1
|
Ovcherenko SS, Shernyukov AV, Nasonov DM, Endutkin AV, Zharkov DO, Bagryanskaya EG. Dynamics of 8-Oxoguanine in DNA: Decisive Effects of Base Pairing and Nucleotide Context. J Am Chem Soc 2023; 145:5613-5617. [PMID: 36867834 DOI: 10.1021/jacs.2c11230] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
8-Oxo-7,8-dihydroguanine (oxoG), an abundant DNA lesion, can mispair with adenine and induce mutations. To prevent this, cells possess DNA repair glycosylases that excise either oxoG from oxoG:C pairs (bacterial Fpg, human OGG1) or A from oxoG:A mispairs (bacterial MutY, human MUTYH). Early lesion recognition steps remain murky and may include enforced base pair opening or capture of a spontaneously opened pair. We adapted the CLEANEX-PM NMR protocol to detect DNA imino proton exchange and analyzed the dynamics of oxoG:C, oxoG:A, and their undamaged counterparts in nucleotide contexts with different stacking energy. Even in a poorly stacking context, the oxoG:C pair did not open easier than G:C, arguing against extrahelical base capture by Fpg/OGG1. On the contrary, oxoG opposite A significantly populated the extrahelical state, which may assist recognition by MutY/MUTYH.
Collapse
Affiliation(s)
- Sergey S Ovcherenko
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Andrey V Shernyukov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Dmitry M Nasonov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anton V Endutkin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| |
Collapse
|
2
|
Ryan BJ, Yang H, Bacurio JHT, Smith MR, Basu AK, Greenberg MM, Freudenthal BD. Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication. J Am Chem Soc 2022; 144:8054-8065. [PMID: 35499923 PMCID: PMC9097547 DOI: 10.1021/jacs.2c00193] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
N6-(2-Deoxy-α,β-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamido pyrimidine (Fapy•dG) is a prevalent form of genomic DNA damage. Fapy•dG is formed in greater amounts under anoxic conditions than the well-studied, chemically related 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxodGuo). Fapy•dG is more mutagenic in mammalian cells than 8-oxodGuo. A distinctive property of Fapy•dG is facile epimerization, but prior works with Fapy•dG analogues have precluded determining its effect on chemistry. We present crystallographic characterization of natural Fapy•dG in duplex DNA and as the template base for DNA polymerase β (Pol β). Fapy•dG adopts the β-anomer when base paired with cytosine but exists as a mixture of α- and β-anomers when promutagenically base paired with adenine. Rotation about the bond between the glycosidic nitrogen atom and the pyrimidine ring is also affected by the opposing nucleotide. Sodium cyanoborohydride soaking experiments trap the ring-opened Fapy•dG, demonstrating that ring opening and epimerization occur in the crystalline state. Ring opening and epimerization are facilitated by propitious water molecules that are observed in the structures. Determination of Fapy•dG mutagenicity in wild type and Pol β knockdown HEK 293T cells indicates that Pol β contributes to G → T transversions but also suppresses G → A transitions. Complementary kinetic studies have determined that Fapy•dG promotes mutagenesis by decreasing the catalytic efficiency of dCMP insertion opposite Fapy•dG, thus reducing polymerase fidelity. Kinetic studies have determined that dCMP incorporation opposite the β-anomer is ∼90 times faster than the α-anomer. This research identifies the importance of anomer dynamics, a feature unique to formamidopyrimidines, when considering the incorporation of nucleotides opposite Fapy•dG and potentially the repair of this structurally unusual lesion.
Collapse
Affiliation(s)
- Benjamin J Ryan
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Haozhe Yang
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Jan Henric T Bacurio
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Mallory R Smith
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Ashis K Basu
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| |
Collapse
|
3
|
Phillips CN, Schowe S, Langeberg CJ, Siddique N, Chapman EG, Resendiz MJE. Processing of RNA Containing 8-Oxo-7,8-Dihydroguanosine (8-oxoG) by the Exoribonuclease Xrn-1. Front Mol Biosci 2021; 8:780315. [PMID: 34869601 PMCID: PMC8634602 DOI: 10.3389/fmolb.2021.780315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/21/2021] [Indexed: 12/31/2022] Open
Abstract
Understanding how oxidatively damaged RNA is handled intracellularly is of relevance due to the link between oxidized RNA and the progression/development of some diseases as well as aging. Among the ribonucleases responsible for the decay of modified (chemically or naturally) RNA is the exonuclease Xrn-1, a processive enzyme that catalyzes the hydrolysis of 5′-phosphorylated RNA in a 5′→3′ direction. We set out to explore the reactivity of this exonuclease towards oligonucleotides (ONs, 20-nt to 30-nt long) of RNA containing 8-oxo-7,8-dihydroguanosine (8-oxoG), obtained via solid-phase synthesis. The results show that Xrn-1 stalled at sites containing 8-oxoG, evidenced by the presence of a slower moving band (via electrophoretic analyses) than that observed for the canonical analogue. The observed fragment(s) were characterized via PAGE and MALDI-TOF to confirm that the oligonucleotide fragment(s) contained a 5′-phosphorylated 8-oxoG. Furthermore, the yields for this stalling varied from app. 5–30% with 8-oxoG located at different positions and in different sequences. To gain a better understanding of the decreased nuclease efficiency, we probed: 1) H-bonding and spatial constraints; 2) anti-syn conformational changes; 3) concentration of divalent cation; and 4) secondary structure. This was carried out by introducing methylated or brominated purines (m1G, m6,6A, or 8-BrG), probing varying [Mg2+], and using circular dichroism (CD) to explore the formation of structured RNA. It was determined that spatial constraints imposed by conformational changes around the glycosidic bond may be partially responsible for stalling, however, the results do not fully explain some of the observed higher stalling yields. We hypothesize that altered π-π stacking along with induced H-bonding interactions between 8-oxoG and residues within the binding site may also play a role in the decreased Xrn-1 efficiency. Overall, these observations suggest that other factors, yet to be discovered/established, are likely to contribute to the decay of oxidized RNA. In addition, Xrn-1 degraded RNA containing m1G, and stalled mildly at sites where it encountered m6,6A, or 8-BrG, which is of particular interest given that the former two are naturally occurring modifications.
