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Shen D, Guo H, Zhang F, Chen X, Tong X, Li H, Wu W, Mei S. Highly-sensitive and logic platform based on spatially-constrained T7 transcription enhanced Cas13a for DNA repair enzyme detection and intracellular imaging. Biosens Bioelectron 2025; 280:117406. [PMID: 40179700 DOI: 10.1016/j.bios.2025.117406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Revised: 02/27/2025] [Accepted: 03/20/2025] [Indexed: 04/05/2025]
Abstract
The activity of DNA repair enzymes, particularly Flap endonuclease 1 (FEN1) and apurinic/apyrimidinic endonuclease 1 (APE1), plays a critical role in disease prevention, diagnosis, and prognosis. Accurate detection of these enzymes is therefore essential. Recent advancements in CRISPR-Cas technology, particularly its programmable and trans-cleavage activity, have paved the way for the development of innovative detection methods. However, there is a need for a simple, low-background, highly sensitive detection platform with logical capabilities for FEN1 and APE1. In this study, we present a novel detection platform that integrates spatially constrained T7 transcription with the CRISPR-Cas13a system. This biosensor minimizes background interference and achieves high sensitivity, with limits of detection as low as 5 × 10-7 U/μL for FEN1 and 2 × 10-8 U/μL for APE1, making it one of the most sensitive methods available for detecting these enzymes. The platform supports both OR and logic detection, offering enhanced versatility. It demonstrates robustness by detecting FEN1 activity at concentrations as low as 1 cell/μL and screening enzyme inhibitors. Additionally, the system was successfully used for intracellular imaging of FEN1 activity in cells and reliably measured APE1 activity in ovarian tissue samples, confirming its clinical applicability. This biosensor represents a promising tool for detecting FEN1 and APE1, further expanding the potential of CRISPR-Cas13a in diagnostic applications.
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Affiliation(s)
- Dongsheng Shen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji University School of Medicine, No.389 Xincun Road, Shanghai, 200065, China
| | - Hong Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji University School of Medicine, No.389 Xincun Road, Shanghai, 200065, China
| | - Fubin Zhang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji University School of Medicine, No.389 Xincun Road, Shanghai, 200065, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, No. 59 Liuting Street, Ningbo, 315010, Zhejiang Province, China
| | - Xixi Chen
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Xiaowen Tong
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji University School of Medicine, No.389 Xincun Road, Shanghai, 200065, China
| | - Huaifang Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji University School of Medicine, No.389 Xincun Road, Shanghai, 200065, China.
| | - Wenjun Wu
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
| | - Shuaikang Mei
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji University School of Medicine, No.389 Xincun Road, Shanghai, 200065, China.
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2
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Nian L, Xiaohua L, Rongcheng L, Song-Bai L. Types of DNA damage and research progress. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:881-901. [PMID: 37948546 DOI: 10.1080/15257770.2023.2277194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 10/11/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023]
Abstract
DNA damage is a modification in the structure of DNA under the influence of endogenous or exogenous factors. DNA damage can cause different types of diseases and is closely related to genetic mutations, cancer, and aging. The cause of the corresponding reaction process is essential for the study of related cancers and other genetically related diseases. Therefore, it is essential to gain a deeper understanding of the various types of DNA damage. This paper provides a comprehensive review of recent advances in the types of DNA damage and associated reaction processes, including damage to DNA bases, nucleotides, and strands, as well as the biological implications of the damage.
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Affiliation(s)
- Liu Nian
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, Suzhou, China
| | - Li Xiaohua
- Thyroid and breast surgery, Wuzhong People's Hospital of Suzhou City, Suzhou, China
| | - Li Rongcheng
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, Suzhou, China
| | - Liu Song-Bai
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, Suzhou, China
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3
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Duan L, Zhao Y, Zhang X, Cui X, Meng Q, Zhang C. Fluorescent adenine analogues with ESPT characteristic utilized for real-time detecting DNA adduct. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 282:121675. [PMID: 35914355 DOI: 10.1016/j.saa.2022.121675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
The 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG) is the representative damaged nucleoside that may increase the risk of developing diseases. Accordingly, the selective detection of 8-oxoG in DNA with minimal disturbance to the native structure is important to have an in-depth understanding of the formation mechanism and becomes an attractive tool for genomic research. To identify the DNA adduct in real-time efficiently, a series of quasi-intrinsic optical probes are performed based on the natural adenine, which has preference to form a stable base pair with 8-oxoG in the syn conformation. The calculations revealed that the A-analogues in solution could bring red-shifted absorption spectra and bright photoluminescence arisen from the additional π-conjugation by means of fluorophore modification and the ring expansion. Especially, A1 possesses large Stokes shifts and the highest fluorescence intensity in emission, which is proposed as the biosensor to monitor the optical changes in the presence and absence of the considered 8-oxoG. It is found that the fluorescence is insensitive to base pairing with thymine, while the excited state intermolecular proton transfer (ESPT) induced efficient fluorescence quenching is observed upon pairing with the 8-oxoG. To evaluate the direct usefulness of the bright adenine analogues in biological environment, we further examined the influences of linking deoxyribose on the absorption and emission, which are consistent with the experimental data.
