The solution structure of DNA decamer duplex containing the Dewar product of thymidylyl(3-5')thymidine by NMR and full relaxation matrix refinement

Lee, Joon-Hwa; Hwang, Geum-Sook; Kim, Jong-Ki; Choi, Byong-Seok

doi:10.1016/s0014-5793(98)00508-0

Cited by 19DNA and Nucleic Acid ChemistryDNA Repair MechanismsProtein Structure and Dynamics

The solution structure of DNA decamer duplex containing the Dewar product of thymidylyl(3-5')thymidine by NMR and full relaxation matrix refinement

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Lee, Joon-Hwa, Hwang, Geum-Sook, Kim, Jong-Ki, Choi, Byong-Seok·1998·FEBS Letters

DOI 10.1016/s0014-5793(98)00508-0

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Abstract

The (6‐4) adducts and their Dewar isomers play an important role in cytotoxicity and mutation in skin cells exposed to sunlight. Structural study of the DNA duplex containing a site‐specific photoproduct is an essential step toward understanding the molecular mechanism of the mutagenesis and the repair activity of UV‐irradiated DNA. Here we use 1 H NMR spectroscopy and full relaxation matrix refinement to investigate the solution structure of the duplex Dewar decamer. We find that the isomerization of the (6‐4) adduct to its Dewar form induces a substantial change in overall structure of the oligonucleotide duplex. Contrasting base stacking of two lesion sites results in a large difference in the structural impacts induced by the two photoproducts, such as differential disruption of hydrogen bonding at the lesion sites and overall helical bending of 44° by the (6‐4) lesion and 21° by the Dewar lesion.

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Dewar valence isomers induce an intermediate distortion in DNA structure of 21 degrees compared to CPDs at 10 degrees and 6-4PPs at 44 degrees.
“Dewar valence isomers induce an intermediate distortion in DNA structure (21 degrees) compared to CPDs (10 degrees) and 6-4PPs (44 degrees) [35].”
From Sunlight damage to cellular DNA: focus on oxidatively generated lesions (2017) · cites this paper as [35]

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NMR Structural Studies of DNA Decamer Duplex Containing the Dewar Photoproduct of Thymidylyl(3′→5′)Thymidine
Hwang, G., Kim, J., & Choi, B. (1996) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1996.00359.x · Cited by 20 · see citing works
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The Solution Structure of DNA Duplex-Decamer Containing the (6-4) Photoproduct of Thymidylyl(3'5')Thymidine by NMR and Relaxation Matrix Refinement
Kim, J.-K., & Choi, B.-S. (1995) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1995.tb20331.x · Cited by 121 · see citing works
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Structure of a DNA Duplex Containing a Site-Specific Dewar Isomer: Structural Influence of the 3'-T.G base pair of the Dewar product.
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The Dewar photoproduct of thymidylyl(3′→5′)- thymidine (Dewar product) exhibits mutagenic behavior in accordance with the “A rule”
Lee, J.-H., Bae, S.-H., & Choi, B.-S. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.080057097 · Cited by 26 · see citing works
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Solution structure of a DNA decamer duplex containing the stable 3′ T⋅G base pair of the pyrimidine(6–4)pyrimidone photoproduct [(6–4) adduct]: Implications for the highly specific 3′ T → C transition of the (6–4) adduct
Lee, J., Hwang, G., & Choi, B. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.12.6632 · Cited by 63 · see citing works
Self-citation

Authors: Lee, J.-H., Hwang, G.-S., Kim, J.-K., & Choi, B.-S.
Affiliations: Korea Advanced Institute of Science and Technology (KR)
Daegu Catholic University (KR)
Corresponding author: Choi, Byong-Seok
ORCID: Lee, Joon-Hwa
Hwang, Geum-Sook
Kim, Jong-Ki
Choi, Byong-Seok
Venue: FEBS Letters
Publisher: Wiley
Published: 1998-05-29
Volume: 428
Issue: 3
Pages: 269-274
ISSN: 0014-5793 (ISSN-L)
1873-3468
DOI: 10.1016/s0014-5793(98)00508-0
OpenAlex: W2052831715
Cited by: 19
References: 20
Citations by year: 2022: 1 · 2021: 1 · 2020: 1 · 2017: 1 · 2015: 1 · 2014: 1
FWCI: 0.70
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor, 18 d)
Locations: FEBS Letters (publishedVersion)
PubMed (publishedVersion)
Funders: Seoul National University
Korea Science and Engineering Foundation
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: Dewar isomers, DNA photoproducts, UV mutagenesis, base stacking, hydrogen bond breaking
MeSH terms: Base Composition, DNA, Models, Molecular, Nucleic Acid Conformation, Oligodeoxyribonucleotides, Skin, Solutions, Sunlight, Ultraviolet Rays, Dinucleoside Phosphates, DNA Adducts, Nuclear Magnetic Resonance, Biomolecular

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The solution structure of DNA decamer duplex containing the Dewar product of thymidylyl(3-5')thymidine by NMR and full relaxation matrix refinement

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