Pyrimidine dimer: Difference between revisions

From Wikipedia, the free encyclopedia
Browse history interactively
← Previous editNext edit →
Content deleted Content added
VisualWikitext
Reconstructed a paragraph and expanded on XP, added in a source for that. Also added in a paragraph about translesion synthesis which is also used in DNA repair due to dimerization.
Added in more information regarding how sunscreen works to reduce dna damage from UV on a molecular level, and added in a source for it.
Line 133: Line 133:


== Effect of topical sunscreen and effect of absorbed sunscreen ==
== Effect of topical sunscreen and effect of absorbed sunscreen ==
Direct DNA damage is reduced by sunscreen. This prevents sunburn. When the sunscreen is at the surface of the skin, it filters the UV rays, which attenuates the intensity. Even when the sunscreen molecules have penetrated into the skin, they protect against direct DNA damage, because the UV light is absorbed by the sunscreen and not by the DNA.<ref name=KnowlandGulston1999>{{cite journal |vauthors=Gulston M, Knowland J |date=July 1999 |title= Illumination of human keratinocytes in the presence of the sunscreen ingredient Padimate-O and through an SPF-15 sunscreen reduces direct photodamage to DNA but increases strand breaks |journal=Mutat. Res. |volume= 444 |issue=1 |pages=49–60 |pmid=10477339 |doi=10.1016/s1383-5718(99)00091-1}}</ref>
Direct DNA damage is reduced by sunscreen, which also reduces the risk of developing a sunburn. When the sunscreen is at the surface of the skin, it filters the UV rays, which attenuates the intensity. Even when the sunscreen molecules have penetrated into the skin, they protect against direct DNA damage, because the UV light is absorbed by the sunscreen and not by the DNA.<ref name=KnowlandGulston1999>{{cite journal |vauthors=Gulston M, Knowland J |date=July 1999 |title= Illumination of human keratinocytes in the presence of the sunscreen ingredient Padimate-O and through an SPF-15 sunscreen reduces direct photodamage to DNA but increases strand breaks |journal=Mutat. Res. |volume= 444 |issue=1 |pages=49–60 |pmid=10477339 |doi=10.1016/s1383-5718(99)00091-1}}</ref>Sunscreen primarily works by absorbing the UV light from the sun through the use of organic compounds, such as oxybenzone or avobenzone. These compounds are able to absorb UV energy from the sun and transition into higher-energy states. Eventually, these molecules return to lower energy states, and in doing so, the initial energy from the UV light can be transformed into heat. This process of absorption works to reduce the risk of DNA damage and the formation of pyrimidine dimers. UVA light makes up 95% of the UV light that reaches earth, whereas UVB light makes up only about 5%. UVB light is the form of UV light that is responsible for tanning and burning. Sunscreens work to protect from both UVA and UVB rays. Overall, sunburns exemplify DNA damage caused by UV rays, and this damage can come in the form of free radical species, as well as dimerization of adjacent nucleotides.<ref>{{Cite journal |last=Sander |first=Megan |last2=Sander |first2=Michael |last3=Burbidge |first3=Toni |last4=Beecker |first4=Jennifer |date=2020-12-14 |title=The efficacy and safety of sunscreen use for the prevention of skin cancer |url=http://www.cmaj.ca/lookup/doi/10.1503/cmaj.201085 |journal=Canadian Medical Association Journal |language=en |volume=192 |issue=50 |pages=E1802–E1808 |doi=10.1503/cmaj.201085 |issn=0820-3946 |pmc=PMC7759112 |pmid=33318091}}</ref>


== See also ==
== See also ==

Revision as of 20:57, 28 April 2023

Formation of thymine dimer lesion in DNA. The photon causes two consecutive bases on one strand to bind together, destroying the normal base-pairing double-strand structure in that area.