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Affiliation(s)
- Lingjie Duan
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Yu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Xiao Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Xixi Cui
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Qingtian Meng
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Changzhe Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
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Kellum AH, Pallan PS, Nilforoushan A, Sturla SJ, Stone MP, Egli M. Conformation and Pairing Properties of an O6-Methyl-2'-deoxyguanosine-Directed Benzimidazole Nucleoside Analog in Duplex DNA. Chem Res Toxicol 2022; 35:1903-1913. [PMID: 35973057 PMCID: PMC9988402 DOI: 10.1021/acs.chemrestox.2c00165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
O6-Methyl-2'-deoxyguanosine (O6-MeG) is one of the most common DNA lesions and arises as a consequence of both xenobiotic carcinogens and endogenous methylation by S-adenosylmethionine. O6-MeG frequently causes G-to-A mutations during DNA replication due to the misincorporation of dTTP and continued DNA synthesis. Efforts to detect DNA adducts such as O6-MeG, and to understand their impacts on DNA structure and function, have motivated the creation of nucleoside analogs with altered base moieties to afford a more favorable interaction with the adduct as compared to the unmodified nucleotide. Such analogs directed at O6-MeG include benzimidazolinone and benzimidazole nucleotides, as well as their extended π surface analogs naphthimidazolinone and napthimidazole derivatives. These analogs form a more stable pair with O6-MeG than with G, most likely due to a combination of H-bonding and stacking. While extending the π surface of the analogs enhances their performance as adduct-directed probes, the precise origins of the increased affinity between the synthetic analogs and O6-MeG remain unclear. To better understand relevant conformational and pairing properties, we used X-ray crystallography and analyzed the structures of the DNA duplexes with naphthimidazolinone inserted opposite G or O6-MeG. The structures reveal a complex interaction of the analog found either in an anti orientation and stacked inside the duplex, either above or below G or O6-MeG, or in a syn orientation and paired opposite G with formation of a single H-bond. The experimental structural data are consistent with the stabilizing effect of the synthetic analog observed in UV melting experiments and calculations and moreover reveal that the origin of these observations appears to be superior stacking between O6-MeG and the extended π system of the synthetic probe.
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Affiliation(s)
- Andrew H Kellum
- Department of Chemistry, Vanderbilt University, College of Arts and Science, Nashville, Tennessee 37235, United States
| | - Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
| | - Arman Nilforoushan
- Department of Health Sciences and Technology, ETH Zürich, Zurich 8092, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, Zurich 8092, Switzerland
| | - Michael P Stone
- Department of Chemistry, Vanderbilt University, College of Arts and Science, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
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Liang Y, Li H, Fan L, Li R, Cui Y, Ji X, Xiao H, Hu J, Wang L. Zwitterionic daptomycin stabilized palladium nanoparticles with enhanced peroxidase-like properties for glucose detection. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2021.127797] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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He X, Gan F, Zhou Y, Zhang Y, Zhao P, Zhao B, Tang Q, Ye L, Bu J, Mei J, Du L, Dai H, Qiu H, Liu P. Nonplanar Helicene Benzo[4]Helicenium for the Precise Treatment of Renal cell Carcinoma. SMALL METHODS 2021; 5:e2100770. [PMID: 34927965 DOI: 10.1002/smtd.202100770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/25/2021] [Indexed: 06/14/2023]
Abstract
Immune and targeted therapy are becoming the first-line treatment for renal cell carcinoma (RCC). However, therapeutic outcomes are limited due to the low efficiency and side effect. Here, it is found that helicenes are able to exhibit an anticancer capability through changing the molecular structure from planar to nonplanar. Furthermore, the cytotoxicity in vitro and cancer inhibition ability of nonplanar helicenes increase with its aromatic rings' number. It is further demonstrated that benzo[4]helicenium shows the specific killing efficiency against the RCC cancer as compared to normal kidney cells. This is majorly originated from a more selective damage of benzo[4]helicenium for mitochondria and DNA in RCC cancer cells, not the normal kidney. The selective killing ability of benzo[4]helicenium makes it have potential to be used as a targeted drug for the precise treatment of RCC.
