1
|
Abstract
DNA repair enzymes continuously provide surveillance throughout our cells, protecting the enclosed DNA from the damage that is constantly arising from oxidation, alkylating species, and radiation. Members of this enzyme class are intimately linked to pathways controlling cancer and inflammation and are promising targets for diagnostics and future therapies. Their study is benefiting widely from the development of new tools and methods aimed at measuring their activities. Here, we provide an Account of our laboratory's work on developing chemical tools to study DNA repair processes in vitro, as well as in cells and tissues, and what we have learned by applying them.We first outline early work probing how DNA repair enzymes recognize specific forms of damage by use of chemical analogs of the damage with altered shapes and H-bonding abilities. One outcome of this was the development of an unnatural DNA base that is incorporated selectively by polymerase enzymes opposite sites of missing bases (abasic sites) in DNA, a very common form of damage.We then describe strategies for design of fluorescent probes targeted to base excision repair (BER) enzymes; these were built from small synthetic DNAs incorporating fluorescent moieties to engender light-up signals as the enzymatic reaction proceeds. Examples of targets for these DNA probes include UDG, SMUG1, Fpg, OGG1, MutYH, ALKBH2, ALKBH3, MTH1, and NTH1. Several such strategies were successful and were applied both in vitro and in cellular settings; moreover, some were used to discover small-molecule modulators of specific repair enzymes. One of these is the compound SU0268, a potent OGG1 inhibitor that is under investigation in animal models for inhibiting hyperinflammatory responses.To investigate cellular nucleotide sanitation pathways, we designed a series of "two-headed" nucleotides containing a damaged DNA nucleotide at one end and ATP at the other; these were applied to studying the three human sanitation enzymes MTH1, dUTPase, and dITPase, some of which are therapeutic targets. The MTH1 probe (ARGO) was used in collaboration with oncologists to measure the enzyme in tumors as a disease marker and also to develop the first small-molecule activators of the enzyme.We proceed to discuss the development of a "universal" probe of base excision repair processes (UBER), which reacts covalently with abasic site intermediates of base excision repair. UBER probes light up in real time as the reaction occurs, enabling the observation of base excision repair as it occurs in live cells and tissues. UBER probes can also be used in efficient and simple methods for fluorescent labeling of DNA. Finally, we suggest interesting directions for the future of this field in biomedicine and human health.
Collapse
Affiliation(s)
- Yong Woong Jun
- Department of Chemistry, Stanford University, 369 North-South Axis, Stauffer I, Stanford, California 94305, United States
| | - Eric T Kool
- Department of Chemistry, Stanford University, 369 North-South Axis, Stauffer I, Stanford, California 94305, United States
| |
Collapse
|
2
|
Farag N, Ercolani G, Del Grosso E, Ricci F. DNA Tile Self‐Assembly Guided by Base Excision Repair Enzymes. Angew Chem Int Ed Engl 2022; 61:e202208367. [DOI: 10.1002/anie.202208367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 12/18/2022]
Affiliation(s)
- Nada Farag
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Gianfranco Ercolani
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Erica Del Grosso
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| |
Collapse
|
3
|
Farag N, Ercolani G, Del Grosso E, Ricci F. DNA Tile Self‐Assembly Guided by Base Excision Repair Enzymes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nada Farag
- Universita degli Studi di Roma Tor Vergata Chemistry ITALY
| | | | | | - Francesco Ricci
- University of Rome, Tor Vergata Department of Chemistry Via della Ricerca Scientifica 00133 Rome ITALY
| |
Collapse
|
4
|
Kasprzyk R, Starek BJ, Ciechanowicz S, Kubacka D, Kowalska J, Jemielity J. Fluorescent Turn-On Probes for the Development of Binding and Hydrolytic Activity Assays for mRNA Cap-Recognizing Proteins. Chemistry 2019; 25:6728-6740. [PMID: 30801798 DOI: 10.1002/chem.201900051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/21/2019] [Indexed: 12/16/2022]
Abstract
The m7 G cap is a unique nucleotide structure at the 5'-end of all eukaryotic mRNAs. The cap specifically interacts with numerous cellular proteins and participates in biological processes that are essential for cell growth and function. To provide small molecular probes to study important cap-recognizing proteins, we synthesized m7 G nucleotides labeled with fluorescent tags via the terminal phosph(on)ate group and studied how their emission properties changed upon protein binding or enzymatic cleavage. Only the pyrene-labeled compounds behaved as sensitive turn-on probes. A pyrene-labeled m7 GTP analogue showed up to eightfold enhanced fluorescence emission upon binding to eukaryotic translation initiation factor 4E (eIF4E) and over 30-fold enhancement upon cleavage by decapping scavenger (DcpS) enzyme. These observations served as the basis for developing binding- and hydrolytic-activity assays. The assay utility was validated with previously characterized libraries of eIF4E ligands and DcpS inhibitors. The DcpS assay was also applied to study hydrolytic activity and inhibition of endogenous enzyme in cytoplasmic extracts from HeLa and HEK cells.
