Repair Reaction Research Articles

UHRF1 is a sensor for DNA interstrand crosslinks

The human genome is guarded against mutations by several DNA repair pathways. Common for all pathways, is the initiating event of detecting the DNA damage. This initial event is followed by the coordinated recruitment of various other DNA repair proteins needed for the repair. For instance, the MSH2/MSH6 complex detects DNA mismatches, while the MRN or KU70/KU80 complexes detect double strand breaks. We have recently identified the UHRF1 protein as a sensor for DNA interstrand crosslinks (ICLs) [1]. DNA interstrand crosslinks (ICLs) are extremely toxic to cells. In human, the Fanconi Anemia (FA) DNA repair pathway repairs such DNA damage [2]. Disruption of the FA pathway in human causes the FA disease, where patients are characterized by developmental abnormalities, bone marrow failure, and a high incidence of cancer. To date, 19 FA genes have been identified. In addition, a number of other gene products cooperate in the FA pathway. In addition to the critical step of detecting the damage, repair of an ICL entails incision of the ICL by nucleases, translesion synthesis, nucleotide excision repair and homologous recombination. The ICL repair reaction has been studied extensively in various model systems. An ICL can be an obstacle to DNA replication, and the convergence of two replication forks from opposite sides of the ICL can trigger the repair reaction as shown in the Xenopus cell free system [3]. At the same time, traverse through an ICL by the replication machinery has been reported in mammalian cells, leaving an unrepaired ICL for later repair [4]. When the MRN complex is recruited to a DNA double strand break, histone H2AX is phosphorylated by ATM, which allows the recruitment of MDC1, RNF8 and RNF168. RNF8 mediates ubiquitination of histone H1 and RNF168 mediates ubiquitination of histone H2A, creating a landing platform to subsequently recruit downstream factors [5]. Unlike the double strand break repair pathway, an actual ICL sensor protein has remained unknown. The identification of UHRF1 opens the possibility that the initial stages of ICL repair might be conceptually similar to the repair of other types of DNA damage. UHRF1 interacts with ICLs both in vitro and in vivo. Using live-cell imaging, we established that UHRF1 is recruited to ICLs within seconds after their appearance in the cell, kinetics similar to that of early stage repair proteins in other DNA repair pathways. The initiating event of UHRF1 recruitment facilitates the subsequent recruitment of the key FA protein, FANCD2. It is currently unclear how UHRF1 mediates this event. It is possible that a direct interaction between the two proteins exists. It has also been suggested that UHRF1 interacts with nucleases, and this might be important for its role early in the ICL repair process [6]. The discovery of UHRF1 as an ICL sensor prompts several questions. For instance, we do not know the nature of the interaction with an ICL. Structural studies will be required to uncover this. Also, it will be interesting to clarify whether the function of UHRF1 is required for ICL repair in a replication-dependent or -independent manner. Association of UHRF1 with an ICL in the G1-phase of the cell cycle could potentially mark the crosslink for later repair when the cell enters S-phase, and might prevent other DNA repair pathways from initiating repair prior to the FA pathway. DNA repair pathways are often deregulated in cancer. Therefore, increased understanding of these pathways could accelerate the development of new therapeutic approaches. UHRF1 is deregulated in a number of cancers, suggesting that it might be a potential therapeutic target [7]. Also, ICL-forming drugs, such as cisplatin and mitomycin C, are currently used effectively in the treatment of various types of cancer. However, occurrence of resistance is a major problem. It is possible that the developed resistance is caused by increased cellular ability to repair ICLs. Therefore, targeting ICL repair pathways directly could potentially sensitize cancer cells to existing therapeutic drugs. Future research will hopefully address these questions.

Visualization of mismatch repair complexes using fluorescence microscopy.