Pyrimidine dimers are molecular lesions formed from thymine or cytosine bases in DNA via photochemical reactions,[1][2] commonly associated with direct DNA damage.[3] Ultraviolet light (UV; particularly UVC) induces the formation of covalent linkages between consecutive bases along the nucleotide chain in the vicinity of their carbon–carbon double bonds.[4] The photo-coupled dimers are fluorescent.[5] The dimerization reaction can also occur among pyrimidine bases in dsRNA (double-stranded RNA)—uracil or cytosine. Two common UV products are cyclobutane pyrimidine dimers (CPDs) and 6–4 photoproducts. These premutagenic lesions alter the structure of the DNA helix and cause non-canonical base pairing. Specifically, adjacent thymines or cytosines in DNA will form a cyclobutane ring when joined together and cause a distortion in the DNA. This distortion prevents replication or transcription machinery beyond the site of the dimerization.[6] Up to 50–100 such reactions per second might occur in a skin cell during exposure to sunlight, but are usually corrected within seconds by photolyase reactivation or nucleotide excision repair. In humans, the most common form of DNA repair is nucleotide excision repair (NER). In contrast, organisms such as bacteria can counterintuitively harvest energy from the sun to fix DNA damage from pyrimidine dimers via photolyase activity. If these lesions are not fixed, polymerase machinery may misread or add in the incorrect nucleotide to the strand. If the damage to the DNA is overwhelming, mutations can arise within the genome of an organism and may lead to the production of cancer cells.[7] Uncorrected lesions can inhibit polymerases, cause misreading during transcription or replication, or lead to arrest of replication. It causes sunburn and it triggers the production of melanin.[8] Pyrimidine dimers are the primary cause of melanomas in humans.

Types of dimers

Left: cyclobutane dimer (CPD). Right: 6,4-dimer (6-4PP)

A cyclobutane pyrimidine dimer (CPD) contains a four membered ring arising from the coupling of the two double-bonded carbons of each of the pyrimidines.[9][10][11] Such dimers interfere with base pairing during DNA replication, leading to mutations.

A 6–4 photoproduct (6–4 pyrimidine–pyrimidone or 6–4 pyrimidine–pyrimidinone) is an alternate dimer consisting of a single covalent bond between the carbon at the 6 position of one ring and carbon at the 4 position of the ring on the next base.[12] This type of conversion occurs at one third the frequency of CPDs but is more mutagenic.[13]

A third type of lesion is a Dewar pyrimidinone, formed by a reversible isomerization of the 6–4 photoproduct upon further exposure to light.[14]

Skin light exposure

Due to the excellent photochemical properties of DNA, this nature-made molecule is damaged by only a tiny fraction of the absorbed photons. DNA transforms more than 99.9% of the photons into harmless heat[15] (but the damage from the remaining < 0.1% is still enough to cause sunburn).[8] The transformation of excitation energy into harmless heat occurs via a photochemical process called internal conversion. In DNA, this internal conversion is extremely fast, and therefore efficient. This ultrafast (subpicosecond) internal conversion is a powerful photoprotection provided by single nucleotides.[15] However, the Ground-State Recovery is much slower (picoseconds) in G·C−DNA duplexes and hairpins.[16] It is presumed to be even slower for double-stranded DNA in conditions of the nucleus. The absorption spectrum of DNA shows a strong absorption for UVB radiation and a much lower absorption for UVA radiation. Since the action spectrum of sunburn is indistinguishable from the absorption spectrum of DNA, it is generally accepted that the direct DNA damages are the cause of sunburn.[8] While the human body reacts to direct DNA damages with a painful warning signal,[8] no such warning signal is generated from indirect DNA damage.

Mutagenesis

Translesion polymerases frequently introduce mutations at pyrimidine dimers, both in prokaryotes (SOS mutagenesis) and in eukaryotes. Although the thymine-thymine CPDs (thymine dimers) are the most frequent lesions caused by UV light, translesion polymerases are biased toward introduction of As, so that TT dimers are often replicated correctly. On the other hand, any cytosine involved in CPDs is prone to be deaminated, inducing a C to T transition.[17]

DNA repair

Further information: DNA repair and ultraviolet light and cancer
Melanoma, a type of skin cancer