Collapse
Affiliation(s)
- Cheyenne N Phillips
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - Shawn Schowe
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - Conner J Langeberg
- Department of Chemistry, University of Denver, Denver, CO, United States
| | - Namoos Siddique
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - Erich G Chapman
- Department of Chemistry, University of Denver, Denver, CO, United States
| | - Marino J E Resendiz
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| |
Collapse
|
4
|
Karakaidos P, Karagiannis D, Rampias T. Resolving DNA Damage: Epigenetic Regulation of DNA Repair. Molecules 2020; 25:molecules25112496. [PMID: 32471288 PMCID: PMC7321228 DOI: 10.3390/molecules25112496] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/18/2022] Open
Abstract
Epigenetic research has rapidly evolved into a dynamic field of genome biology. Chromatin regulation has been proved to be an essential aspect for all genomic processes, including DNA repair. Chromatin structure is modified by enzymes and factors that deposit, erase, and interact with epigenetic marks such as DNA and histone modifications, as well as by complexes that remodel nucleosomes. In this review we discuss recent advances on how the chromatin state is modulated during this multi-step process of damage recognition, signaling, and repair. Moreover, we examine how chromatin is regulated when different pathways of DNA repair are utilized. Furthermore, we review additional modes of regulation of DNA repair, such as through the role of global and localized chromatin states in maintaining expression of DNA repair genes, as well as through the activity of epigenetic enzymes on non-nucleosome substrates. Finally, we discuss current and future applications of the mechanistic interplays between chromatin regulation and DNA repair in the context cancer treatment.
Collapse
Affiliation(s)
| | - Dimitris Karagiannis
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA;
| | - Theodoros Rampias
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
- Correspondence: ; Tel.: +30-210-659-7469
| |
Collapse
|
5
|
Dynamic DNA Energy Landscapes and Substrate Complexity in Triplet Repeat Expansion and DNA Repair. Biomolecules 2019; 9:biom9110709. [PMID: 31698848 PMCID: PMC6920812 DOI: 10.3390/biom9110709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 12/14/2022] Open
Abstract
DNA repeat domains implicated in DNA expansion diseases exhibit complex conformational and energy landscapes that impact biological outcomes. These landscapes include ensembles of entropically driven positional interchanges between isoenergetic, isomeric looped states referred to as rollamers. Here, we present evidence for the position-dependent impact on repeat DNA energy landscapes of an oxidative lesion (8oxodG) and of an abasic site analogue (tetrahydrofuran, F), the universal intermediate in base excision repair (BER). We demonstrate that these lesions modulate repeat bulge loop distributions within the wider dynamic rollamer triplet repeat landscapes. We showed that the presence of a lesion disrupts the energy degeneracy of the rollameric positional isomers. This lesion-induced disruption leads to the redistribution of loop isomers within the repeat loop rollamer ensemble, favoring those rollameric isomers where the lesion is positioned to be energetically least disruptive. These dynamic ensembles create a highly complex energy/conformational landscape of potential BER enzyme substrates to select for processing or to inhibit processing. We discuss the implications of such lesion-induced alterations in repeat DNA energy landscapes in the context of potential BER repair outcomes, thereby providing a biophysical basis for the intriguing in vivo observation of a linkage between pathogenic triplet repeat expansion and DNA repair.
Collapse
|
6
|
McCauley MJ, Furman L, Dietrich CA, Rouzina I, Núñez ME, Williams MC. Quantifying the stability of oxidatively damaged DNA by single-molecule DNA stretching. Nucleic Acids Res 2019. [PMID: 29522114 PMCID: PMC5934642 DOI: 10.1093/nar/gky148] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
One of the most common DNA lesions is created when reactive oxygen alters guanine. 8-oxo-guanine may bind in the anti-conformation with an opposing cytosine or in the syn-conformation with an opposing adenine paired by transversion, and both conformations may alter DNA stability. Here we use optical tweezers to measure the stability of DNA hairpins containing 8-oxoguanine (8oxoG) lesions, comparing the results to predictive models of base-pair energies in the absence of the lesion. Contrasted with either a canonical guanine-cytosine or adenine-thymine pair, an 8oxoG-cytosine base pair shows significant destabilization of several kBT. The magnitude of destabilization is comparable to guanine-thymine ‘wobble’ and cytosine-thymine mismatches. Furthermore, the measured energy of 8oxoG-adenine corresponds to theoretical predictions for guanine-adenine pairs, indicating that oxidative damage does not further destabilize this mismatch in our experiments, in contrast to some previous observations. These results support the hypothesis that oxidative damage to guanine subtly alters the direction of the guanine dipole, base stacking interactions, the local backbone conformation, and the hydration of the modified base. This localized destabilization under stress provides additional support for proposed mechanisms of enzyme repair.