DNA mismatch repair (MMR) is a surveillance mechanism present in most living organisms, which repairs errors introduced by DNA polymerases. Importantly, loss of MMR function due to inactivating mutations and/or epigenetic silencing results in the accumulation of mutations and as consequence increased cancer susceptibility, as observed in Lynch syndrome patients. During the past decades important progress has been made in the MMR field resulting in the identification and characterization of essential MMR components, culminating in the in vitro reconstitution of 5' and 3' nick-directed MMR. However, several mechanistic aspects of the MMR reaction remain not fully understood, therefore alternative approaches and further investigations are needed. Recently, the use of imaging techniques and, more specifically, visualization of MMR components in living cells, has broadened our mechanistic understanding of the repair reaction providing more detailed information about the spatio-temporal organization of MMR in vivo. In this review we would like to comment on mechanistic aspects of the MMR reaction in light of these and other recent findings. Moreover, we will discuss the current limitations and provide future perspectives regarding imaging of mismatch repair components in diverse organisms.

Protein-protein interactions in DNA mismatch repair.

The principal DNA mismatch repair proteins MutS and MutL are versatile enzymes that couple DNA mismatch or damage recognition to other cellular processes. Besides interaction with their DNA substrates this involves transient interactions with other proteins which is triggered by the DNA mismatch or damage and controlled by conformational changes. Both MutS and MutL proteins have ATPase activity, which adds another level to control their activity and interactions with DNA substrates and other proteins. Here we focus on the protein-protein interactions, protein interaction sites and the different levels of structural knowledge about the protein complexes formed with MutS and MutL during the mismatch repair reaction.

The structures of the SNM1A and SNM1B/Apollo nuclease domains reveal a potential basis for their distinct DNA processing activities.

The human SNM1A and SNM1B/Apollo proteins are members of an extended family of eukaryotic nuclease containing a motif related to the prokaryotic metallo-β-lactamase (MBL) fold. SNM1A is a key exonuclease during replication-dependent and transcription-coupled interstrand crosslink repair, while SNM1B/Apollo is required for maintaining telomeric overhangs. Here, we report the crystal structures of SNM1A and SNM1B at 2.16 Å. While both proteins contain a typical MBL-β-CASP domain, a region of positive charge surrounds the active site of SNM1A, which is absent in SNM1B and explains the greater apparent processivity of SNM1A. The structures of both proteins also reveal a putative, wide DNA-binding groove. Extensive mutagenesis of this groove, coupled with detailed biochemical analysis, identified residues that did not impact on SNM1A catalytic activity, but drastically reduced its processivity. Moreover, we identified a key role for this groove for efficient digestion past DNA interstrand crosslinks, facilitating the key DNA repair reaction catalysed by SNM1A. Together, the architecture and dimensions of this groove, coupled to the surrounding region of high positive charge, explain the remarkable ability of SNM1A to accommodate and efficiently digest highly distorted DNA substrates, such as those containing DNA lesions.

Deoxyinosine repair in nuclear extracts of human cells.

BackgroundDeamination of adenine can occur spontaneously under physiological conditions generating the highly mutagenic lesion, hypoxanthine. This process is enhanced by ROS from exposure of DNA to ionizing radiation, UV light, nitrous acid, or heat. Hypoxanthine in DNA can pair with cytosine which results in A:T to G:C transition mutations after DNA replication. In Escherichia coli, deoxyinosine (hypoxanthine deoxyribonucleotide, dI) is removed through an alternative excision repair pathway initiated by endonuclease V. However, the correction of dI in mammalian cells appears more complex and was not fully understood.ResultsAll four possible dI-containing heteroduplex DNAs, including A-I, C-I, G-I, and T-I were introduced to repair reactions containing extracts from human cells. The repair reaction requires magnesium, dNTPs, and ATP as cofactors. We found G-I was the best substrate followed by T-I, A-I and C-I, respectively. Moreover, judging from the repair requirements and sensitivity to specific polymerase inhibitors, there were overlapping repair activities in processing of dI in DNA. Indeed, a hereditable non-polyposis colorectal cancer cell line (HCT116) demonstrated lower dI repair activity that was partially attributed to lack of mismatch repair.ConclusionsA plasmid-based convenient and non-radioisotopic method was created to study dI repair in human cells. Mutagenic dI lesions processed in vitro can be scored by restriction enzyme cleavage to evaluate the repair. The repair assay described in this study provides a good platform for further investigation of human repair pathways involved in dI processing and their biological significance in mutation prevention.