Pyrimidine dimers introduce local conformational changes in the DNA structure, which allow recognition of the lesion by repair enzymes.[18] In most organisms (excluding placental mammals such as humans) they can be repaired by photoreactivation.[19] Photoreactivation is a repair process in which photolyase enzymes directly reverse CPDs via photochemical reactions. In addition, there are photolyases that can also repair 6-4 photoproducts of UV induced DNA damage. Photolyase enzymes utilize flavin adenine dinucleotide (FAD) as a cofactor in the repair process. Bacteria and other prokaryotes utilize UV energy to directly excite this FAD molecule. The FAD molecule then gives an electron to the CPD, resulting in radical species of FAD and CPD. The CPD radical anion is then cleaved out and gives it's electron back to FAD, restoring FAD back to its original state.[20] In essence, photolyases use energy from the sun to correct pyrimidine dimerization from UV light. Lesions on the DNA strand are recognized by these enzymes, followed by the absorption of light wavelengths >300 nm (i.e. fluorescent and sunlight). This absorption enables the photochemical reactions to occur, which results in the elimination of the pyrimidine dimer, returning it to its original state.[21]

The UV dose that reduces a population of wild-type yeast cells to 37% survival is equivalent (assuming a Poisson distribution of hits) to the UV dose that causes an average of one lethal hit to each of the cells of the population.[22] The number of pyrimidine dimers induced per haploid genome at this dose was measured as 27,000.[22] A mutant yeast strain defective in the three pathways by which pyrimidine dimers were known to be repaired in yeast was also tested for UV sensitivity. It was found in this case that only one or, at most, two unrepaired pyrimidine dimers per haploid genome are lethal to the cell.[22] These findings thus indicate that the repair of thymine dimers in wild-type yeast is highly efficient.

Nucleotide excision repair, sometimes termed "dark reactivation", is a more general mechanism for repair of lesions and is the most common form of DNA repair for pyrimidine dimers in humans. This process works by using cellular machinery to locate the dimerized nucleotides and excise the lesion. Once the CPD is removed, there is a gap in the DNA strand that must be filled. DNA machinery uses the undamaged complementary strand to synthesize nucleotides off of and consequently fill in the gap on the previously damaged strand.[6]

Xeroderma pigmentosum (XP) is a rare genetic disease in humans in which genes that encode for NER proteins are mutated and result in decreased ability to combat pyrimidine dimers that form as a result of UV damage. Individuals with XP are also at a much higher risk of cancer than others, with a greater than 5,000 fold increased risk of developing skin cancers.[7] Some common features and symptoms of XP include skin discoloration, and the formation of multiple tumors proceeding UV exposure.

A few organisms have other ways to perform repairs:

Another type of repair mechanism that is conserved in humans and other non-mammals is translesion synthesis. Typically, the lesion associated with with the pyrimidine dimer blocks cellular machinery from synthesizing past the damaged site. However, in translesion synthesis, the CPD is bypassed by translesion polymerases, and replication and or transcription machinery can continue past the lesion. One specific translesion DNA polymerase, DNA polymerase η, is deficient in individuals with XPD.[24]

Sunscreen and melanoma

A study by Hanson suggests sunscreen that penetrates into the skin and thereby amplifies the amount of free radicals and oxidative stress [25] contributes to the formation of melanoma, but this idea has not been validated by other researchers.

Effect of topical sunscreen and effect of absorbed sunscreen

Direct DNA damage is reduced by sunscreen, which also reduces the risk of developing a sunburn. When the sunscreen is at the surface of the skin, it filters the UV rays, which attenuates the intensity. Even when the sunscreen molecules have penetrated into the skin, they protect against direct DNA damage, because the UV light is absorbed by the sunscreen and not by the DNA.[26]Sunscreen primarily works by absorbing the UV light from the sun through the use of organic compounds, such as oxybenzone or avobenzone. These compounds are able to absorb UV energy from the sun and transition into higher-energy states. Eventually, these molecules return to lower energy states, and in doing so, the initial energy from the UV light can be transformed into heat. This process of absorption works to reduce the risk of DNA damage and the formation of pyrimidine dimers. UVA light makes up 95% of the UV light that reaches earth, whereas UVB light makes up only about 5%. UVB light is the form of UV light that is responsible for tanning and burning. Sunscreens work to protect from both UVA and UVB rays. Overall, sunburns exemplify DNA damage caused by UV rays, and this damage can come in the form of free radical species, as well as dimerization of adjacent nucleotides.[27]

