Visualizing the DNA repair process by a photolyase at atomic resolution.
Manuel Maestre-ReynaPo-Hsun WangEriko NangoYuhei HosokawaMartin SaftAntonia FurrerCheng-Han YangEka-Putra Gusti-Ngurah-PutuWen-Jin WuHans-Joachim EmmerichNicolas CaramelloSophie Franz-BadurChao YangSylvain EngilbergeMaximilian WranikHannah Louise GloverTobias WeinertHsiang-Yi WuCheng-Chung LeeWei-Cheng HuangKai-Fa HuangYao-Kai ChangJiahn-Haur LiaoJui-Hung WengWael GadChiung-Wen ChangAllan H PangKai-Chun YangWei-Ting LinYu-Chen ChangDardan GashiEmma V BealeDmitry OzerovKarol NassGregor KnoppPhilip J M JohnsonClaudio CirelliChristopher J MilneCamila BacellarMichihiro SugaharaShigeki OwadaYasumasa JotiAyumi YamashitaRie TanakaTomoyuki TanakaFangjia LuoKensure TonoWiktoria ZarzyckaPavel MüllerMaisa Alkheder AlahmadFilipp BezoldValerie FuchsPetra GnauStephan KiontkeLukas KorfViktoria ReithoferChristian Joshua RosnerElisa Marie SeilerMohamed WatadLaura WerelRoberta SpadacciniJunpei YamamotoSo IwataDongping ZhongJoerg StandfussAntoine RoyantYoshitaka BesshoLars-Oliver EssenMing-Daw TsaiPublished in: Science (New York, N.Y.) (2023)
Photolyases, a ubiquitous class of flavoproteins, use blue light to repair DNA photolesions. In this work, we determined the structural mechanism of the photolyase-catalyzed repair of a cyclobutane pyrimidine dimer (CPD) lesion using time-resolved serial femtosecond crystallography (TR-SFX). We obtained 18 snapshots that show time-dependent changes in four reaction loci. We used these results to create a movie that depicts the repair of CPD lesions in the picosecond-to-nanosecond range, followed by the recovery of the enzymatic moieties involved in catalysis, completing the formation of the fully reduced enzyme-product complex at 500 nanoseconds. Finally, back-flip intermediates of the thymine bases to reanneal the DNA were captured at 25 to 200 microseconds. Our data cover the complete molecular mechanism of a photolyase and, importantly, its chemistry and enzymatic catalysis at work across a wide timescale and at atomic resolution.
Keyphrases
- dna repair
- single molecule
- circulating tumor
- dna damage
- cell free
- hydrogen peroxide
- dna damage response
- living cells
- big data
- room temperature
- genome wide
- machine learning
- gene expression
- dna methylation
- oxidative stress
- drug discovery
- circulating tumor cells
- artificial intelligence
- electron transfer
- fluorescent probe