Activation of Saccharomyces cerevisiae Mlh1-Pms1 Endonuclease in a Reconstituted Mismatch Repair System

Previous studies reported the reconstitution of an Mlh1-Pms1-independent 5' nick-directed mismatch repair (MMR) reaction using Saccharomyces cerevisiae proteins. Here we describe the reconstitution of a mispair-dependent Mlh1-Pms1 endonuclease activation reaction requiring Msh2-Msh6 (or Msh2-Msh3), proliferating cell nuclear antigen (PCNA), and replication factor C (RFC) and a reconstituted Mlh1-Pms1-dependent 3' nick-directed MMR reaction requiring Msh2-Msh6 (or Msh2-Msh3), exonuclease 1 (Exo1), replication protein A (RPA), RFC, PCNA, and DNA polymerase δ. Both reactions required Mg(2+) and Mn(2+) for optimal activity. The MMR reaction also required two reaction stages in which the first stage required incubation of Mlh1-Pms1 with substrate DNA, with or without Msh2-Msh6 (or Msh2-Msh3), PCNA, and RFC but did not require nicking of the substrate, followed by a second stage in which other proteins were added. Analysis of different mutant proteins demonstrated that both reactions required a functional Mlh1-Pms1 endonuclease active site, as well as mispair recognition and Mlh1-Pms1 recruitment by Msh2-Msh6 but not sliding clamp formation. Mutant Mlh1-Pms1 and PCNA proteins that were defective for Exo1-independent but not Exo1-dependent MMR in vivo were partially defective in the Mlh1-Pms1 endonuclease and MMR reactions, suggesting that both reactions reflect the activation of Mlh1-Pms1 seen in Exo1-independent MMR in vivo. The availability of this reconstituted MMR reaction should now make it possible to better study both Exo1-independent and Exo1-dependent MMR.

Theoretical investigation of an in situ k-restore process for damaged ultra-low-k materials based on plasma enhanced fragmentation

The authors present theoretical investigations of a k-restore process for damaged porous ultra-low-k (ULK) materials. The process is based on plasma enhanced fragmented silylation precursors to replace k-value damaging, polar Si-OH and Si-H bonds by k-value lowering Si-CH3 bonds. The authors employ density functional theory to determine the favored fragments of silylation precursors and show the successful repair of damaged bonds on our model system. This model system consists of a small set of ULK-fragments, which represent various damaged states of ULK materials. Our approach provides a fast scanning method for a wide variety of possible repair reactions. Further, the authors show that oxygen containing fragments are required to repair Si-H bonds and fragments with dangling Si-bonds are most effective to repair polar Si-OH bonds.

Plants Possess a Cyclic Mitochondrial Metabolic Pathway similar to the Mammalian Metabolic Repair Mechanism Involving Malate Dehydrogenase and l-2-Hydroxyglutarate Dehydrogenase.