See also

References

  1. ^ David S. Goodsell (2001). "The Molecular Perspective: Ultraviolet Light and Pyrimidine Dimers". The Oncologist. 6 (3): 298–299. doi:10.1634/theoncologist.6-3-298. PMID 11423677. S2CID 36511461.
  2. ^ E. C. Friedberg; G. C. Walker; W. Siede; R. D. Wood; R. A. Schultz & T. Ellenberger (2006). DNA repair and mutagenesis. Washington: ASM Press. p. 1118. ISBN 978-1-55581-319-2.
  3. ^ Effects of Solar Ultraviolet Photons on Mammalian Cell DNA
  4. ^ S. E. Whitmore; C. S. Potten; C. A. Chadwick; P. T. Strickland; W. L. Morison (2001). "Effect of photoreactivating light on UV radiation-induced alterations in human skin". Photodermatol. Photoimmunol. Photomed. 17 (5): 213–217. doi:10.1111/j.1600-0781.2001.170502.x. PMID 11555330. S2CID 11529493.
  5. ^ Gregory T. Carroll, Angela Mammana (2023). "Intrinsic fluorescence of UV-irradiated DNA". Journal of Photochemistry and Photobiology A. 437: 114484. doi:10.1016/j.jphotochem.2022.114484.
  6. ^ a b Cooper, Geoffrey M. (2000). "DNA Repair". The Cell: A Molecular Approach. 2nd edition.
  7. ^ a b Kemp, Michael G.; Sancar, Aziz (2012-08-15). "DNA excision repair: Where do all the dimers go?". Cell Cycle. 11 (16): 2997–3002. doi:10.4161/cc.21126. ISSN 1538-4101. PMC 3442910. PMID 22825251.{{cite journal}}: CS1 maint: PMC format (link)
  8. ^ a b c d John A. Parrish; Kurt F. Jaenicke; R. Rox Anderson (1982). "Erythema and melanogenesis action spectra of normal human skin". Photochemistry and Photobiology. 36 (2): 187–191. doi:10.1111/j.1751-1097.1982.tb04362.x. PMID 7122713. S2CID 38940583.
  9. ^ R. B. Setlow (1966). "Cyclobutane-Type Pyrimidine Dimers in Polynucleotides". Science. 153 (3734): 379–386. Bibcode:1966Sci...153..379S. doi:10.1126/science.153.3734.379. PMID 5328566. S2CID 11210761.
  10. ^ Expert reviews in molecular medicine (2 December 2002). "Structure of the major UV-induced photoproducts in DNA" (PDF). Cambridge University Press. Archived from the original (PDF) on 21 March 2005.
  11. ^ Christopher Mathews & K.E. Van Holde (1990). Biochemistry (2nd ed.). Benjamin Cummings Publication. p. 1168. ISBN 978-0-8053-5015-9.
  12. ^ R. E. Rycyna; J. L. Alderfer (1985). "UV irradiation of nucleic acids: formation, purification and solution conformational analysis of the '6–4 lesion' of dTpdT". Nucleic Acids Res. 13 (16): 5949–5963. doi:10.1093/nar/13.16.5949. PMC 321925. PMID 4034399.
  13. ^ Van Holde, K. E.; Mathews, Christopher K. (1990). Biochemistry. Menlo Park, Calif: Benjamin/Cummings Pub. Co. ISBN 978-0-8053-5015-9.[pages needed]
  14. ^ J.-S. Taylor; M. Cohrs (1987). "DNA, light and Dewar pyrimidinones: the structure and significance of TpT3". J. Am. Chem. Soc. 109 (9): 2834–2835. doi:10.1021/ja00243a052.
  15. ^ a b "Ultrafast Photodynamics of Nucleic Acids". Archived from the original on 2008-06-05. Retrieved 2008-02-13.
  16. ^ Ground-State Recovery Following UV Excitation is Much Slower in G·C−DNA Duplexes and Hairpins Than in Mononucleotides: Carlos E. Crespo-Hernndez†, Kimberly de La Harpe and Bern Kohler. http://pubs.acs.org/doi/abs/10.1021/ja802183s
