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Chemical Compound Review

thymine     5-methyl-1H-pyrimidine-2,4- dione

Synonyms: Thymin, Thymine-t, CHEMBL993, PubChem9313, Thymine-2-14C, ...
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Disease relevance of thymine

  • Ultraviolet irradiation forms covalent crosslinks between E. coli RNA polymerase and the lac UV5 promoter substituted with bromouracil in the place of thymine [1].
  • McArdle's disease is genetically heterogeneous, but the most common mutation is the substitution of thymine for cytosine at codon 49 [2].
  • The linkages are susceptible to direct photoreversal by 254 nm UV, as expected for cyclobutane-type thymine dimers, but they are not cleaved by the bacteriophage T4 endonuclease V, a dimer-specific DNA repair enzyme [3].
  • Excision of thymine dimers from specifically incised DNA by extracts of xeroderma pigmentosum cells [4].
  • In 24 (69%) of the 35 papillary thyroid carcinomas examined, we found a missense thymine (T)-->adenine (A) transversion at nucleotide 1796 in the BRAF gene (T1796A) [5].

Psychiatry related information on thymine

  • The reactivity of FCDI with the guanine bases was smaller than that with the thymine ones and the prolongation of the reaction time resulted in a lower yield [6].
  • Our previous study suggested that the tumour necrosis factor-alpha gene with thymine residue at position -857 in its promoter region [TNF-alpha(-857T)] could be associated with human narcolepsy independently of a strong association of the human leucocyte antigen (HLA)-DRB1*1501 with the disorder [7].

High impact information on thymine

  • Dpo4 is also captured in the crystal translocating two template bases to the active site at once, suggesting a possible mechanism for bypassing thymine dimers [8].
  • Vertebrate genomic DNA is generally CpG depleted, possibly because methylation of cytosines at 80% of CpG dinucleotides results in their frequent mutation to thymine, and thus CpG to TpG dinucleotides [9].
  • In E. coli, the enzyme recognizes a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine [10].
  • Analysis of 347 plaques obtained after transfection of this modified DNA indicated that mispairs were corrected in 343 cases (99%), revealing 314 repair events in favor of guanine (90%) and 29 in favor of thymine (8%) [11].
  • The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites [12].

Chemical compound and disease context of thymine


Biological context of thymine

  • TFIID binding shows phosphate contacts with the same residues that were found to be essential for TFIID interactions by methylation and thymine-specific modification interference assays [18].
  • Age-dependent excision repair of damaged thymine from gamma-irradiated DNA by isolated nuclei from human fibroblasts [19].
  • Hydrolytic deamination of 5-methylcytosine bases in DNA leads to thymine residues, and hence to T/G mismatches, pre-mutagenic DNA lesions consisting of two natural DNA constituents and thus devoid of an obvious marker of the damaged DNA strand [20].
  • Recombinant human DNA polymerase eta corrects the inability of XP-V cell extracts to carry out DNA replication by bypassing thymine dimers on damaged DNA [21].
  • We report here that thymidine oligonucleotides annealed to polydeoxyadenylate can be ligated end-to-end by UV irradiation, via thymine dimerization of the terminal nucleotides in adjacent oligonucleotides [3].

Anatomical context of thymine

  • Using an improved cell-free assay for trans-lesion DNA synthesis, we have recently isolated a DNA polymerase from HeLa cells that continues replication on damaged DNA by bypassing ultraviolet-induced thymine dimers in XP-V cell extracts [21].
  • Induction and repair of thymine glycols were studied in irradiated A549 cells (a human lung carcinoma cell line) [22].
  • Since 1971 thymine-requiring (thy-) pathogens have been isolated from the urine of 8 patients with renal calculi, and from the sputum of 1 patient with chronic chest infection [23].
  • Crude extracts of normal human diploid fibroblasts and of human peripheral blood lymphocytes excise thymine dimers from purified ultraviolet-irradiated DNA, or from the DNA presumably present as chromatin in unfractionated cell-free preparations of cells that had been labeled with [3H]thymidine [24].
  • Thymine glycols were produced in DNA in a dose-dependent manner after exposure of human mammary epithelial cells to benzo[a]pyrene [25].