Enzymatic side reactions can give rise to the formation of wasteful and toxic products that are removed by metabolite repair pathways. In this work, we identify and characterize a mitochondrial metabolic repair mechanism in Arabidopsis thaliana involving malate dehydrogenase (mMDH) and l-2-hydroxyglutarate dehydrogenase (l-2HGDH). We analyze the kinetic properties of both A. thaliana mMDH isoforms, and show that they produce l-2-hydroxyglutarate (l-2HG) from 2-ketoglutarate (2-KG) at low rates in side reactions. We identify A. thaliana l-2HGDH as a mitochondrial FAD-containing oxidase that converts l-2HG back to 2-KG. Using loss-of-function mutants, we show that the electrons produced in the l-2HGDH reaction are transferred to the mitochondrial electron transport chain through the electron transfer protein (ETF). Thus, plants possess the biochemical components of an l-2HG metabolic repair system identical to that found in mammals. While deficiencies in the metabolism of l-2HG result in fatal disorders in mammals, accumulation of l-2HG in plants does not adversely affect their development under a range of tested conditions. However, orthologs of l-2HGDH are found in all examined genomes of viridiplantae, indicating that the repair reaction we identified makes an essential contribution to plant fitness in as yet unidentified conditions in the wild.

New Synthetic Routes to Iron-Sulfur Clusters: Deciphering the Repair Chemistry of [2Fe-2S] Clusters from Mononitrosyl Iron Complexes.

The nitrosylation of inorganic protein cofactors, specifically that of [Fe-S] clusters to form iron nitrosyls, plays a number of important roles in biological systems. In some of these cases, it is expected that a repair process reverts the nitrosylated iron species to intact [Fe-S] clusters. The repair of nitrosylated [2Fe-2S] cluster, primarily in the form of protein-bound dinitrosyl iron complexes (DNICs), has been observed in vitro and in vivo, but the mechanism of this process remains uncertain. The present work expands upon a previous observation (Fitzpatrick et al. J. Am. Chem. Soc. 2014, 136, 7229) of the ability of mononitrosyl iron complexes (MNICs) to be converted into [2Fe-2S] clusters by the addition of nothing other than a cysteine analogue. Herein, each of the critical elementary steps in the cluster repair has been dissected to elucidate the roles of the cysteine analogue. Systematic variations of a cysteine analogue employed in the repair reaction suggest that (i) the bidentate coordination of a cysteine analogue to MNIC promotes NO release from iron, and (ii) deprotonation of the α carbon of the ferric-bound cysteine analogue leads to the C-S cleavage en route to the formation of [2Fe-2S] cluster. The [2Fe-2S] cluster bearing a cysteine analogue has also been synthesized from thiolate-bridged iron dimers of the form [Fe2(μ-SR)2(SR)4](0/2-), which implies that such species may be present as intermediates in the cluster repair. In addition to MNICs, mononuclear tetrathiolate ferric or ferrous species have been established as another form of iron from which [2Fe-2S] clusters can be generated without need for any other reagent but a cysteine analogue. The results of these experiments bring to light new chemistry of classic coordination complexes and provides further insight into the repair of NO-modified [2Fe-2S] clusters.

The molecular origin of high DNA-repair efficiency by photolyase.

The primary dynamics in photomachinery such as charge separation in photosynthesis and bond isomerization in sensory photoreceptor are typically ultrafast to accelerate functional dynamics and avoid energy dissipation. The same is also true for the DNA repair enzyme, photolyase. However, it is not known how the photoinduced step is optimized in photolyase to attain maximum efficiency. Here, we analyse the primary reaction steps of repair of ultraviolet-damaged DNA by photolyase using femtosecond spectroscopy. With systematic mutations of the amino acids involved in binding of the flavin cofactor and the cyclobutane pyrimidine dimer substrate, we report our direct deconvolution of the catalytic dynamics with three electron-transfer and two bond-breaking elementary steps and thus the fine tuning of the biological repair function for optimal efficiency. We found that the maximum repair efficiency is not enhanced by the ultrafast photoinduced process but achieved by the synergistic optimization of all steps in the complex repair reaction.