Collapse
Affiliation(s)
- Micah J McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Leah Furman
- Department of Chemistry, Wellesley College, Wellesley, MA 02481, USA
| | | | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, The Ohio State University, Center for Retroviral Research, and Center for RNA Biology, Columbus, OH 43210, USA
| | - Megan E Núñez
- Department of Chemistry, Wellesley College, Wellesley, MA 02481, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| |
Collapse
|
7
|
Killelea T, Palud A, Akcha F, Lemor M, L'haridon S, Godfroy A, Henneke G. The interplay at the replisome mitigates the impact of oxidative damage on the genetic integrity of hyperthermophilic Archaea. eLife 2019; 8:45320. [PMID: 31184586 PMCID: PMC6559790 DOI: 10.7554/elife.45320] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022] Open
Abstract
8-oxodeoxyguanosine (8-oxodG), a major oxidised base modification, has been investigated to study its impact on DNA replication in hyperthermophilic Archaea. Here we show that 8-oxodG is formed in the genome of growing cells, with elevated levels following exposure to oxidative stress. Functional characterisation of cell-free extracts and the DNA polymerisation enzymes, PolB, PolD, and the p41/p46 complex, alone or in the presence of accessory factors (PCNA and RPA) indicates that translesion synthesis occurs under replicative conditions. One of the major polymerisation effects was stalling, but each of the individual proteins could insert and extend past 8-oxodG with differing efficiencies. The introduction of RPA and PCNA influenced PolB and PolD in similar ways, yet provided a cumulative enhancement to the polymerisation performance of p41/p46. Overall, 8-oxodG translesion synthesis was seen to be potentially mutagenic leading to errors that are reminiscent of dA:8-oxodG base pairing.
Collapse
Affiliation(s)
- Tom Killelea
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Adeline Palud
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Farida Akcha
- Laboratoire d'Ecotoxicologie, Ifremer, Nantes, France
| | - Mélanie Lemor
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Stephane L'haridon
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Anne Godfroy
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Ghislaine Henneke
- Univ Brest, Ifremer, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| |
Collapse
|
8
|
Kumari B, Sinha KK, DAS P. Complex interplay of lesion-specific DNA repair enzyme on bistranded clustered DNA damage harboring Tg:G mismatch in nucleosome core particles. J Biosci 2018; 43:575-583. [PMID: 30207305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
5,6-Dihydroxy-5,6-dihydrothymine (thymine glycol) and 7,8-dihydro-8-oxo-20-deoxyguanosine (8-oxodG) are major DNA damage lesions produced by endogenous oxidative stress, as well as inflicted by carcinogens and ionizing radiation. The processing of Tg:G mismatch and 8-oxodG in close proximity of each other in a bistranded clustered environment in DNA oligomer duplexes as well as in a nucleosome core particle (NCP) model are reported here. The processing of the lesions was evaluated by purified enzyme cocktails of hNTH1 and hOGG1 as well as with a HeLa cell extract. Interestingly, the yield of double-strand breaks (DSBs) resulting from the processing of the bistranded lesions are appreciably lower when the DNA is treated with the HeLa cell extract compared with the relevant purified enzyme cocktail in both models. Clustered bistranded lesions become more repair refractive when reconstituted as an NCP. This indicates a complex interplay between the repair enzymes that influence the processing of the bistranded cluster damage positively to avoid the formation of DSBs under cellular conditions. In addition to position and orientation of the lesions, the type of the lesions in the cluster environment in DNA along with the relative abundance of the lesion-specific enzymes in the cells strongly prevents the processing of the oxidized nucleobases.
Collapse
Affiliation(s)
- Bhavini Kumari
- Department of Chemistry, Indian Institute of Technology Patna, Bihta, Bihar 801 103, India
| | | | | |
Collapse
|
9
|
Complex interplay of lesion-specific DNA repair enzyme on bistranded clustered DNA damage harboring Tg:G mismatch in nucleosome core particles. J Biosci 2018. [DOI: 10.1007/s12038-018-9786-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
10
|
Kumari B, Jha P, Sinha KK, Das P. Vicinal abasic site impaired processing of a Tg:G mismatch and 8-oxoguanine lesions in three-component bistranded clustered DNA damage. RSC Adv 2018; 8:17921-17926. [PMID: 35542077 PMCID: PMC9080475 DOI: 10.1039/c8ra01992d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/03/2018] [Indexed: 11/23/2022] Open
Abstract
The occurrence of 7,8-dihydro-8-oxo-2′deoxyguanosine (8-oxodG), thymine glycol:guanine (Tg:G) mismatch and abasic site DNA damage lesions in close proximity induce repair refractive multicomponent clustered DNA damage. Herein, the influence of abasic sites in the processing of 8-oxodG lesion and Tg:G mismatch bistranded cluster is evaluated. Abasic sites are found to impart conformational destabilization that appreciably hinders the repair activity of the other lesions whenever present in a cluster combination. The repair process reduces the formation of double strand breaks (DSBs) and renders this three-lesion combination a non-DSB forming cluster. The stability of the DNA duplex harbouring these three lesions is highly compromised due to altered base helicity and base stacking phenomena leading to impaired repair. The occurrence of 7,8-dihydro-8-oxo-2′deoxyguanosine (8-oxodG), thymine glycol:guanine (Tg:G) mismatch and abasic site DNA damage lesions in close proximity induce repair refractive non-DSB cluster.![]()
Collapse
Affiliation(s)
| | - Pravin Jha
- Department of Biotechnology
- NIPER Hajipur
- India
| | | | - Prolay Das
- Department of Chemistry
- IIT Patna
- Patna-801103
- India
| |
Collapse
|
11
|
Li H, Endutkin AV, Bergonzo C, Fu L, Grollman A, Zharkov DO, Simmerling C. DNA Deformation-Coupled Recognition of 8-Oxoguanine: Conformational Kinetic Gating in Human DNA Glycosylase. J Am Chem Soc 2017; 139:2682-2692. [PMID: 28098999 DOI: 10.1021/jacs.6b11433] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
8-Oxoguanine (8-oxoG), a mutagenic DNA lesion generated under oxidative stress, differs from its precursor guanine by only two substitutions (O8 and H7). 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 a 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.