Associations of thymine with other chemical compounds


Gene context of thymine

  • This structure indicates a more invasive interaction with dsDNA than observed with other UDGs and reveals an elegant water displacement/replacement mechanism that allows SMUG1 to exclude thymine from its active site while accepting HmU [32].
  • DME and ROS1 show a preference for 5-meC over thymine in the symmetric dinucleotide CpG context, where most plant DNA methylation occurs [33].
  • The ER mutant HE84, which contains a single amino acid exchange, Glu-203 to Gly, in the knuckle of ER, creates a promiscuous ER that is able to bind to GRE/PREs by contacting this thymine [34].
  • Using reverse transcription-PCR, single-strand conformational polymorphism, and sequencing analysis, the COOH-terminal domain of SMAD4 was found to be mutated: a single thymine was inserted between nt 1521 and 1522 in 2 of 20 tumors analyzed [35].
  • Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4 [36].

Analytical, diagnostic and therapeutic context of thymine


  1. The molecular topography of RNA polymerase-promoter interaction. Simpson, R.B. Cell (1979) [Pubmed]
  2. Molecular genetic heterogeneity of myophosphorylase deficiency (McArdle's disease). Tsujino, S., Shanske, S., DiMauro, S. N. Engl. J. Med. (1993) [Pubmed]
  3. Ligation of oligonucleotides by pyrimidine dimers--a missing 'link' in the origin of life? Lewis, R.J., Hanawalt, P.C. Nature (1982) [Pubmed]
  4. Excision of thymine dimers from specifically incised DNA by extracts of xeroderma pigmentosum cells. Cook, K., Friedberg, E.C., Cleaver, J.E. Nature (1975) [Pubmed]
  5. BRAF mutation in papillary thyroid carcinoma. Cohen, Y., Xing, M., Mambo, E., Guo, Z., Wu, G., Trink, B., Beller, U., Westra, W.H., Ladenson, P.W., Sidransky, D. J. Natl. Cancer Inst. (2003) [Pubmed]
  6. Investigation of ferrocenyl carbodiimide (FCDI) in the modification reaction of nucleic acids. Mukumoto, K., Nojima, T., Takenaka, S. Nucleic acids symposium series (2004) (2005) [Pubmed]
  7. Haplotype analyses with the human leucocyte antigen and tumour necrosis factor-alpha genes in narcolepsy families. Hohjoh, H., Terada, N., Miki, T., Honda, Y., Tokunaga, K. Psychiatry and clinical neurosciences. (2001) [Pubmed]
  8. Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Ling, H., Boudsocq, F., Woodgate, R., Yang, W. Cell (2001) [Pubmed]
  9. Large-scale human promoter mapping using CpG islands. Ioshikhes, I.P., Zhang, M.Q. Nat. Genet. (2000) [Pubmed]
  10. Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex. Tsutakawa, S.E., Jingami, H., Morikawa, K. Cell (1999) [Pubmed]
  11. A specific mismatch repair event protects mammalian cells from loss of 5-methylcytosine. Brown, T.C., Jiricny, J. Cell (1987) [Pubmed]
  12. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Hendrich, B., Hardeland, U., Ng, H.H., Jiricny, J., Bird, A. Nature (1999) [Pubmed]
  13. High-fidelity in vivo replication of DNA base shape mimics without Watson-Crick hydrogen bonds. Delaney, J.C., Henderson, P.T., Helquist, S.A., Morales, J.C., Essigmann, J.M., Kool, E.T. Proc. Natl. Acad. Sci. U.S.A. (2003) [Pubmed]
  14. Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. Ostrander, E.A., Jong, P.M., Rine, J., Duyk, G. Proc. Natl. Acad. Sci. U.S.A. (1992) [Pubmed]
  15. Genetic effects of thymine glycol: site-specific mutagenesis and molecular modeling studies. Basu, A.K., Loechler, E.L., Leadon, S.A., Essigmann, J.M. Proc. Natl. Acad. Sci. U.S.A. (1989) [Pubmed]
  16. Bromodeoxyuridine mutagenesis in mammalian cells: mutagenesis is independent of the amount of bromouracil in DNA. Kaufman, E.R., Davidson, R.L. Proc. Natl. Acad. Sci. U.S.A. (1978) [Pubmed]
  17. Base excision of oxidative purine and pyrimidine DNA damage in Saccharomyces cerevisiae by a DNA glycosylase with sequence similarity to endonuclease III from Escherichia coli. Eide, L., Bjørås, M., Pirovano, M., Alseth, I., Berdal, K.G., Seeberg, E. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  18. Interaction of TFIID in the minor groove of the TATA element. Lee, D.K., Horikoshi, M., Roeder, R.G. Cell (1991) [Pubmed]
