5-Bromouridine

5-Bromouridine
Names
	IUPAC name 5-Bromouridine
	Systematic IUPAC name 1-[(2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-bromoimidazole-2,4(1H,3H)-dione
	Other names 5-Bromouracil ribonucleoside; 1-β-Ribofuranosyl-5-bromo-uracil; 5-Bromouridin
Identifiers
CAS Number	957-75-5 ;
3D model (JSmol)	Interactive image;
Abbreviations	BrUrd
Beilstein Reference	33664
ChEBI	CHEBI:20553;
ChemSpider	82616;
ECHA InfoCard	100.012.260
EC Number	213-486-6;
PubChem CID	91494;
UNII	KEY8PG1BRC ;
CompTox Dashboard (EPA)	DTXSID401317210 ;
	InChI InChI=1S/C9H11BrN2O6/c10-3-1-12(9(17)11-7(3)16)8-6(15)5(14)4(2-13)18-8/h1,4-6,8,13-15H,2H2,(H,11,16,17)/t4-,5-,6-,8-/m1/s1 Key: AGFIRQJZCNVMCW-UAKXSSHOSA-N; InChI=1/C9H11BrN2O6/c10-3-1-12(9(17)11-7(3)16)8-6(15)5(14)4(2-13)18-8/h1,4-6,8,13-15H,2H2,(H,11,16,17)/t4-,5-,6-,8-/m1/s1 Key: AGFIRQJZCNVMCW-UAKXSSHOBS;
	SMILES BrC=1C(=O)NC(=O)N(C=1)[C@@H]2O[C@@H]([C@@H](O)[C@H]2O)CO;
Properties
Chemical formula	C9H11BrN2O6
Molar mass	323.099 g·mol−1
Appearance	Crystalline, white solid
Density	2.043 g/cm3
Melting point	180 to 182 °C (356 to 360 °F; 453 to 455 K) (decomposes)
Chiral rotation ([α]D)	[α]22/D −11°, c = 2 in H2O
Hazards
Autoignition; temperature	Hazardous decomposition products formed under fire conditions. - Carbon oxides, nitrogen oxides (NOx), Hydrogen bromide gas
	Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). Infobox references

5-Bromouridine (abbreviated BrUrd, 5BrU, br5Urd or rarely the one letter code B)^[2] is a uridine derivative with a bromo substituent at the fifth carbon.^[3] BrUrd is incorporated into RNA and can be detected immunocytochemically and analysed by cytometry. It causes DNA damage through base substitution and increases the number of mutations.^[4]

Uses

Detecting half-Life activity

5-Bromouridine has also been used to detect the half-life of RNA molecules. In a method called 5'-bromo-uridine immunoprecipitation chase-deep sequencing analysis (BRIC-seq), 5'-bromouridine is used to label RNA and enable the measurement of RNA levels over time. This method was used in Tani et al.'s study determining RNA half-lives to investigate the function of non-coding RNAs.^[5]

Splicing of pre-mRNA

5-Bromouridine was also used to study in vitro splicing of pre-mRNA in a study by Wansink. 5-Bromoruridine 5'-triphosphate (BruUTP) was used to label pre-mRNA and investigate the efficiency of splicing. They found that splicing is inhibited if uridines in RNA transcript were replaced by BrU, which suggested that Us were critical for the splicing reaction.^[6]

Detection of RNA synthesis in individual cells

Incorporation of 5-bromouridine by individual cells was detected immunocytochemically using antibodies against BrdU followed by flow cytometry.^[7]