Interaction with Single-stranded DNA-binding Protein Stimulates Escherichia coli Ribonuclease HI Enzymatic Activity

Single-stranded (ss) DNA-binding proteins (SSBs) bind and protect ssDNA intermediates formed during replication, recombination, and repair reactions. SSBs also directly interact with many different genome maintenance proteins to stimulate their enzymatic activities and/or mediate their proper cellular localization. We have identified an interaction formed between Escherichia coli SSB and ribonuclease HI (RNase HI), an enzyme that hydrolyzes RNA in RNA/DNA hybrids. The RNase HI·SSB complex forms by RNase HI binding the intrinsically disordered C terminus of SSB (SSB-Ct), a mode of interaction that is shared among all SSB interaction partners examined to date. Residues that comprise the SSB-Ct binding site are conserved among bacterial RNase HI enzymes, suggesting that RNase HI·SSB complexes are present in many bacterial species and that retaining the interaction is important for its cellular function. A steady-state kinetic analysis shows that interaction with SSB stimulates RNase HI activity by lowering the reaction Km. SSB or RNase HI protein variants that disrupt complex formation nullify this effect. Collectively our findings identify a direct RNase HI/SSB interaction that could play a role in targeting RNase HI activity to RNA/DNA hybrid substrates within the genome.

Reconstitution and structure of a bacterial Pnkp1-Rnl-Hen1 RNA repair complex.

Ribotoxins cleave essential RNAs for cell killing, and RNA repair neutralizes the damage inflicted by ribotoxins for cell survival. Here we report a new bacterial RNA repair complex that performs RNA repair linked to immunity. This new RNA repair complex is a 270-kDa heterohexamer composed of three proteins—Pnkp1, Rnl and Hen1—that are required to repair ribotoxin-cleaved RNA in vitro. The crystal structure of the complex reveals the molecular architecture of the heterohexamer as two rhomboid-shaped ring structures of Pnkp1–Rnl–Hen1 heterotrimer fused at the Pnkp1 dimer interface. The four active sites required for RNA repair are located on the inner rim of each ring. The architecture and the locations of the active sites of the Pnkp1–Rnl–Hen1 heterohexamer suggest an ordered series of repair reactions at the broken RNA ends that confer immunity to recurrent damage.

Effects of DNA3'pp5'G capping on 3' end repair reactions and of an embedded pyrophosphate-linked guanylate on ribonucleotide surveillance.

When DNA breakage results in a 3′-PO4 terminus, the end is considered ‘dirty’ because it cannot prime repair synthesis by DNA polymerases or sealing by classic DNA ligases. The noncanonical ligase RtcB can guanylylate the DNA 3′-PO4 to form a DNA3′pp5′GOH cap. Here we show that DNA capping precludes end joining by classic ATP-dependent and NAD+-dependent DNA ligases, prevents template-independent nucleotide addition by mammalian terminal transferase, blocks exonucleolytic proofreading by Escherichia coli DNA polymerase II and inhibits proofreading by E. coli DNA polymerase III, while permitting templated DNA synthesis from the cap guanosine 3′-OH primer by E. coli DNA polymerase II (B family) and E. coli DNA polymerase III (C family). Human DNA polymerase β (X family) extends the cap primer predominantly by a single templated addition step. Cap-primed synthesis by templated polymerases embeds a pyrophosphate-linked ribonucleotide in DNA. We find that the embedded ppG is refractory to surveillance and incision by RNase H2.

Fluorogenic DNA ligase and base excision repair enzyme assays using substrates labeled with single fluorophores