Collapse
Affiliation(s)
| | - Anton V Endutkin
- Novosibirsk State University , 2 Pirogova Street, Novosibirsk 630090, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine , 8 Lavrentieva Avenue, Novosibirsk 630090, Russia
| | | | - Lin Fu
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
| | | | - Dmitry O Zharkov
- Novosibirsk State University , 2 Pirogova Street, Novosibirsk 630090, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine , 8 Lavrentieva Avenue, Novosibirsk 630090, Russia
| | | |
Collapse
|
12
|
La Rosa G, Zacharias M. Global deformation facilitates flipping of damaged 8-oxo-guanine and guanine in DNA. Nucleic Acids Res 2016; 44:9591-9599. [PMID: 27651459 PMCID: PMC5175360 DOI: 10.1093/nar/gkw827] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/04/2016] [Accepted: 09/08/2016] [Indexed: 01/20/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Giuseppe La Rosa
- Physik-Department T38, Technische Universität München, James-Franck-Straße 1, D-85748 Garching, Germany
| | - Martin Zacharias
- Physik-Department T38, Technische Universität München, James-Franck-Straße 1, D-85748 Garching, Germany
| |
Collapse
|
13
|
Cravens SL, Stivers JT. Comparative Effects of Ions, Molecular Crowding, and Bulk DNA on the Damage Search Mechanisms of hOGG1 and hUNG. Biochemistry 2016; 55:5230-42. [PMID: 27571472 DOI: 10.1021/acs.biochem.6b00482] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The energetic nature of the interactions of DNA base excision repair glycosylases with undamaged and damaged DNA and the nuclear environment are expected to significantly impact the time it takes for these enzymes to search for damaged DNA bases. In particular, the high concentration of monovalent ions, macromolecule crowding, and densely packed DNA chains in the cell nucleus could alter the search mechanisms of these enzymes as compared to findings in dilute buffers typically used in in vitro experiments. Here we utilize an in vitro system where the concerted effects of monovalent ions, macromolecular crowding, and high concentrations of bulk DNA chains on the activity of two paradigm human DNA glycosylases can be determined. We find that the energetic nature of the observed binding free energies of human 8-oxoguanine DNA glycosylase (hOGG1) and human uracil DNA glycosylase (hUNG) for undamaged DNA are derived from different sources. Although hOGG1 uses primarily nonelectrostatic binding interactions with nonspecific DNA, hUNG uses a salt-dependent electrostatic binding mode. Both enzymes turn to a nonelectrostatic mode in their specific complexes with damaged bases in DNA, which enhances damage site specificity at physiological ion concentrations. Neither enzyme was capable of efficiently locating and removing their respective damaged bases in the combined presence of physiological ions and a bulk DNA chain density approximating that found in the nucleus. However, the addition of an inert crowding agent to mimic macromolecular crowding in the nucleus largely restored their ability to track DNA chains and locate damaged sites. These findings suggest how the concerted action of monovalent ions and crowding could contribute to efficient DNA damage recognition in cells.
Collapse
Affiliation(s)
- Shannen L Cravens
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
| |
Collapse
|
14
|
Norabuena EM, Barnes Williams S, Klureza MA, Goehring LJ, Gruessner B, Radhakrishnan ML, Jamieson ER, Núñez ME. Effect of the Spiroiminodihydantoin Lesion on Nucleosome Stability and Positioning. Biochemistry 2016; 55:2411-21. [PMID: 27074396 DOI: 10.1021/acs.biochem.6b00093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA is constantly under attack by oxidants, generating a variety of potentially mutagenic covalently modified species, including oxidized guanine base products. One such product is spiroiminodihydantoin (Sp), a chiral, propeller-shaped lesion that strongly destabilizes the DNA helix in its vicinity. Despite its unusual shape and thermodynamic effect on double-stranded DNA structure, DNA duplexes containing the Sp lesion form stable nucleosomes upon being incubated with histone octamers. Indeed, among six different combinations of lesion location and stereochemistry, only two duplexes display a diminished ability to form nucleosomes, and these only by ∼25%; the other four are statistically indistinguishable from the control. Nonetheless, kinetic factors also play a role: when the histone proteins have less time during assembly of the core particle to sample both lesion-containing and normal DNA strands, they are more likely to bind the Sp lesion DNA than during slower assembly processes that better approximate thermodynamic equilibrium. Using DNase I footprinting and molecular modeling, we discovered that the Sp lesion causes only a small perturbation (±1-2 bp) on the translational position of the DNA within the nucleosome. Each diastereomeric pair of lesions has the same effect on nucleosome positioning, but lesions placed at different locations behave differently, illustrating that the location of the lesion and not its shape serves as the primary determinant of the most stable DNA orientation.
