Energetic Preference of 8-oxoG Eversion Pathways in a DNA Glycosylase

Bergonzo, Christina; Campbell, Arthur J.; Santos, Carlos de los; Grollman, Arthur P.; Simmerling, Carlos

doi:10.1021/ja205142d

Cited by 32 publications

(71 citation statements)

References 19 publications

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“…Crystallographic studies have proposed a major groove path for OGG1 10, 15–16, 36 , and OGG1’s functional analog Fpg also prefers base eversion through the major groove 19 . Thus, in this work we focus only on comparing eversion and recognition through the major groove.…”

Section: Resultsmentioning

confidence: 99%

“…For example, the crystal structure of uracil DNA glycosylase (UDG) suggested a major groove eversion mechanism, as UDG, like OGG1, binds DNA from the minor groove and the minor groove path is sterically hindered 18 . Also, computational studies on the Fpg-DNA complex strongly indicate that the eversion of 8-oxoG through the major groove is energetically more favorable than through the minor groove 19 . Thus, it is plausible that OGG1 also everts 8-oxoG through a major groove pathway.…”

Section: Introductionmentioning

confidence: 99%

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DNA Deformation-Coupled Recognition of 8-Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase

Li¹,

Endutkin

Bergonzo³

et al. 2017

J. Am. Chem. Soc.

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8-Oxoguanine (8-oxoG), a mutagenic DNA lesion generated under oxidative stress, differs from its precursor guanine by only two substitutions (O8 andH7). Human 8-oxoguanine glycosylase 1 (OGG1) can locate and remove 8-oxoG through extrusion and excision. To date, it remains unclear how OGG1 efficiently distinguishes 8-oxoG from a large excess of undamaged DNA bases. We recently showed that formamidopyrimidine–DNA glycosylase (Fpg), a bacterial functional analog of OGG1, can selectively facilitate eversion of oxoG by stabilizing several intermediate states, and it is intriguing whether OGG1 also employs a similar mechanism in lesion recognition. Here, we use molecular dynamics simulations to explore the mechanism by which OGG1 discriminates between 8-oxoG and guanine along the base eversion pathway. The MD results suggest an important role for kinking of the DNA by the glycosylase, which positions DNA phosphates in a way that assists lesion recognition during base eversion. The computational predictions were validated through experimental enzyme assays on phosphorothioate substrate analogs. Our simulations suggest that OGG1 distinguishes between 8-oxoG and G using their chemical dissimilarities not only at the active site, but also at earlier stages during base eversion, and this mechanism is at least partially conserved in Fpg despite lack of structural homology. The similarity also suggests that lesion recognition through multiple gating steps may be a common theme in DNA repair. Our results provide new insight into how enzymes can exploit kinetics and DNA conformational changes to probe the chemical modifications present in DNA lesions.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

DNA Deformation-Coupled Recognition of 8-Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase

Li¹,

Endutkin

Bergonzo³

et al. 2017

J. Am. Chem. Soc.

Self Cite

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“…The template for this reaction was prepared by linearizing the plasmid pBS-5SLv (22) at a KpnI site immediately adjacent to the 5 S ribosomal DNA-containing nucleosome positioning sequence from Lytechinus variegatus. To this DNA we added buffer, TaqDNA polymerase (Invitrogen), and a 25-fold molar excess of a lesion-containing primer (Midland Certified Reagent Co.) that had been 5Ј end-labeled with [␥- 32 P]ATP by polynucleotide kinase (New England Biolabs). After 22 cycles of denaturation (95°C), annealing (53°C) and extension (72°C), we purified the resulting "top strand" DNA by denaturing PAGE, quantified it by scintillation counting, and mixed it with equimolar amounts of three "bottom strand" oligodeoxyribonucleotides.…”

Section: Methodsmentioning

confidence: 99%

Nucleosomes Suppress the Formation of Double-strand DNA Breaks during Attempted Base Excision Repair of Clustered Oxidative Damages

Cannan

Tsang

Wallace

et al. 2014

Journal of Biological Chemistry

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Background: Ionizing radiation can produce clustered lesions in DNA; attempted base excision repair of these lesions can generate double-strand breaks (DSBs). Results: The extent to which nucleosomes suppress DSB formation is governed by their structural and dynamic properties. Conclusion: Nucleosomes suppress formation of radiation-induced DSBs. Significance: This study helps elucidate mechanisms responsible for potentially mutagenic or lethal DSBs.

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“…Free energy simulations on flipping a damaged 8oxoG indicate that the presence of the protein but also DNA deformation facilitate the flipping process after an initial encounter binding (23,31,32). This is further supported by experimental studies indicating that negative DNA supercoiling (untwisting) can stimulate endonuclease and DNA repair activity (33).…”

Section: Introductionmentioning

confidence: 99%

Global deformation facilitates flipping of damaged 8-oxo-guanine and guanine in DNA

Rosa¹,

Zacharias²

2016

Nucleic Acids Res

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Oxidation of guanine (Gua) to form 7,8-dihydro-8-oxoguanine (8oxoG) is a frequent mutagenic DNA lesion. DNA repair glycosylases such as the bacterial MutM can effciently recognize and eliminate the 8oxoG damage by base excision. The base excision requires a 8oxoG looping out (flipping) from an intrahelical base paired to an extrahelical state where the damaged base is in the enzyme active site. It is still unclear how the damage is identified and flipped from an energetically stable stacked and paired state without any external energy source. Free energy simulations have been employed to study the flipping process for globally deformed DNA conformational states. DNA deformations were generated by systematically untwisting the DNA to mimic its conformation in repair enzyme encounter complex. The simulations indicate that global DNA untwisting deformation toward the enzyme bound form alone (without protein) significantly reduces the penalty for damage flipping to about half of the penalty observed in regular DNA. The finding offers a mechanistic explanation how binding free energy that is transformed to binding induced DNA deformation facilitates flipping and helps to rapidly detect a damaged base. It is likely of general relevance since repair enzyme binding frequently results in significant deformation of the target DNA.

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Energetic Preference of 8-oxoG Eversion Pathways in a DNA Glycosylase

Cited by 32 publications

References 19 publications

DNA Deformation-Coupled Recognition of 8-Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase

DNA Deformation-Coupled Recognition of 8-Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase

Nucleosomes Suppress the Formation of Double-strand DNA Breaks during Attempted Base Excision Repair of Clustered Oxidative Damages

Global deformation facilitates flipping of damaged 8-oxo-guanine and guanine in DNA

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