but may be available through custom synthesis. To ensure cost efficiency, the minimum order quantity is 1 gram. The estimated lead time is 2 to 4 months, with pricing dependent on the complexity of the synthesis (typically high for intricate chemistries). Quotes for quantities below 1 gram will not be provided. To request a quote, please click the button below. Note: If this product becomes available in stock in the future, pricing will be listed accordingly.
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Related CAS #
No Data
Synonym
Wybutosine; Nucleoside Y;
IUPAC/Chemical Name
methyl (S)-4-(3-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-4,6-dimethyl-9-oxo-4,9-dihydro-3H-imidazo[1,2-a]purin-7-yl)-2-((methoxycarbonyl)amino)butanoate
InChi Key
QAOHCFGKCWTBGC-QHOAOGIMSA-N
InChi Code
1S/C21H28N6O9/c1-9-11(6-5-10(19(32)34-3)24-21(33)35-4)27-17(31)13-16(25(2)20(27)23-9)26(8-22-13)18-15(30)14(29)12(7-28)36-18/h8,10,12,14-15,18,28-30H,5-7H2,1-4H3,(H,24,33)/t10-,12+,14+,15+,18+/m0/s1
SMILES Code
COC(=O)N[C@@H](CCC1=C(C)N=C2N1C(=O)C3=C(N(C=N3)[C@@H]4O[C@H](CO)[C@@H](O)[C@H]4O)N2C)C(=O)OC
Appearance
To be determined
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
To be determined
Shelf Life
>2 years if stored properly
Drug Formulation
To be determined
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
More Info

Preparing Stock Solutions

The following data is based on the product molecular weight 508.49 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
1: Perche-Letuvée P, Molle T, Forouhar F, Mulliez E, Atta M. Wybutosine biosynthesis: structural and mechanistic overview. RNA Biol. 2014;11(12):1508-18. doi: 10.4161/15476286.2014.992271. PMID: 25629788; PMCID: PMC4615248. 2: Young AP, Bandarian V. Radical mediated ring formation in the biosynthesis of the hypermodified tRNA base wybutosine. Curr Opin Chem Biol. 2013 Aug;17(4):613-8. doi: 10.1016/j.cbpa.2013.05.035. Epub 2013 Jul 12. PMID: 23856057; PMCID: PMC4320972. 3: Sun C, Guo R, Ye X, Tang S, Chen M, Zhou P, Yang M, Liao C, Li H, Lin B, Zang C, Qi Y, Han D, Sun Y, Li N, Zhu D, Xu K, Hu H. Wybutosine hypomodification of tRNAphe activates HERVK and impairs neuronal differentiation. iScience. 2024 Apr 16;27(5):109748. doi: 10.1016/j.isci.2024.109748. PMID: 38706838; PMCID: PMC11066470. 4: Nostramo RT, Hopper AK. A Simple Method for the Detection of Wybutosine- Modified tRNAPheGAA as a Readout of Retrograde tRNA Nuclear Import and Re-export: HCl/Aniline Cleavage and Nonradioactive Northern Hybridization. Methods Mol Biol. 2023;2666:1-14. doi: 10.1007/978-1-0716-3191-1_1. PMID: 37166653; PMCID: PMC10370157. 5: Fandilolu PM, Kamble AS, Dound AS, Sonawane KD. Role of Wybutosine and Mg2+ Ions in Modulating the Structure and Function of tRNAPhe: A Molecular Dynamics Study. ACS Omega. 2019 Dec 2;4(25):21327-21339. doi: 10.1021/acsomega.9b02238. PMID: 31867527; PMCID: PMC6921629. 6: Young AP, Bandarian V. TYW1: A Radical SAM Enzyme Involved in the Biosynthesis of Wybutosine Bases. Methods Enzymol. 2018;606:119-153. doi: 10.1016/bs.mie.2018.04.024. Epub 2018 Jun 6. PMID: 30097090; PMCID: PMC6448148. 7: Noma A, Kirino Y, Ikeuchi Y, Suzuki T. Biosynthesis of wybutosine, a hyper- modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 2006 May 17;25(10):2142-54. doi: 10.1038/sj.emboj.7601105. Epub 2006 Apr 27. PMID: 16642040; PMCID: PMC1462984. 