Accommodation and repair of a UV photoproduct in DNA at different rotational settings on the nucleosome surface

Zeljko M Svedruzić; Chenbo Wang; Joseph V Kosmoski; Michael J Smerdon

doi:10.1074/jbc.M509478200

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Accommodation and repair of a UV photoproduct in DNA at different rotational settings on the nucleosome surface

Journal article

Open access

Peer reviewed

Accommodation and repair of a UV photoproduct in DNA at different rotational settings on the nucleosome surface

Zeljko M Svedruzić, Chenbo Wang, Joseph V Kosmoski and Michael J Smerdon

The Journal of biological chemistry, Vol.280(48), pp.40051-40057

12/02/2005

DOI: https://doi.org/10.1074/jbc.M509478200

Handle:

https://hdl.handle.net/2376/105412

PMID: 16210312

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Abstract

Binding, Competitive

Histones - chemistry

Nucleosomes - chemistry

Oocytes - metabolism

Xenopus laevis

Models, Molecular

Nucleosomes - metabolism

Hydroxyl Radical

Thermodynamics

DNA - chemistry

Animals

Cell Nucleus - metabolism

Ultraviolet Rays

Time Factors

DNA Repair

Pyrimidine Dimers - chemistry

Protein Conformation

DNA Damage

Nucleic Acid Conformation

Dimerization

Chromatin - chemistry

Cyclobutane-thymine dimers (CTDs), the most common DNA lesion induced by UV radiation, cause 30 degrees bending and 9 degrees unwinding of the DNA helix. We prepared site-specific CTDs within a short sequence bracketed by strong nucleosome-positioning sequences. The rotational setting of CTDs over one turn of the helix near the dyad center on the histone surface was analyzed by hydroxyl radical footprinting. Surprisingly, the position of CTDs over one turn of the helix does not affect the rotational setting of DNA on the nucleosome surface. Gel-shift analysis indicates that one CTD destabilizes histone-DNA interactions by 0.6 or 1.1 kJ/mol when facing away or toward the histone surface, respectively. Thus, 0.5 kJ/mol energy penalty for a buried CTD is not enough to change the rotational setting of sequences with strong rotational preference. The effect of rotational setting on CTD removal by nucleotide excision repair (NER) was examined using Xenopus oocyte nuclear extracts. The NER rates are only 2-3 times lower in nucleosomes and change by only 1.5-fold when CTDs face away or toward the histone surface. Therefore, in Xenopus nuclear extracts, the rotational orientation of CTDs on nucleosomes has surprisingly little effect on rates of repair. These results indicate that nucleosome dynamics and/or chromatin remodeling may facilitate NER in gaining access to DNA damage in nucleosomes.

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Title: Accommodation and repair of a UV photoproduct in DNA at different rotational settings on the nucleosome surface
Creators: Zeljko M Svedruzić - Department of Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA
Chenbo Wang
Joseph V Kosmoski
Michael J Smerdon
Publication Details: The Journal of biological chemistry, Vol.280(48), pp.40051-40057
Academic Unit: Molecular Biosciences, School of
Publisher: United States
Grant note: ES04106 / NIEHS NIH HHS ES02614 / NIEHS NIH HHS
Identifiers: 99900547077901842
Language: English
Resource Type: Journal article