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Szabó JE, Surányi ÉV, Mébold BS, Trombitás T, Cserepes M, Tóth J. A user-friendly, high-throughput tool for the precise fluorescent quantification of deoxyribonucleoside triphosphates from biological samples. Nucleic Acids Res 2020; 48:e45. [PMID: 32103262 PMCID: PMC7192609 DOI: 10.1093/nar/gkaa116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 02/05/2020] [Accepted: 02/17/2020] [Indexed: 12/24/2022] Open
Abstract
Cells maintain a fine-tuned, dynamic concentration balance in the pool of deoxyribonucleoside 5′-triphosphates (dNTPs). This balance is essential for physiological processes including cell cycle control or antiviral defense. Its perturbation results in increased mutation frequencies, replication arrest and may promote cancer development. An easily accessible and relatively high-throughput method would greatly accelerate the exploration of the diversified consequences of dNTP imbalances. The dNTP incorporation based, fluorescent TaqMan-like assay published by Wilson et al. has the aforementioned advantages over mass spectrometry, radioactive or chromatography based dNTP quantification methods. Nevertheless, the assay failed to produce reliable data in several biological samples. Therefore, we applied enzyme kinetics analysis on the fluorescent dNTP incorporation curves and found that the Taq polymerase exhibits a dNTP independent exonuclease activity that decouples signal generation from dNTP incorporation. Furthermore, we found that both polymerization and exonuclease activities are unpredictably inhibited by the sample matrix. To resolve these issues, we established a kinetics based data analysis method which identifies the signal generated by dNTP incorporation. We automated the analysis process in the nucleoTIDY software which enables even the inexperienced user to calculate the final and accurate dNTP amounts in a 96-well-plate setup within minutes.
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Affiliation(s)
- Judit Eszter Szabó
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary.,Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest 1111, Hungary
| | - Éva Viola Surányi
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary.,Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest 1111, Hungary
| | - Bence Sándor Mébold
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Tamás Trombitás
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary.,Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest 1111, Hungary
| | - Mihály Cserepes
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary.,Department of Experimental Pharmacology, National Institute of Oncology, Budapest, Hungary
| | - Judit Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
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