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. 2021 Dec 22;3(1):101059.
doi: 10.1016/j.xpro.2021.101059. eCollection 2022 Mar 18.

Mapping atypical UV photoproducts in vitro and across the S. cerevisiae genome

Kaitlynne A Bohm  1 , Smitha Sivapragasam  1 , John J Wyrick  1   2
Affiliations

Mapping atypical UV photoproducts in vitro and across the S. cerevisiae genome

Kaitlynne A Bohm et al. STAR Protoc. .

Abstract

Exposure to ultraviolet (UV) light induces DNA damage, predominantly cyclobutane pyrimidine dimers (CPD) and 6,4-photoproducts (6,4-PP), as well as rare, atypical photoproducts at thymidine-adenine (TA) sequences. We have recently shown 'TA' photoproducts are induced in UV-irradiated oligonucleotides and across the budding yeast genome. Here, we describe a protocol for mapping atypical 'TA' photoproducts in vitro and in vivo. This protocol overcomes the technical challenges involved in accurately mapping such rare photoproducts by using ultraviolet damage endonuclease (UVDE) enzymes. For complete details on the use and execution of this protocol, please refer to Laughery et al. (2020).

Keywords: Bioinformatics; Model Organisms; Molecular Biology; Sequence analysis; Sequencing.

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Conflict of interest statement

The authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
In vitro and in vivo ‘TA’ photoproduct cleavage protocol overview
Figure 2
Figure 2
In vitro characterization of ‘TA’ photoproduct (adapted from Laughery et al., 2020)
Figure 3
Figure 3
Agarose gel confirmation of proper sample sonication
Figure 4
Figure 4
Agarose gel confirmation of sample standardization
Figure 5
Figure 5
Agarose gel confirmation of first adapter ligation
Figure 6
Figure 6
Agarose gel confirmation of final library preparation
Figure 7
Figure 7
Bioinformatic analysis of lesion distribution (adapted from Laughery et al., 2020)
See this image and copyright information in PMC

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