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Vemulapalli S, Hashemi M, Chen Y, Pramanik S, Bhakat KK, Lyubchenko YL. Nanoscale Interaction of Endonuclease APE1 with DNA. Int J Mol Sci 2024; 25:5145. [PMID: 38791183 PMCID: PMC11121393 DOI: 10.3390/ijms25105145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/17/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) is involved in DNA repair and transcriptional regulation mechanisms. This multifunctional activity of APE1 should be supported by specific structural properties of APE1 that have not yet been elucidated. Herein, we applied atomic force microscopy (AFM) to characterize the interactions of APE1 with DNA containing two well-separated G-rich segments. Complexes of APE1 with DNA containing G-rich segments were visualized, and analysis of the complexes revealed the affinity of APE1 to G-rich DNA sequences, and their yield was as high as 53%. Furthermore, APE1 is capable of binding two DNA segments leading to the formation of loops in the DNA-APE1 complexes. The analysis of looped APE1-DNA complexes revealed that APE1 can bridge G-rich segments of DNA. The yield of loops bridging two G-rich DNA segments was 41%. Analysis of protein size in various complexes was performed, and these data showed that loops are formed by APE1 monomer, suggesting that APE1 has two DNA binding sites. The data led us to a model for the interaction of APE1 with DNA and the search for the specific sites. The implication of these new APE1 properties in organizing DNA, by bringing two distant sites together, for facilitating the scanning for damage and coordinating repair and transcription is discussed.
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Affiliation(s)
- Sridhar Vemulapalli
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA; (S.V.); (M.H.)
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA; (S.V.); (M.H.)
- Department of Physics, Auburn University, Auburn, AL 36849-5318, USA
| | - Yingling Chen
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198-5805, USA; (Y.C.); (S.P.)
| | - Suravi Pramanik
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198-5805, USA; (Y.C.); (S.P.)
| | - Kishor K. Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198-5805, USA; (Y.C.); (S.P.)
| | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA; (S.V.); (M.H.)
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Stitch M, Avagliano D, Graczyk D, Clark IP, González L, Towrie M, Quinn SJ. Good Vibrations Report on the DNA Quadruplex Binding of an Excited State Amplified Ruthenium Polypyridyl IR Probe. J Am Chem Soc 2023; 145:21344-21360. [PMID: 37736878 PMCID: PMC10557146 DOI: 10.1021/jacs.3c06099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Indexed: 09/23/2023]
Abstract
The nitrile containing Ru(II)polypyridyl complex [Ru(phen)2(11,12-dCN-dppz)]2+ (1) is shown to act as a sensitive infrared probe of G-quadruplex (G4) structures. UV-visible absorption spectroscopy reveals enantiomer sensitive binding for the hybrid htel(K) and antiparallel htel(Na) G4s formed by the human telomer sequence d[AG3(TTAG3)3]. Time-resolved infrared (TRIR) of 1 upon 400 nm excitation indicates dominant interactions with the guanine bases in the case of Λ-1/htel(K), Δ-1/htel(K), and Λ-1/htel(Na) binding, whereas Δ-1/htel(Na) binding is associated with interactions with thymine and adenine bases in the loop. The intense nitrile transient at 2232 cm-1 undergoes a linear shift to lower frequency as the solution hydrogen bonding environment decreases in DMSO/water mixtures. This shift is used as a sensitive reporter of the nitrile environment within the binding pocket. The lifetime of 1 in D2O (ca. 100 ps) is found to increase upon DNA binding, and monitoring of the nitrile and ligand transients as well as the diagnostic DNA bleach bands shows that this increase is related to greater protection from the solvent environment. Molecular dynamics simulations together with binding energy calculations identify the most favorable binding site for each system, which are in excellent agreement with the observed TRIR solution study. This study shows the power of combining the environmental sensitivity of an infrared (IR) probe in its excited state with the TRIR DNA "site effect" to gain important information about the binding site of photoactive agents and points to the potential of such amplified IR probes as sensitive reporters of biological environments.
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Affiliation(s)
- Mark Stitch
- School
of Chemistry, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Davide Avagliano
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 19, 1090 Vienna, Austria
- Department
of Chemistry, Chemical Physics Theory Group, University of Toronto, 80 St. George St., Toronto, Ontario M5S 3H6, Canada
| | - Daniel Graczyk
- School
of Chemistry, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Ian P. Clark
- Central
Laser Facility, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K.