Continuing our work on fluorogenic substrates labeled with single fluorophores for nucleic acid modifying enzymes, here we describe the development of such substrates for DNA ligases and some base excision repair enzymes. These substrates are hairpin-type synthetic DNA molecules with a single fluorophore located on a base close to the 3′ ends, an arrangement that results in strong fluorescence quenching. When such substrates are subjected to an enzymatic reaction, the position of the dyes relative to that end of the molecules is altered, resulting in significant fluorescence intensity changes. The ligase substrates described here were 5′ phosphorylated and either blunt-ended or carrying short, self-complementary single-stranded 5′ extensions. The ligation reactions resulted in the covalent joining of the ends of the molecules, decreasing the quenching effect of the terminal bases on the dyes. To generate fluorogenic substrates for the base excision repair enzymes formamido–pyrimidine–DNA glycosylase (FPG), human 8-oxo-G DNA glycosylase/AP lyase (hOGG1), endonuclease IV (EndoIV), and apurinic/apyrimidinic endonuclease (APE1), we introduced abasic sites or a modified nucleotide, 8-oxo-dG, at such positions that their enzymatic excision would result in the release of a short fluorescent fragment. This was also accompanied by strong fluorescence increases. Overall fluorescence changes ranged from approximately 4-fold (ligase reactions) to more than 20-fold (base excision repair reactions).

Comparative insight into nucleotide excision repair components of Plasmodium falciparum.

Nucleotide excision repair (NER) is one of the DNA repair pathways crucial for maintenance of genome integrity and deals with repair of DNA damages arising due to exogenous and endogenous factors. The multi-protein transcription initiation factor TFIIH plays a critical role in NER and transcription and is highly conserved throughout evolution. The malaria parasite Plasmodium falciparum has been a challenge for the researchers for a long time because of emergence of drug resistance. The availability of its genome sequence has opened new avenues for research. Antimalarial drugs like chloroquine and mefloquine have been reported to inhibit NER pathway mediated repair reactions and thus promote mutagenesis. Previous studies have validated existence and implied possible association of defective or altered DNA repair pathways with development of drug resistant phenotype in certain P. falciparum strains. We conjecture that a compromised NER pathway in combination with other DNA repair pathways might be conducive for the emergence and sustenance of drug resistance in P. falciparum. Therefore we decided to unravel the components of NER pathway in P. falciparum and using bioinformatics based approaches here we report a genome wide in silico analysis of NER components from P. falciparum and their comparison with the human host. Our results reveal that P. falciparum genome contains almost all the components of NER but we were unable to find clear homologue for p62 and XPC in its genome. The structure modeling of all the components further suggests that their structures are significantly conserved. Furthermore this study lays a foundation to perform similar comparative studies between drug resistant and drug sensitive strains of parasite in order to understand DNA repair-related mechanisms of drug resistance.

2-Hydrazinobenzothiazole-based etheno-adduct repair protocol (HERP): a method for quantitative determination of direct repair of etheno-bases.

Etheno-DNA adducts are mutagenic and lead to genomic instability. Enzymes belonging to Fe(II)/2-oxoglutarate-dependent dioxygenase family repair etheno-DNA adducts by directly removing alkyl chain as glyoxal. Presently there is no simple method to assess repair reaction of etheno-adducts. We have developed a rapid and sensitive assay for studying etheno-DNA adduct repair by Fe(II)/2-oxoglutarate-dependent dioxygenases. Using AlkB as model Fe(II)/2-oxoglutarate-dependent dioxygenases, we performed in vitro repair of etheno-adducts containing DNA and detected glyoxal by reacting with 2-hydrazinobenzothiazole which forms complex yellow color compound with distinct absorption spectrum with a peak absorption at 365 nm. We refer this method as 2-hydrazinobenzothiazole-based etheno-adduct repair protocol or HERP. Our novel approach for determining repair of etheno-adducts containing DNA overcomes several drawbacks of currently available radioisotope-based assay.

A proton-electron sequential transfer mechanism: theoretical evidence about its biological relevance.

Density functional theory calculations, using the SMD continuum model, indicate that hydrogen transfer from totally protonated uric to a tryptophanyl radical in proteins corresponds to a sequential mechanism. Modeling in methyl butanoate indicates that this mechanism is more important in a hydrophobic medium than in water.

A new approach to elucidating repair reactions of resveratrol.