Collapse
Affiliation(s)
- Erika M Norabuena
- Department of Chemistry and Program in Biochemistry, Mount Holyoke College , South Hadley, Massachusetts 01075, United States
| | - Sara Barnes Williams
- Department of Chemistry and Program in Biochemistry, Mount Holyoke College , South Hadley, Massachusetts 01075, United States
| | - Margaret A Klureza
- Department of Chemistry and Program in Biochemistry, Wellesley College , Wellesley, Massachusetts 02481, United States
| | - Liana J Goehring
- Department of Chemistry and Program in Biochemistry, Wellesley College , Wellesley, Massachusetts 02481, United States
| | - Brian Gruessner
- Department of Chemistry and Program in Biochemistry, Smith College , Northampton, Massachusetts 01063, United States
| | - Mala L Radhakrishnan
- Department of Chemistry and Program in Biochemistry, Wellesley College , Wellesley, Massachusetts 02481, United States
| | - Elizabeth R Jamieson
- Department of Chemistry and Program in Biochemistry, Smith College , Northampton, Massachusetts 01063, United States
| | - Megan E Núñez
- Department of Chemistry and Program in Biochemistry, Wellesley College , Wellesley, Massachusetts 02481, United States
| |
Collapse
|
15
|
Jana K, Ganguly B. In silico studies with substituted adenines to achieve a remarkable stability of mispairs with thymine nucleobase. NEW J CHEM 2016. [DOI: 10.1039/c5nj02311d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The modified adenine and thymine mispair achieves a remarkable stability, which can presumably help the DNA lesions to be less cytotoxic.
Collapse
Affiliation(s)
- Kalyanashis Jana
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR – Central Salt and Marine Chemicals Research Institute
- Bhavnagar – 364002
- India
- Academy of Scientific and Innovative Research
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR – Central Salt and Marine Chemicals Research Institute
- Bhavnagar – 364002
- India
- Academy of Scientific and Innovative Research
| |
Collapse
|
16
|
Buechner CN, Maiti A, Drohat AC, Tessmer I. Lesion search and recognition by thymine DNA glycosylase revealed by single molecule imaging. Nucleic Acids Res 2015; 43:2716-29. [PMID: 25712093 PMCID: PMC4357730 DOI: 10.1093/nar/gkv139] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The ability of DNA glycosylases to rapidly and efficiently detect lesions among a vast excess of nondamaged DNA bases is vitally important in base excision repair (BER). Here, we use single molecule imaging by atomic force microscopy (AFM) supported by a 2-aminopurine fluorescence base flipping assay to study damage search by human thymine DNA glycosylase (hTDG), which initiates BER of mutagenic and cytotoxic G:T and G:U mispairs in DNA. Our data reveal an equilibrium between two conformational states of hTDG–DNA complexes, assigned as search complex (SC) and interrogation complex (IC), both at target lesions and undamaged DNA sites. Notably, for both hTDG and a second glycosylase, hOGG1, which recognizes structurally different 8-oxoguanine lesions, the conformation of the DNA in the SC mirrors innate structural properties of their respective target sites. In the IC, the DNA is sharply bent, as seen in crystal structures of hTDG lesion recognition complexes, which likely supports the base flipping required for lesion identification. Our results support a potentially general concept of sculpting of glycosylases to their targets, allowing them to exploit the energetic cost of DNA bending for initial lesion sensing, coupled with continuous (extrahelical) base interrogation during lesion search by DNA glycosylases.
Collapse
Affiliation(s)
- Claudia N Buechner
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Atanu Maiti
- Department of Biochemistry and Molecular Biology and Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology and Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| |
Collapse
|
17
|
Szulik M, Pallan PS, Nocek B, Voehler M, Banerjee S, Brooks S, Joachimiak A, Egli M, Eichman BF, Stone MP. Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. Biochemistry 2015; 54:1294-305. [PMID: 25632825 PMCID: PMC4325598 DOI: 10.1021/bi501534x] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson-Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T(8)X(9)G(10)-3' sequence of the DDD, were compared. The presence of 5caC at the X(9) base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A(5):T(8), whereas 5caC did not. At the oxidized base pair G(4):X(9), 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C(3):G(10). No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G(4):X(9); each favored Watson-Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N(4) exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.
Collapse
Affiliation(s)
- Marta
W. Szulik
- Department
of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt
Ingram Cancer Center, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Pradeep S. Pallan
- Department
of Biochemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt
Ingram Cancer Center, and Center for Structural Biology, School of
Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Boguslaw Nocek
- Bioscience
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Markus Voehler
- Department
of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt
Ingram Cancer Center, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Surajit Banerjee
- Northeastern
Collaborative Access Team and Department of Chemistry and Chemical
Biology, Cornell University, Argonne National
Laboratory, Argonne, Illinois 60439, United
States
| | - Sonja Brooks
- Department
of Biological Sciences, Vanderbilt Institute of Chemical Biology,
and Center for Structural Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Andrzej Joachimiak
- Bioscience
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Martin Egli
- Department
of Biochemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt
Ingram Cancer Center, and Center for Structural Biology, School of
Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Brandt F. Eichman
- Department
of Biological Sciences, Vanderbilt Institute of Chemical Biology,
and Center for Structural Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Michael P. Stone
- Department
of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt
Ingram Cancer Center, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States,(M.P.S.) Tel.: 615-322-2589; E-mail:
| |
Collapse
|
18
|
Szulik MW, Voehler M, Stone MP. NMR analysis of base-pair opening kinetics in DNA. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2014; 59:7.20.1-18. [PMID: 25501592 PMCID: PMC4274747 DOI: 10.1002/0471142700.nc0720s59] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Base pairing in nucleic acids plays a crucial role in their structure and function. Differences in the base-pair opening and closing kinetics of individual double-stranded DNA sequences or between chemically modified base pairs provide insight into the recognition of these base pairs by DNA processing enzymes. This unit describes how to quantify the kinetics for localized base pairs by observing changes in the imino proton signals by nuclear magnetic resonance spectroscopy. The determination of all relevant parameters using state-of-the art techniques and NMR instrumentation, including cryoprobes, is discussed.