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 19, 1090 Vienna, Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währingerstr. 19, 1090 Vienna, Austria
| | - Michael Towrie
- Central
Laser Facility, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K.
| | - Susan J Quinn
- School
of Chemistry, University College Dublin, Dublin, D04 V1W8, Ireland
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Gillard M, Bonnet H, Lartia R, Yacoub H, Dejeu J, Defrancq E, Elias B. Luminescent Ruthenium(II) Complexes Used for the Detection of 8-Oxoguanine in the Human Telomeric Sequence. Bioconjug Chem 2023; 34:414-421. [PMID: 36689988 DOI: 10.1021/acs.bioconjchem.2c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Detecting cancer at the early stage of the disease is crucial to keep the best chance for successful treatment. The recent development of genomic screening, a methodology that is addressed to asymptomatic patients presumably at risk of carcinogenesis, has stimulated the quest for new tools able to signal the level of risk. Carcinogenesis has been associated to chronic oxidative stress exceeding the antioxidant defenses and leading to critical genome alteration levels. The telomeric regions are presumably the most exposed to oxidative stress due to their high concentration of guanine (i.e., the easiest oxidizable nucleic base). Accumulation of 8-oxoguanine in telomeres, thus oxidative lesions, was reportedly associated with telomeric crisis and carcinogenesis. In this study, we report on the capacity of Ru(II) polyazaaromatic complexes to photoprobe 8-oxoguanine into the human telomeric sequence with the view of developing new tools for cancer risk screening.
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Affiliation(s)
- Martin Gillard
- Molecular Chemistry, Materials and Catalysis (MOST), Université catholique de Louvain (UCLouvain), Institut de la Matière Condensée et des Nanosciences (IMCN), Place Louis Pasteur 1, bte L4.01.02, B-1348 Louvain-la-Neuve, Belgium
| | - Hugues Bonnet
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble-Alpes (UGA), CS 40700, 38058 Grenoble, France
| | - Rémy Lartia
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble-Alpes (UGA), CS 40700, 38058 Grenoble, France
| | - Hiba Yacoub
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble-Alpes (UGA), CS 40700, 38058 Grenoble, France
| | - Jérôme Dejeu
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble-Alpes (UGA), CS 40700, 38058 Grenoble, France.,CNRS UMR-6174, FEMTO-ST Institute, Université de Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Eric Defrancq
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble-Alpes (UGA), CS 40700, 38058 Grenoble, France
| | - Benjamin Elias
- Molecular Chemistry, Materials and Catalysis (MOST), Université catholique de Louvain (UCLouvain), Institut de la Matière Condensée et des Nanosciences (IMCN), Place Louis Pasteur 1, bte L4.01.02, B-1348 Louvain-la-Neuve, Belgium
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Wu S, Jiang L, Lei L, Fu C, Huang J, Hu Y, Dong Y, Chen J, Zeng Q. Crosstalk between G-quadruplex and ROS. Cell Death Dis 2023; 14:37. [PMID: 36653351 PMCID: PMC9849334 DOI: 10.1038/s41419-023-05562-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 12/25/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023]
Abstract
The excessive production of reactive oxygen species (ROS) can lead to single nucleic acid base damage, DNA strand breakage, inter- and intra-strand cross-linking of nucleic acids, and protein-DNA cross-linking involved in the pathogenesis of cancer, neurodegenerative diseases, and aging. G-quadruplex (G4) is a stacked nucleic acid structure that is ubiquitous across regulatory regions of multiple genes. Abnormal formation and destruction of G4s due to multiple factors, including cations, helicases, transcription factors (TFs), G4-binding proteins, and epigenetic modifications, affect gene replication, transcription, translation, and epigenetic regulation. Due to the lower redox potential of G-rich sequences and unique structural characteristics, G4s are highly susceptible to oxidative damage. Additionally, the formation, stability, and biological regulatory role of G4s are affected by ROS. G4s are involved in regulating gene transcription, translation, and telomere length maintenance, and are therefore key players in age-related degeneration. Furthermore, G4s also mediate the antioxidant process by forming stress granules and activating Nrf2, which is suggestive of their involvement in developing ROS-related diseases. In this review, we have summarized the crosstalk between ROS and G4s, and the possible regulatory mechanisms through which G4s play roles in aging and age-related diseases.
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Affiliation(s)
- Songjiang Wu
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Ling Jiang
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Li Lei
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Chuhan Fu
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Jinhua Huang
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Yibo Hu
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Yumeng Dong
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Jing Chen
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China.
| | - Qinghai Zeng
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China.
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Miclot T, Hognon C, Bignon E, Terenzi A, Grandemange S, Barone G, Monari A. Never Cared for What They Do: High Structural Stability of Guanine-Quadruplexes in the Presence of Strand-Break Damage. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103256. [PMID: 35630732 PMCID: PMC9146567 DOI: 10.3390/molecules27103256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022]
Abstract
DNA integrity is an important factor that assures genome stability and, more generally, the viability of cells and organisms. In the presence of DNA damage, the normal cell cycle is perturbed when cells activate their repair processes. Although efficient, the repair system is not always able to ensure complete restoration of gene integrity. In these cases, mutations not only may occur, but the accumulation of lesions can either lead to carcinogenesis or reach a threshold that induces apoptosis and programmed cell death. Among the different types of DNA lesions, strand breaks produced by ionizing radiation are the most toxic due to the inherent difficultly of repair, which may lead to genomic instability. In this article we show, by using classical molecular simulation techniques, that compared to canonical double-helical B-DNA, guanine-quadruplex (G4) arrangements show remarkable structural stability, even in the presence of two strand breaks. Since G4-DNA is recognized for its regulatory roles in cell senescence and gene expression, including oncogenes, this stability may be related to an evolutionary cellular response aimed at minimizing the effects of ionizing radiation.