  19. Age-dependent excision repair of damaged thymine from gamma-irradiated DNA by isolated nuclei from human fibroblasts. Mattern, M.R., Cerutti, P.A. Nature (1975) [Pubmed]
  20. The vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease. Hennecke, F., Kolmar, H., Bründl, K., Fritz, H.J. Nature (1991) [Pubmed]
  21. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase eta. Masutani, C., Kusumoto, R., Yamada, A., Dohmae, N., Yokoi, M., Yuasa, M., Araki, M., Iwai, S., Takio, K., Hanaoka, F. Nature (1999) [Pubmed]
  22. Inducible repair of thymine glycol detected by an ultrasensitive assay for DNA damage. Le, X.C., Xing, J.Z., Lee, J., Leadon, S.A., Weinfeld, M. Science (1998) [Pubmed]
  23. Thymine-requiring bacteria associated with co-trimoxazole therapy. Maskell, R., Okubadejo, O.A., Payne, R.H. Lancet (1976) [Pubmed]
  24. Defective thymine dimer excision by cell-free extracts of xeroderma pigmentosum cells. Mortelmans, K., Friedberg, E.C., Slor, H., Thomas, G., Cleaver, J.E. Proc. Natl. Acad. Sci. U.S.A. (1976) [Pubmed]
  25. Production of oxidative DNA damage during the metabolic activation of benzo[a]pyrene in human mammary epithelial cells correlates with cell killing. Leadon, S.A., Stampfer, M.R., Bartley, J. Proc. Natl. Acad. Sci. U.S.A. (1988) [Pubmed]
  26. In vivo synthesis and properties of uracil-containing DNA. Warner, H.R., Duncan, B.K. Nature (1978) [Pubmed]
  27. Reverse banding on chromosomes produced by a guanosine-cytosine specific DNA binding antibiotic: olivomycin. van de Sande, J.H., Lin, C.C., Jorgenson, K.F. Science (1977) [Pubmed]
  28. The unusual varl gene of yeast mitochondrial DNA. Butow, R.A., Perlman, P.S., Grossman, L.I. Science (1985) [Pubmed]
  29. Echinomycin binding sites on DNA. Van Dyke, M.M., Dervan, P.B. Science (1984) [Pubmed]
  30. Yeast DNA polymerase zeta (zeta) is essential for error-free replication past thymine glycol. Johnson, R.E., Yu, S.L., Prakash, S., Prakash, L. Genes Dev. (2003) [Pubmed]
  31. Ring opening of the cyclobutane in a thymine dimer radical anion. Chatgilialoglu, C., Guerra, M., Kaloudis, P., Houée-Lévin, C., Marignier, J.L., Swaminathan, V.N., Carell, T. Chemistry (2007) [Pubmed]
  32. Structure and specificity of the vertebrate anti-mutator uracil-DNA glycosylase SMUG1. Wibley, J.E., Waters, T.R., Haushalter, K., Verdine, G.L., Pearl, L.H. Mol. Cell (2003) [Pubmed]
  33. DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases. Morales-Ruiz, T., Ortega-Galisteo, A.P., Ponferrada-Marín, M.I., Martínez-Macías, M.I., Ariza, R.R., Roldán-Arjona, T. Proc. Natl. Acad. Sci. U.S.A. (2006) [Pubmed]
  34. Functional interaction of hybrid response elements with wild-type and mutant steroid hormone receptors. Truss, M., Chalepakis, G., Slater, E.P., Mader, S., Beato, M. Mol. Cell. Biol. (1991) [Pubmed]
  35. A novel SMAD4 gene mutation in seminoma germ cell tumors. Bouras, M., Tabone, E., Bertholon, J., Sommer, P., Bouvier, R., Droz, J.P., Benahmed, M. Cancer Res. (2000) [Pubmed]
  36. Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4. Wu, P., Qiu, C., Sohail, A., Zhang, X., Bhagwat, A.S., Cheng, X. J. Biol. Chem. (2003) [Pubmed]
  37. Thymine glycol and thymidine glycol in human and rat urine: a possible assay for oxidative DNA damage. Cathcart, R., Schwiers, E., Saul, R.L., Ames, B.N. Proc. Natl. Acad. Sci. U.S.A. (1984) [Pubmed]
  38. Enhancement of DNA repair in human skin cells by thymidine dinucleotides: evidence for a p53-mediated mammalian SOS response. Eller, M.S., Maeda, T., Magnoni, C., Atwal, D., Gilchrest, B.A. Proc. Natl. Acad. Sci. U.S.A. (1997) [Pubmed]
  39. Molecular and cellular basis for type I heparin cofactor II deficiency (heparin cofactor II Awaji). Kondo, S., Tokunaga, F., Kario, K., Matsuo, T., Koide, T. Blood (1996) [Pubmed]
  40. Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Gitan, R.S., Shi, H., Chen, C.M., Yan, P.S., Huang, T.H. Genome Res. (2002) [Pubmed]
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