The repair by co-antioxidants of the phenoxy radical of resveratrol, the famous health-preserving ingredient of red wine, is a key step of radical scavenging cascades in nature. To generate that radical, we employed 355 nm photoionization as a direct and selective access that reduces the chemical complexity and is equally applicable in organized phases; to monitor it, we used its hitherto unreported absorption in the red where no other species in our systems interfere. With this novel approach, we measured rate constants and H/D kinetic isotope effects for the repairs by ascorbate, trolox (a vitamin E analogue) and 4-aminophenol, and identified the mechanisms as one-step hydrogen abstractions. Cysteine and glutathione are unreactive. In micellar solution (SDS), the repair by ascorbate is much slower and involves only the hydrophilic phenoxy moieties protruding from the micelles. The new experimental strategy also led to a reevaluation of extinction coefficients, rate constants and mechanisms.

Abstract 3654: The role of structure-specific endonuclease MUS81 in the induction of cytosolic DNA in tumor cells

Abstract Genomic DNA is constantly damaged by endogenous and exogenous agents. The DNA damage response (DDR) is vital for recognizing DNA damage and instigating DNA repair reactions to ensure genome stability. MUS81 is a structure-specific endonuclease that is required for resolving stalled replication forks at sites of DNA damage to initiate Homologous Recombination repair. Our preliminary data suggests that the potentially detrimental DNA structures cleaved by MUS81 accumulate in the cytosol of many tumor cells. Furthermore, we found that DNA cleaved by MUS81 induces type I interferon expression in a STING-dependent manner, and initiates an innate immune response in vivo. Cytosolic DNA in tumor cells was also abrogated upon inhibition of DNA damage sensors, ATM/ATR and PARP1. In addition, genetic inhibition of Mus81 in different tumor cells lines impaired expression of cytosolic DNA and type I interferon. In summary, our data suggest that the structure-specific endonuclease MUS81 cleaves damaged nuclear DNA leading to accumulation of genomic DNA in the cytosol of tumor cells, activating immunosurveillance mechanisms. Citation Format: Samantha Ho, Stephan Gasser. The role of structure-specific endonuclease MUS81 in the induction of cytosolic DNA in tumor cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3654. doi:10.1158/1538-7445.AM2014-3654

Mechanism of repair of acrolein- and malondialdehyde-derived exocyclic guanine adducts by the α-ketoglutarate/Fe(II) dioxygenase AlkB.

The structurally related exocyclic guanine adducts α-hydroxypropano-dG (α-OH-PdG), γ-hydroxypropano-dG (γ-OH-PdG), and M1dG are formed when DNA is exposed to the reactive aldehydes acrolein and malondialdehyde (MDA). These lesions are believed to form the basis for the observed cytotoxicity and mutagenicity of acrolein and MDA. In an effort to understand the enzymatic pathways and chemical mechanisms that are involved in the repair of acrolein- and MDA-induced DNA damage, we investigated the ability of the DNA repair enzyme AlkB, an α-ketoglutarate/Fe(II) dependent dioxygenase, to process α-OH-PdG, γ-OH-PdG, and M1dG in both single- and double-stranded DNA contexts. By monitoring the repair reactions using quadrupole time-of-flight (Q-TOF) mass spectrometry, it was established that AlkB can oxidatively dealkylate γ-OH-PdG most efficiently, followed by M1dG and α-OH-PdG. The AlkB repair mechanism involved multiple intermediates and complex, overlapping repair pathways. For example, the three exocyclic guanine adducts were shown to be in equilibrium with open-ring aldehydic forms, which were trapped using (pentafluorobenzyl)hydroxylamine (PFBHA) or NaBH4. AlkB repaired the trapped open-ring form of γ-OH-PdG but not the trapped open-ring of α-OH-PdG. Taken together, this study provides a detailed mechanism by which three-carbon bridge exocyclic guanine adducts can be processed by AlkB and suggests an important role for the AlkB family of dioxygenases in protecting against the deleterious biological consequences of acrolein and MDA.