  17. ^ J. H. Choi; A. Besaratinia; D. H. Lee; C. S. Lee; G. P. Pfeifer (2006). "The role of DNA polymerase ι in UV mutational spectra". Mutat. Res. 599 (1–2): 58–65. doi:10.1016/j.mrfmmm.2006.01.003. PMID 16472831.
  18. ^ Kemmink Johan; Boelens Rolf; Koning Thea M.G.; Kaptein Robert; Van, der Morel Gijs A.; Van Boom Jacques H. (1987). "Conformational Changes in the oligonucleotide duplex d(GCGTTGCG)•d(GCGAAGCG) induced by formation of a cis–syn thymine dimer". European Journal of Biochemistry. 162 (1): 31–43. doi:10.1111/j.1432-1033.1987.tb10538.x. PMID 3028790.
  19. ^ Essen LO, Klar T (2006). "Light-driven DNA repair by photolyases". Cell Mol Life Sci. 63 (11): 1266–77. doi:10.1007/s00018-005-5447-y. PMID 16699813. S2CID 5897571.
  20. ^ Xu, Lei; Zhu, Guoping (2010). "The Roles of Several Residues of Escherichia coli DNA Photolyase in the Highly Efficient Photo-Repair of Cyclobutane Pyrimidine Dimers". Journal of Nucleic Acids. 2010: 1–7. doi:10.4061/2010/794782. ISSN 2090-021X. PMC 2939405. PMID 20871655.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  21. ^ Errol C. Friedberg (23 January 2003). "DNA Damage and Repair". Nature. 421 (6921): 436–439. Bibcode:2003Natur.421..436F. doi:10.1038/nature01408. PMID 12540918.
  22. ^ a b c Cox B, Game J. Repair systems in Saccharomyces. Mutat Res. 1974 Aug;26(4):257-64. doi: 10.1016/s0027-5107(74)80023-0. PMID: 4605044
  23. ^ Jeffrey M. Buis; Jennifer Cheek; Efthalia Kalliri & Joan B. Broderick (2006). "Characterization of an Active Spore Photoproduct Lyase, a DNA Repair Enzyme in the Radical S-Adenosylmethionine Superfamily". Journal of Biological Chemistry. 281 (36): 25994–26003. doi:10.1074/jbc.M603931200. PMID 16829680.
  24. ^ Takasawa, K. (2004-03-08). "Chemical synthesis and translesion replication of a cis-syn cyclobutane thymine-uracil dimer". Nucleic Acids Research. 32 (5): 1738–1745. doi:10.1093/nar/gkh342. ISSN 1362-4962. PMC 390339. PMID 15020710.{{cite journal}}: CS1 maint: PMC format (link)
  25. ^ Hanson Kerry M.; Gratton Enrico; Bardeen Christopher J. (2006). "Sunscreen enhancement of UV-induced reactive oxygen species in the skin". Free Radical Biology and Medicine. 41 (8): 1205–1212. doi:10.1016/j.freeradbiomed.2006.06.011. PMID 17015167.
  26. ^ Gulston M, Knowland J (July 1999). "Illumination of human keratinocytes in the presence of the sunscreen ingredient Padimate-O and through an SPF-15 sunscreen reduces direct photodamage to DNA but increases strand breaks". Mutat. Res. 444 (1): 49–60. doi:10.1016/s1383-5718(99)00091-1. PMID 10477339.
  27. ^ Sander, Megan; Sander, Michael; Burbidge, Toni; Beecker, Jennifer (2020-12-14). "The efficacy and safety of sunscreen use for the prevention of skin cancer". Canadian Medical Association Journal. 192 (50): E1802–E1808. doi:10.1503/cmaj.201085. ISSN 0820-3946. PMC 7759112. PMID 33318091.{{cite journal}}: CS1 maint: PMC format (link)
Retrieved from "https://en.wikipedia.org/w/index.php?title=Pyrimidine_dimer&oldid=1152206733"