Collapse
Affiliation(s)
- Marta W Szulik
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennesee; These authors contributed equally to this work
| | | | | |
Collapse
|
19
|
Development of ABEEMσπ polarizable force field for oxidized adenine base pairs: investigation of the interaction and mutagenic mechanism. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1469-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
20
|
Liu C, Wang Y, Zhao D, Gong L, Yang Z. Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field. J Mol Graph Model 2014; 47:62-76. [DOI: 10.1016/j.jmgm.2013.10.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/21/2013] [Accepted: 10/21/2013] [Indexed: 12/21/2022]
|
21
|
Wenke BB, Huiting LN, Frankel EB, Lane BF, Núñez ME. Base pair opening in a deoxynucleotide duplex containing a cis-syn thymine cyclobutane dimer lesion. Biochemistry 2013; 52:9275-85. [PMID: 24328089 DOI: 10.1021/bi401312r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cis-syn thymine cyclobutane dimer is a DNA photoproduct implicated in skin cancer. We compared the stability of individual base pairs in thymine dimer-containing duplexes to undamaged parent 10-mer duplexes. UV melting thermodynamic measurements, CD spectroscopy, and 2D NOESY NMR spectroscopy confirm that the thymine dimer lesion is locally and moderately destabilizing within an overall B-form duplex conformation. We measured the rates of exchange of individual imino protons by NMR using magnetization transfer from water and determined the equilibrium constant for the opening of each base pair K(op). In the normal duplex K(op) decreases from the frayed ends of the duplex toward the center, such that the central TA pair is the most stable with a K(op) of 8 × 10⁻⁷. In contrast, base pair opening at the 5'T of the thymine dimer is facile. The 5'T of the dimer has the largest equilibrium constant (K(op) = 3 × 10⁻⁴) in its duplex, considerably larger than even the frayed penultimate base pairs. Notably, base pairing by the 3'T of the dimer is much more stable than by the 5'T, indicating that the predominant opening mechanism for the thymine dimer lesion is not likely to be flipping out into solution as a single unit. The dimer asymmetrically affects the stability of the duplex in its vicinity, destabilizing base pairing on its 5' side more than on the 3' side. The striking differences in base pair opening between parent and dimer duplexes occur independently of the duplex-single strand melting transitions.
Collapse
Affiliation(s)
- Belinda B Wenke
- Department of Chemistry, Mount Holyoke College , South Hadley, Massachusetts 01075, United States
| | | | | | | | | |
Collapse
|
22
|
Szulik MW, Voehler MW, Ganguly M, Gold B, Stone MP. Site-specific stabilization of DNA by a tethered major groove amine, 7-aminomethyl-7-deaza-2'-deoxyguanosine. Biochemistry 2013; 52:7659-68. [PMID: 24131376 PMCID: PMC3812902 DOI: 10.1021/bi400695r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
A cationic
7-aminomethyl-7-deaza-2′-deoxyguanosine (7amG)
was incorporated site-specifically into the self-complementary duplex
d(G1A2G3A4X5C6G7C8T9C10T11C12)2 (X = 7amG). This construct placed two positively charged amines adjacent
to the major groove edges of two symmetry-related guanines, providing
a model for probing how cation binding in the major groove modulates
the structure and stability of DNA. Molecular dynamics calculations
restrained by nuclear magnetic resonance (NMR) data revealed that
the tethered cationic amines were in plane with the modified base
pairs. The tethered amines did not form salt bridges to the phosphodiester
backbone. There was also no indication of the amines being capable
of hydrogen bonding to flanking DNA bases. NMR spectroscopy as a function
of temperature revealed that the X5 imino resonance remained
sharp at 55 °C. Additionally, two 5′-neighboring base
pairs, A4:T9 and G3:C10, were stabilized with respect to the exchange of their imino protons
with solvent. The equilibrium constant for base pair opening at the
A4:T9 base pair determined by magnetization
transfer from water in the absence and presence of added ammonia base
catalyst decreased for the modified duplex compared to that of the
A4:T9 base pair in the unmodified duplex, which
confirmed that the overall fraction of the A4:T9 base pair in the open state of the modified duplex decreased. This
was also observed for the G3:C10 base pair,
where αKop for the G3:C10 base pair in the modified duplex was 3.0 × 106 versus 4.1 × 106 for the same base pair in
the unmodified duplex. In contrast, equilibrium constants for base
pair opening at the X5:C8 and C6:G7 base pairs did not change at 15 °C. These results argue
against the notion that electrostatic interactions with DNA are entirely
entropic and suggest that major groove cations can stabilize DNA via
enthalpic contributions to the free energy of duplex formation.
Collapse
Affiliation(s)
- Marta W Szulik
- Department of Chemistry and Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37235, United States
| | | | | | | | | |
Collapse
|
23
|
Dršata T, Kara M, Zacharias M, Lankaš F. Effect of 8-oxoguanine on DNA structure and deformability. J Phys Chem B 2013; 117:11617-22. [PMID: 24028561 DOI: 10.1021/jp407562t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
8-Oxoguanine (oxoG) is an abundant product of oxidative DNA damage. It is removed by repair glycosylases, but exactly how the enzymes recognize oxoG in the large surplus of undamaged bases is not fully understood. The lesion may induce changes in the properties of naked DNA that facilitate the recognition. In this work, we assess the effect of oxoG on DNA structure and mechanical deformability. We performed extensive unrestrained, atomic resolution molecular dynamics simulations to parametrize a nonlocal, rigid base mechanical model of DNA. Our data indicate that oxoG induces unwinding of the base pair step at the 5'-side of the lesion. This brings the damaged DNA closer to its conformation in the initial complex with bacterial glycosylase MutM. The untwisting is partially caused by different BII substate populations and is further enhanced by the base-sugar repulsion within oxoG. On the other hand, our analysis shows that damaged and undamaged DNA have very similar harmonic stiffness. These results suggest an indirect readout component of the MutM-DNA initial complex formation. They also help one to understand the effect of oxoG on the formation of nucleosomes and looped gene regulatory complexes.