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Affiliation(s)
- Tom Miclot
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo, viale delle Scienze, Ed. 17, 90128 Palermo, Italy; (T.M.); (A.T.)
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France; (C.H.); (E.B.)
| | - Cécilia Hognon
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France; (C.H.); (E.B.)
| | - Emmanuelle Bignon
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France; (C.H.); (E.B.)
| | - Alessio Terenzi
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo, viale delle Scienze, Ed. 17, 90128 Palermo, Italy; (T.M.); (A.T.)
| | | | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo, viale delle Scienze, Ed. 17, 90128 Palermo, Italy; (T.M.); (A.T.)
- Correspondence: (G.B.); (A.M.)
| | - Antonio Monari
- Université Paris Cité and CNRS, ITODYS, F-75006 Paris, France
- Correspondence: (G.B.); (A.M.)
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6
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Impact of G-Quadruplexes and Chronic Inflammation on Genome Instability: Additive Effects during Carcinogenesis. Genes (Basel) 2021; 12:genes12111779. [PMID: 34828385 PMCID: PMC8619830 DOI: 10.3390/genes12111779] [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: 09/29/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 02/07/2023] Open
Abstract
Genome instability is an enabling characteristic of cancer, essential for cancer cell evolution. Hotspots of genome instability, from small-scale point mutations to large-scale structural variants, are associated with sequences that potentially form non-B DNA structures. G-quadruplex (G4) forming motifs are enriched at structural variant endpoints in cancer genomes. Chronic inflammation is a physiological state underlying cancer development, and oxidative DNA damage is commonly invoked to explain how inflammation promotes genome instability. We summarize where G4s and oxidative stress overlap, with a focus on DNA replication. Guanine has low ionization potential, making G4s vulnerable to oxidative damage. Impacts to G4 structure are dependent upon lesion type, location, and G4 conformation. Occasionally, G4s pose a challenge to replicative DNA polymerases, requiring specialized DNA polymerases to maintain genome stability. Therefore, chronic inflammation creates a dual challenge for DNA polymerases to maintain genome stability: faithful G4 synthesis and bypassing unrepaired oxidative lesions. Inflammation is also accompanied by global transcriptome changes that may impact mutagenesis. Several studies suggest a regulatory role for G4s within cancer- and inflammatory-related gene promoters. We discuss the extent to which inflammation could influence gene regulation by G4s, thereby impacting genome instability, and highlight key areas for new investigation.
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Pavlova AV, Kubareva EA, Monakhova MV, Zvereva MI, Dolinnaya NG. Impact of G-Quadruplexes on the Regulation of Genome Integrity, DNA Damage and Repair. Biomolecules 2021; 11:1284. [PMID: 34572497 PMCID: PMC8472537 DOI: 10.3390/biom11091284] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/19/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
DNA G-quadruplexes (G4s) are known to be an integral part of the complex regulatory systems in both normal and pathological cells. At the same time, the ability of G4s to impede DNA replication plays a critical role in genome integrity. This review summarizes the results of recent studies of G4-mediated genomic and epigenomic instability, together with associated DNA damage and repair processes. Although the underlying mechanisms remain to be elucidated, it is known that, among the proteins that recognize G4 structures, many are linked to DNA repair. We analyzed the possible role of G4s in promoting double-strand DNA breaks, one of the most deleterious DNA lesions, and their repair via error-prone mechanisms. The patterns of G4 damage, with a focus on the introduction of oxidative guanine lesions, as well as their removal from G4 structures by canonical repair pathways, were also discussed together with the effects of G4s on the repair machinery. According to recent findings, there must be a delicate balance between G4-induced genome instability and G4-promoted repair processes. A broad overview of the factors that modulate the stability of G4 structures in vitro and in vivo is also provided here.
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Affiliation(s)
- Anzhela V. Pavlova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (M.I.Z.); (N.G.D.)
| | - Elena A. Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (E.A.K.); (M.V.M.)
| | - Mayya V. Monakhova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (E.A.K.); (M.V.M.)
| | - Maria I. Zvereva
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (M.I.Z.); (N.G.D.)
| | - Nina G. Dolinnaya
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (M.I.Z.); (N.G.D.)
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