Collapse
Affiliation(s)
- Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Beata J Starek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Sylwia Ciechanowicz
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Dorota Kubacka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| |
Collapse
|
5
|
Edwards SK, Ono T, Wang S, Jiang W, Franzini RM, Jung JW, Chan KM, Kool ET. In Vitro Fluorogenic Real-Time Assay of the Repair of Oxidative DNA Damage. Chembiochem 2015; 16:1637-46. [PMID: 26073452 PMCID: PMC4586133 DOI: 10.1002/cbic.201500184] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 01/09/2023]
Abstract
The repair of oxidative damage to DNA is essential to avoid mutations that lead to cancer. Oxidized DNA bases, such as 8-oxoguanine, are a main source of these mutations, and the enzyme 8-oxoguanine glycosylase 1 (OGG1) is the chief human enzyme that excises 8-oxoguanine from DNA. The activity of OGG1 has been linked to human inflammation responses and to cancer, and researchers are beginning to search for inhibitors of the enzyme. However, measuring the activity of the enzyme typically requires laborious gel-based measurements of radiolabeled DNAs. Here we report the design and properties of fluorogenic probes that directly report on the activity of OGG1 (and its bacterial homologue Fpg) in real time as the oxidized base is excised. The probes are short, modified DNA oligomers containing fluorescent DNA bases and are designed to utilize 8-oxoguanine itself as a fluorescence quencher. Screening of combinations of fluorophores and 8-oxoguanine revealed two fluorophores, pyrene and tCo, that are strongly quenched by the damaged base. We tested 42 potential probes containing these fluorophores: the optimum probe, OGR1, yields a 60-fold light-up signal in vitro with OGG1 and Fpg. It can report on oxidative repair activity in mammalian cell lysate and with bacterial cells overexpressing a repair enzyme. Such probes might prove useful in quantifying enzyme activity and performing competitive inhibition assays.
Collapse
Affiliation(s)
- Sarah K Edwards
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
| | - Toshikazu Ono
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
- Present Address: Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395 (Japan)
| | - Shenliang Wang
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
| | - Wei Jiang
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
| | | | - Jong Wha Jung
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
- Present Address: College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 702-701 (Republic of Korea)
| | - Ke Min Chan
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA).
| |
Collapse
|
6
|
Dziuba D, Karpenko IA, Barthes NPF, Michel BY, Klymchenko AS, Benhida R, Demchenko AP, Mély Y, Burger A. Rational Design of a Solvatochromic Fluorescent Uracil Analogue with a Dual-Band Ratiometric Response Based on 3-Hydroxychromone. Chemistry 2014; 20:1998-2009. [DOI: 10.1002/chem.201303399] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Indexed: 12/24/2022]
|
7
|
Jung JW, Edwards SK, Kool ET. Selective fluorogenic chemosensors for distinct classes of nucleases. Chembiochem 2013; 14:440-4. [PMID: 23371801 PMCID: PMC3770146 DOI: 10.1002/cbic.201300001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Indexed: 12/26/2022]
Abstract
NUCLEASE SENSOR TRIO: Fluorogenic DNA sensors were developed for distinct classes of nucleases: 3'-exonucleases, 5'-exonucleases, and endonucleases. The highly selective sensors, built from very small modified DNA oligomers containing the unnatural fluorescent base pyrene, and employing thymine as a quencher, were found to function in a variety of complex biological media.
Collapse
Affiliation(s)
- Jong-Wha Jung
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 702-701 (Korea)
| | - Sarah K. Edwards
- Department of Chemistry, Stanford University, Stanford, CA, 94305 (USA)
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA, 94305 (USA)
| |
Collapse
|