Collapse
Affiliation(s)
- Tomáš Dršata
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstı́ 2, 166 10, Praha 6, Czech Republic
| | | | | | | |
Collapse
|
24
|
Every AE, Russu IM. Opening dynamics of 8-oxoguanine in DNA. J Mol Recognit 2013; 26:175-80. [PMID: 23456741 DOI: 10.1002/jmr.2262] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 12/18/2012] [Accepted: 12/22/2012] [Indexed: 12/15/2022]
Abstract
8-oxoguanine is a major lesion of genomic DNA that results from oxidation of guanine by reactive oxygen species. The repair of this lesion is initiated by 8-oxoguanine glycosylases, which excise the damaged base by "flipping" it outside the DNA double helix. The molecular mechanisms involved in the specific recognition of the damaged base by the enzyme are not yet fully understood. Several models have proposed that, in DNA, the base pair between 8-oxoguanine and cytosine may possess altered dynamic properties that could help the enzyme locate the lesion and could favor the selective extra-helical flipping of the damaged base. To test this proposal, we have characterized the spontaneous opening of the base pair between 8-oxoguanine and cytosine in a DNA double helix using NMR spectroscopy and proton exchange. The results show that the rate of spontaneous opening of 8-oxoguanine and the lifetime of the base in the extra-helical state are the same as those of a canonical guanine-cytosine base pair, in the same base sequence context. This finding suggests that the opening dynamics of 8-oxoguanine, when paired with cytosine in DNA, does not play a significant role in the recognition of the lesion by glycosylases.
Collapse
Affiliation(s)
- Alicia E Every
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459, USA
| | | |
Collapse
|
25
|
Fleming AM, Burrows CJ. G-quadruplex folds of the human telomere sequence alter the site reactivity and reaction pathway of guanine oxidation compared to duplex DNA. Chem Res Toxicol 2013; 26:593-607. [PMID: 23438298 DOI: 10.1021/tx400028y] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Telomere shortening occurs during oxidative and inflammatory stress with guanine (G) as the major site of damage. In this work, a comprehensive profile of the sites of oxidation and structures of products observed from G-quadruplex and duplex structures of the human telomere sequence was studied in the G-quadruplex folds (hybrid (K(+)), basket (Na(+)), and propeller (K(+) + 50% CH3CN)) resulting from the sequence 5'-(TAGGGT)4T-3' and in an appropriate duplex containing one telomere repeat. Oxidations with four oxidant systems consisting of riboflavin photosensitization, carbonate radical generation, singlet oxygen, and the copper Fenton-like reaction were analyzed under conditions of low product conversion to determine relative reactivity. The one-electron oxidants damaged the 5'-G in G-quadruplexes leading to spiroiminodihydantoin (Sp) and 2,2,4-triamino-2H-oxazol-5-one (Z) as major products as well as 8-oxo-7,8-dihydroguanine (OG) and 5-guanidinohydantoin (Gh) in low relative yields, while oxidation in the duplex context produced damage at the 5'- and middle-Gs of GGG sequences and resulted in Gh being the major product. Addition of the reductant N-acetylcysteine (NAC) to the reaction did not alter the riboflavin-mediated damage sites but decreased Z by 2-fold and increased OG by 5-fold, while not altering the hydantoin ratio. However, NAC completely quenched the CO3(•-) reactions. Singlet oxygen oxidations of the G-quadruplex showed reactivity at all Gs on the exterior faces of G-quartets and furnished the product Sp, while no oxidation was observed in the duplex context under these conditions, and addition of NAC had no effect. Because a long telomere sequence would have higher-order structures of G-quadruplexes, studies were also conducted with 5'-(TAGGGT)8-T-3', and it provided oxidation profiles similar to those of the single G-quadruplex. Lastly, Cu(II)/H2O2-mediated oxidations were found to be indiscriminate in the damage patterns, and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih) was found to be a major duplex product, while nearly equal yields of 2Ih and Sp were observed in G-quadruplex contexts. These findings indicate that the nature of the secondary structure of folded DNA greatly alters both the reactivity of G toward oxidative stress as well as the product outcome and suggest that recognition of damage in telomeric sequences by repair enzymes may be profoundly different from that of B-form duplex DNA.
Collapse
Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | | |
Collapse
|
26
|
Lukin M, Zaliznyak T, Attaluri S, Johnson F, de Los Santos C. Solution structure of duplex DNA containing a β-carba-Fapy-dG lesion. Chem Res Toxicol 2012; 25:2423-31. [PMID: 22897814 DOI: 10.1021/tx300290b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The addition of hydroxyl radicals to the C8 position of guanine can lead to the formation of a 2,6-diamino-4-hydroxy-5-formamido-2'-deoxypyrimidine (Fapy-dG) lesion, whose endogenous levels in cellular DNA rival those of 8-oxo-7,8-dihydroxy-2'-deoxyguanosine. Despite its prevalence, the structure of duplex DNA containing Fapy-dG is unknown. We have prepared an undecameric duplex containing a centrally located β-cFapy-dG residue paired to dC and determined its solution structure by high-resolution NMR spectroscopy and restrained molecular dynamic simulations. The damaged duplex adopts a right-handed helical structure with all residues in an anti conformation, forming Watson-Crick base pair alignments, and 2-deoxyribose conformations in the C2'-endo/C1'-exo range. The formamido group of Fapy rotates out of the pyrimidine plane and is present in the Z and E configurations that equilibrate with an approximate 2:1 population ratio. The two isomeric duplexes show similar lesion-induced deviations from a canonical B-from DNA conformation that are minor and limited to the central three-base-pair segment of the duplex, affecting the stacking interactions with the 5-lesion-neighboring residue. We discuss the implications of our observations for translesion synthesis during DNA replication and the recognition of Fapy-dG by DNA glycosylases.