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Affiliation(s)
- Xiaozhen He
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, China
- Central Laboratory, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fuwei Gan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yan Zhou
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, China
- Central Laboratory, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yuanliang Zhang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Peipei Zhao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, China
- Central Laboratory, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Bingru Zhao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, China
- Central Laboratory, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Qianyun Tang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, China
- Central Laboratory, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Li Ye
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, China
- Central Laboratory, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jun Bu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, China
- Central Laboratory, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Junyang Mei
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, China
- Central Laboratory, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Ling Du
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, China
- Central Laboratory, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Huili Dai
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, China
- Central Laboratory, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Huibin Qiu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Peifeng Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, China
- Central Laboratory, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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Aloisi CMN, Sandell ES, Sturla SJ. A Chemical Link between Meat Consumption and Colorectal Cancer Development? Chem Res Toxicol 2021; 34:12-23. [PMID: 33417435 DOI: 10.1021/acs.chemrestox.0c00395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
O6-carboxymethylguanine (O6-CMG) is a mutagenic DNA adduct that forms at increased levels when people eat meat. It has been studied as a potential initiating event in colorectal carcinogenesis. It can arise from alkylation of guanine in DNA by electrophilic degradation products of N-nitroso compounds. There is significant data regarding biochemical and cellular process, including DNA repair and translesion DNA synthesis that control O6-CMG accumulation, persistence, and mutagenicity. Mutation spectra arising from the adduct closely resemble common mutations in colorectal cancer; however, gaps remain in understanding the biochemical processes that regulate how and where the damage persists in the genome. Addressing such questions relies on advances in chemistry such as synthesis approaches and bioanalytical methods. Results of research in this area help advance our understanding of the toxicological relevance of O6-CMG-modified DNA. Further attention should focus on understanding how a combination of genetic and environmental factors control its biological persistence and how this information can be used as a basis of biomoniotoring and prevention efforts to help mitigate colon cancer risk.
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Affiliation(s)
- Claudia M N Aloisi
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Emma S Sandell
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
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Aloisi CMN, Nilforoushan A, Ziegler N, Sturla SJ. Sequence-Specific Quantitation of Mutagenic DNA Damage via Polymerase Amplification with an Artificial Nucleotide. J Am Chem Soc 2020; 142:6962-6969. [PMID: 32196326 PMCID: PMC7192524 DOI: 10.1021/jacs.9b11746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
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DNA mutations can result from replication
errors due to different
forms of DNA damage, including low-abundance DNA adducts induced by
reactions with electrophiles. The lack of strategies to measure DNA
adducts within genomic loci, however, limits our understanding of
chemical mutagenesis. The use of artificial nucleotides incorporated
opposite DNA adducts by engineered DNA polymerases offers a potential
basis for site-specific detection of DNA adducts, but the availability
of effective artificial nucleotides that insert opposite DNA adducts
is extremely limited, and furthermore, there has been no report of
a quantitative strategy for determining how much DNA alkylation occurs
in a sequence of interest. In this work, we synthesized an artificial
nucleotide triphosphate that is selectively inserted opposite O6-carboxymethyl-guanine DNA by an engineered
polymerase and is required for DNA synthesis past the adduct. We characterized
the mechanism of this enzymatic process and demonstrated that the
artificial nucleotide is a marker for the presence and location in
the genome of O6-carboxymethyl-guanine.
Finally, we established a mass spectrometric method for quantifying
the incorporated artificial nucleotide and obtained a linear relationship
with the amount of O6-carboxymethyl-guanine
in the target sequence. In this work, we present a strategy to identify,
locate, and quantify a mutagenic DNA adduct, advancing tools for linking
DNA alkylation to mutagenesis and for detecting DNA adducts in genes
as potential diagnostic biomarkers for cancer prevention.
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Affiliation(s)
- Claudia M N Aloisi
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Arman Nilforoushan
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Nathalie Ziegler
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
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