Kinetics of cyclobutane thymine dimer splitting by DNA photolyase directly monitored in the UV

Abstract

CPD photolyase uses light to repair cyclobutane pyrimidine dimers (CPDs) formed between adjacent pyrimidines in UV-irradiated DNA. The enzyme harbors an FAD cofactor in fully reduced state (FADH − ). The CPD repair mechanism involves electron transfer from photoexcited FADH − to the CPD, splitting of its intradimer bonds, and electron return to restore catalytically active FADH − . The two electron transfer processes occur on time scales of 10 −10 and 10 −9 s, respectively. Until now, CPD splitting itself has only been poorly characterized by experiments. Using a previously unreported transient absorption setup, we succeeded in monitoring cyclobutane thymine dimer repair in the main UV absorption band of intact thymine at 266 nm. Flavin transitions that overlay DNA-based absorption changes at 266 nm were monitored independently in the visible and subtracted to obtain the true repair kinetics. Restoration of intact thymine showed a short lag and a biexponential rise with time constants of 0.2 and 1.5 ns. We assign these two time constants to splitting of the intradimer bonds (creating one intact thymine and one thymine anion radical T ∘− ) and electron return from T ∘− to the FAD cofactor with recovery of the second thymine, respectively. Previous model studies and computer simulations yielded various CPD splitting times between <1 ps and <100 ns. Our experimental results should serve as a benchmark for future efforts to model enzymatic photorepair. The technique and methods developed here may be applied to monitor other photoreactions involving DNA.DNA repair | flavin adenine dinucleotide | transient absorption spectroscopy | UV damage E xposure of living organisms to UV light from the sun induces harmful lesions in DNA. To overcome this threat, specific repair enzymes have evolved, probably the most ancient and widespread one being CPD photolyase (1, 2). It uses light to repair cis-syn cyclobutane pyrimidine dimer (CPD) lesions, formed by a UV-induced [2 þ 2] cycloaddition of two adjacent pyrimidines (mostly thymines) in the same strand (Fig. 1). CPD photolyase has been found in organisms from all kingdoms of life, except placental mammals (including humans) that rely on nucleotide excision repair for CPD lesions. Among the various DNA repair mechanisms known, that of CPD photolyase is considered the most "cost-efficient" and least error-prone (3, 4). Note, however, that for CPDs containing cytosine, deamination of the cytosine may occur prior to repair. Uracil containing CPD cleavage by photolyase would then result in harmful cytosine-to-uracil mutations (5).Photolyase is a globular single chain protein of approximately 60 kDa that harbors two buried cofactors: flavin adenine dinucleotide (FAD) in its fully reduced state (FADH − ), which is the essential catalytic cofactor, and an antenna pigment, either a folate or a flavin derivative that absorbs blue or near UV light much stronger than FADH − does and efficiently transfers the excitation energy to FADH − .It is widely accepted (1, 2) that CPD repair by phot...

Variable Electron Transfer Pathways in an Amphibian Cryptochrome

“…For class I cyclobutane pyrimidine dimer PLs, mechanistic details of the primary processes after light excitation have been elucidated (23)(24)(25), whereas unquestionable mechanisms for the remaining members of the Cry/PL family are still missing (26,27). The growing body of evidence that Crys perform highly diverse tasks in the distinct phyla of life points toward a similar diversity of the detailed primary processes taking place after the initial light excitation of the FAD at the molecular level.…”

Reply to Brettel and Byrdin: On the efficiency of DNA repair by photolyase

“…In conclusion, both the Thiagarajan et al article (8) and a related article in Biochemistry (9) by the same group involve misinterpretation of the steady-state data and low resolution of the dynamics data. Thus, their arguments regarding the shorter unproductive back ET time are not valid.…”

“…Actually, from the "minimal scheme" in the Thiagarajan et al article (8), the back ET is parallel to the bond splitting. So, only the overall rate of these two steps (the sum of two rates of back ET and bond splitting) can be observed.…”

“…The quantum yield of photolyase is in the range of 0.7-0.9, as measured in vivo (4,5) and in vitro (5,6) and under single turnover (5) and steady-state (6, 7) reaction conditions by three different groups. An inspection of the supplementary information in the Thiagarajan et al article (8) shows that only two data points were used for determining substrate saturation. A systematic concentration titration is needed to determine the accurate binding constant.…”

A C1 orf 124/Spartan szerepe a DNS-hiba tolerancia útvonalban

“…A nukleinsav bázisok által elnyelt UV sugárzás leggyakrabban ciklobután-pirimidin, és pirimidin-pirimidin dimerek kialakulását okozza, amely a legtöbb esetben T-T, kisebb számban T-C illetve C-C kovalens kapcsolatokat jelent, amely az egyik bázis 6-os, és a szomszédos bázis 4-es pozíciójában található szén atomjai között alakul ki (17). Az ilyen típusú károsodások is képesek meggátolni a replikációs apparátus haladását a DNS-szálon.…”