8: Tuorto F, Lyko F. Genome recoding by tRNA modifications. Open Biol. 2016 Dec;6(12):160287. doi: 10.1098/rsob.160287. PMID: 27974624; PMCID: PMC5204126. 9: Noma A, Suzuki T. Ribonucleome analysis identified enzyme genes responsible for wybutosine synthesis. Nucleic Acids Symp Ser (Oxf). 2006;(50):65-6. doi: 10.1093/nass/nrl032. PMID: 17150819. 10: Iyer LM, Abhiman S, de Souza RF, Aravind L. Origin and evolution of peptide- modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase. Nucleic Acids Res. 2010 Sep;38(16):5261-79. doi: 10.1093/nar/gkq265. Epub 2010 Apr 27. PMID: 20423905; PMCID: PMC2938197. 11: Kalhor HR, Penjwini M, Clarke S. A novel methyltransferase required for the formation of the hypermodified nucleoside wybutosine in eucaryotic tRNA. Biochem Biophys Res Commun. 2005 Aug 26;334(2):433-40. doi: 10.1016/j.bbrc.2005.06.111. PMID: 16005430. 12: Hienzsch A, Deiml C, Reiter V, Carell T. Total synthesis of the hypermodified RNA bases wybutosine and hydroxywybutosine and their quantification together with other modified RNA bases in plant materials. Chemistry. 2013 Mar 25;19(13):4244-8. doi: 10.1002/chem.201204209. Epub 2013 Feb 18. PMID: 23417961. 13: Urbonavičius J, Tauraitė D. Biochemical Pathways Leading to the Formation of Wyosine Derivatives in tRNA of Archaea. Biomolecules. 2020 Dec 2;10(12):1627. doi: 10.3390/biom10121627. PMID: 33276555; PMCID: PMC7761594. 14: Suzuki Y, Noma A, Suzuki T, Ishitani R, Nureki O. Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4. Nucleic Acids Res. 2009 May;37(9):2910-25. doi: 10.1093/nar/gkp158. Epub 2009 Mar 14. PMID: 19287006; PMCID: PMC2685095. 15: Rodriguez V, Vasudevan S, Noma A, Carlson BA, Green JE, Suzuki T, Chandrasekharappa SC. Structure-function analysis of human TYW2 enzyme required for the biosynthesis of a highly modified Wybutosine (yW) base in phenylalanine- tRNA. PLoS One. 2012;7(6):e39297. doi: 10.1371/journal.pone.0039297. Epub 2012 Jun 28. PMID: 22761755; PMCID: PMC3386263. 16: Umitsu M, Nishimasu H, Noma A, Suzuki T, Ishitani R, Nureki O. Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2. Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15616-21. doi: 10.1073/pnas.0905270106. Epub 2009 Aug 26. PMID: 19717466; PMCID: PMC2747168. 17: Djumagulov M, Demeshkina N, Jenner L, Rozov A, Yusupov M, Yusupova G. Accuracy mechanism of eukaryotic ribosome translocation. Nature. 2021 Dec;600(7889):543-546. doi: 10.1038/s41586-021-04131-9. Epub 2021 Dec 1. PMID: 34853469; PMCID: PMC8674143. 18: Landgraf BJ, McCarthy EL, Booker SJ. Radical S-Adenosylmethionine Enzymes in Human Health and Disease. Annu Rev Biochem. 2016 Jun 2;85:485-514. doi: 10.1146/annurev-biochem-060713-035504. Epub 2016 May 4. PMID: 27145839. 19: Han L, Phizicky EM. A rationale for tRNA modification circuits in the anticodon loop. RNA. 2018 Oct;24(10):1277-1284. doi: 10.1261/rna.067736.118. Epub 2018 Jul 19. PMID: 30026310; PMCID: PMC6140457. 20: Wang P, Shah GL, Landau H, Coulter ME, Walsh CA, Roider E, Kramer CS, Beuning PJ, Giese RW. Jettison-MS of Nucleic Acid Species. J Am Soc Mass Spectrom. 2020 Jul 9. doi: 10.1021/jasms.0c00084. Epub ahead of print. PMID: 32551641.