The structure of d(CGCGAAT[ ]TCGCG)-d(CGCGAATTCGCG): the incorporation of a thymine photodimer into a B-DNA helix
Open accessAbstract
In the light of the biological significance of thymine photodimers , studies of the energetics of the dodecanucleotide fragment d( CGCGAATTCGCG )2 have been carried out using the methods of molecular mechanics, with and without incorporation of a thymine dimer in the cis-syn configuration. The results of the calculations suggest that the thymine dimerized structures show no gross distortion in the double helix with the conformational changes relative to the normal B-DNA double helix restricted largely to the dimer region. The energetics of dTp[]dT reveal a number of conformers which are energetically almost equally favorable and are, as a group, qualitatively consistent with NMR studies on this molecule. The biological implications of the results of the conformational studies, reported here, have been examined vis-a-vis the currently available models for the recognition of DNA "damage" by repair enzymes.
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trans-syn CPD causes greater distortion than cis-syn CPD through a kink or dislocation at the 5′ side of the dimer in double-stranded DNA.
“It was revealed that the presence of trans-syn CPD causes distortion to a great extent than the cis-syn product by means of a kink or dislocation at the 5′-side of the dimer in double-stranded DNA [77].”
From Molecular Mechanisms of Ultraviolet Radiation‐Induced DNA Damage and Repair (2010) · cites this paper as [77]
The Discussion (page unavailable) reports little overall distortion and only minimal kinks in the cis-syn thymine-dimer models. Our copy does not address trans-syn CPDs or compare their distortion with cis-syn CPDs; searches for trans-syn and a 5′-side kink or dislocation found no passage establishing the claim. (LLM, conf=0.76)
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Molecular Mechanisms of Ultraviolet Radiation‐Induced DNA Damage and Repair
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“It was revealed that the presence of trans-syn CPD causes distortion to a great extent than the cis-syn product by means of a kink or dislocation at the 5′-side of the dimer in double-stranded DNA [77].”
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- Authors
- Rao, S. N., Keepers, J. W., & Koliman, P.
- Affiliations
- University of California, San Francisco (US)
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1984
- Volume
- 12
- Issue
- 11
- Pages
- 4789-4807
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC318875
- OpenAlex
- W2019860157
- Cited by
- 65
- References
- 13
- Citations by year
- 2022: 1 · 2016: 1
- FWCI
- 2.89
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- B-DNA, DNA conformation, helix distortion, DNA damage recognition, DNA repair enzymes, molecular mechanics
- MeSH terms
- DNA, Hydrogen Bonding, Models, Molecular, Nucleic Acid Conformation, Oligodeoxyribonucleotides, Oligonucleotides, Photochemistry, Pyrimidine Dimers, Thermodynamics
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