Collapse
Affiliation(s)
- Mark Lukin
- Department of Pharmacological Sciences, Stony Brook University-School of Medicine, Stony Brook, NY 11794-8651, USA
| | | | | | | | | |
Collapse
|
27
|
Yennie CJ, Delaney S. Thermodynamic consequences of the hyperoxidized guanine lesion guanidinohydantoin in duplex DNA. Chem Res Toxicol 2012; 25:1732-9. [PMID: 22780843 DOI: 10.1021/tx300190a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Guanidinohydantoin (Gh) is a hyperoxidized DNA lesion produced by oxidation of 8-oxo-7,8-dihydroguanine (8-oxoG). Previous work has shown that Gh is potently mutagenic in both in vitro and in vivo coding for G → T and G → C transversion mutations. In this work, analysis by circular dichroism shows that the Gh lesion does not significantly alter the global structure of a 15-mer duplex and that the DNA remains in the B-form. However, we find that Gh causes a large decrease in the thermal stability, decreasing the duplex melting temperature by ~17 °C relative to an unmodified duplex control. Using optical melting analysis and differential scanning calorimetry, the thermodynamic parameters describing duplex melting were also determined. We find that the Gh lesion causes a dramatic decrease in the enthalpic stability of the duplex. This enthalpic destabilization is somewhat tempered by entropic stabilization; yet, Gh results in an overall decrease in thermodynamic stability of the duplex relative to a control that lacks DNA damage, with a ΔΔG° of -7 kcal/mol. These results contribute to our understanding of the consequences of hyperoxidation of G and provide insight into how the thermal and thermodynamic destabilization caused by Gh may influence replication and/or repair of the lesion.
Collapse
Affiliation(s)
- Craig J Yennie
- Department of Chemistry, Brown University, Providence, RI 02912, USA
| | | |
Collapse
|
28
|
Crenshaw CM, Nam K, Oo K, Kutchukian PS, Bowman BR, Karplus M, Verdine GL. Enforced presentation of an extrahelical guanine to the lesion recognition pocket of human 8-oxoguanine glycosylase, hOGG1. J Biol Chem 2012; 287:24916-28. [PMID: 22511791 PMCID: PMC3408145 DOI: 10.1074/jbc.m111.316497] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A poorly understood aspect of DNA repair proteins is their ability to identify exceedingly rare sites of damage embedded in a large excess of nearly identical undamaged DNA, while catalyzing repair only at the damaged sites. Progress toward understanding this problem has been made by comparing the structures and biochemical behavior of these enzymes when they are presented with either a target lesion or a corresponding undamaged nucleobase. Trapping and analyzing such DNA-protein complexes is particularly difficult in the case of base extrusion DNA repair proteins because of the complexity of the repair reaction, which involves extrusion of the target base from DNA followed by its insertion into the active site where glycosidic bond cleavage is catalyzed. Here we report the structure of a human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, in which a normal guanine from DNA has been forcibly inserted into the enzyme active site. Although the interactions of the nucleobase with the active site are only subtly different for G versus oxoG, hOGG1 fails to catalyze excision of the normal nucleobase. This study demonstrates that even if hOGG1 mistakenly inserts a normal base into its active site, the enzyme can still reject it on the basis of catalytic incompatibility.
Collapse
Affiliation(s)
- Charisse M. Crenshaw
- From the Departments of Molecular and Cellular Biology, ,Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Kwangho Nam
- Chemical and Chemical Biology, and ,Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138
| | | | - Peter S. Kutchukian
- Chemical and Chemical Biology, and ,Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Brian R. Bowman
- Chemical and Chemical Biology, and ,Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Martin Karplus
- Chemical and Chemical Biology, and ,the L'Institut de Science et d'Ingénierie Supramoléculaires, Université Louis Pasteur, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Gregory L. Verdine
- Chemical and Chemical Biology, and ,Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, ,the Program in Cancer Chemical Biology and Chemical Biology Initiative, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, and , To whom correspondence should be addressed. 12 Oxford St., Cambridge, MA 02138. Fax: 617-495-8755; E-mail:
| |
Collapse
|
29
|
Delaney S, Jarem DA, Volle CB, Yennie CJ. Chemical and biological consequences of oxidatively damaged guanine in DNA. Free Radic Res 2012; 46:420-41. [PMID: 22239655 DOI: 10.3109/10715762.2011.653968] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Of the four native nucleosides, 2'-deoxyguanosine (dGuo) is most easily oxidized. Two lesions derived from dGuo are 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fapy)∙dGuo. Furthermore, while steady-state levels of 8-oxodGuo can be detected in genomic DNA, it is also known that 8-oxodGuo is more easily oxidized than dGuo. Thus, 8-oxodGuo is susceptible to further oxidation to form several hyperoxidized dGuo products. This review addresses the structural impact, the mutagenic and genotoxic potential, and biological implications of oxidatively damaged DNA, in particular 8-oxodGuo, Fapy∙dGuo, and the hyperoxidized dGuo products.
Collapse
Affiliation(s)
- Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI 02912, USA.
| | | | | | | |
Collapse
|