References

^ 5-bromouridine in Linstrom, Peter J.; Mallard, William G. (eds.); NIST Chemistry WebBook, NIST Standard Reference Database Number 69, National Institute of Standards and Technology, Gaithersburg (MD) (retrieved 2012)
^ IUPAC-IUB Commission on Biochemical Nomenclature (1970). "Abbreviations and symbols for nucleic acids, polynucleotides, and their constituents". Biochemistry. 9 (20): 4022–4027. doi:10.1021/bi00822a023.
^ CSID:82616, http://www.chemspider.com/Chemical-Structure.82616.html (accessed 22:51, Oct 19, 2012)
^ "5-bromouridine (CHEBI:20553)." EBI.ac.uk. European Bioinformatics Institute, 30 Nov. 2010. Web. 26 Oct. 2012.<http://www.ebi.ac.uk/chebi/advancedSearchFT.do;jsessionid=29B3462C81CE2E1F80223B50A927F832?chebiId=20553&structureSearchMethod=substructure>
^ Tani, H; Mizutani, R; Salam, KA; Tano, K; Ijiri, K; Wakamatsu, A; Isogai, T; Suzuki, Y; Akimitsu, N (2012). "Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals". Genome Research. 22 (5): 947–56. doi:10.1101/gr.130559.111. PMC 3337439. PMID 22369889.
^ Wansink, DG; Nelissen, RL; De Jong, L (1994). "In vitro splicing of pre-mRNA containing bromouridine". Molecular Biology Reports. 19 (2): 109–13. doi:10.1007/BF00997156. hdl:11245/1.105890. PMID 8072491. S2CID 10367635.
^ Larsen, J. K.; Jensen, P. Ø.; Larsen, J (2001). Flow cytometric analysis of RNA synthesis by detection of bromouridine incorporation. Vol. 12. pp. 7.12.1–7.12.11. doi:10.1002/0471142956.cy0712s12. ISBN 978-0471142959. PMID 18770724. S2CID 39703414. {{cite book}}: |journal= ignored (help)

External links

5-bromouridine in Linstrom, Peter J.; Mallard, William G. (eds.); NIST Chemistry WebBook, NIST Standard Reference Database Number 69, National Institute of Standards and Technology, Gaithersburg (MD) (retrieved 2012)

[1] 5-bromouridine in Linstrom, Peter J.; Mallard, William G. (eds.); NIST Chemistry WebBook, NIST Standard Reference Database Number 69, National Institute of Standards and Technology, Gaithersburg (MD) (retrieved 2012)

[2] IUPAC-IUB Commission on Biochemical Nomenclature (1970). "Abbreviations and symbols for nucleic acids, polynucleotides, and their constituents". Biochemistry. 9 (20): 4022–4027. doi:10.1021/bi00822a023.

[3] CSID:82616, http://www.chemspider.com/Chemical-Structure.82616.html (accessed 22:51, Oct 19, 2012)

[4] "5-bromouridine (CHEBI:20553)." EBI.ac.uk. European Bioinformatics Institute, 30 Nov. 2010. Web. 26 Oct. 2012.<http://www.ebi.ac.uk/chebi/advancedSearchFT.do;jsessionid=29B3462C81CE2E1F80223B50A927F832?chebiId=20553&structureSearchMethod=substructure>

[5] Tani, H; Mizutani, R; Salam, KA; Tano, K; Ijiri, K; Wakamatsu, A; Isogai, T; Suzuki, Y; Akimitsu, N (2012). "Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals". Genome Research. 22 (5): 947–56. doi:10.1101/gr.130559.111. PMC 3337439. PMID 22369889.

[6] Wansink, DG; Nelissen, RL; De Jong, L (1994). "In vitro splicing of pre-mRNA containing bromouridine". Molecular Biology Reports. 19 (2): 109–13. doi:10.1007/BF00997156. hdl:11245/1.105890. PMID 8072491. S2CID 10367635.

[7] Larsen, J. K.; Jensen, P. Ø.; Larsen, J (2001). Flow cytometric analysis of RNA synthesis by detection of bromouridine incorporation. Vol. 12. pp. 7.12.1–7.12.11. doi:10.1002/0471142956.cy0712s12. ISBN 978-0471142959. PMID 18770724. S2CID 39703414. {{cite book}}: |journal= ignored (help)

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