Highly sensitive fluorescence assay of T4 polynucleotide kinase activity and inhibition via enzyme-assisted signal amplification

Analytical Biochemistry

Volumn 464, Issue , 2014, Pages 63-69

  Tao, Mangjuan ^a   Zhang, Jing ^a   Jin, Yan ^a   Li, Baoxin ^a  

^a SHAANXI NORMAL UNIVERSITY   (China)

Author keywords

DNA phosphorylation; Polynucleotide kinase activity; Signal amplification

Indexed keywords

ENZYME ACTIVITY; ENZYME INHIBITION; FLUORESCENCE; NUCLEIC ACIDS; OLIGONUCLEOTIDES; PHOSPHORYLATION;

AMPLIFICATION STRATEGY; FLUORESCENCE ASSAY; FLUORESCENCE SIGNALS; KINASE ACTIVITY; MONITORING ACTIVITIES; NICKING ENDONUCLEASE; SIGNAL AMPLIFICATIONS; T4 POLYNUCLEOTIDE KINASE;

AMPLIFICATION;

ADENOSINE TRIPHOSPHATE; DNA FRAGMENT; EXONUCLEASE; OLIGONUCLEOTIDE; PHOSPHOTRANSFERASE INHIBITOR; POLYNUCLEOTIDE 5' HYDROXYL KINASE; POLYNUCLEOTIDE 5' HYDROXYL KINASE INHIBITOR; RESTRICTION ENDONUCLEASE; UNCLASSIFIED DRUG; PRIMER DNA;

ARTICLE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME ASSISTED SIGNAL AMPLIFICATION; ENZYME INHIBITION; ENZYME PHOSPHORYLATION; ENZYME SYNTHESIS; FLUORESCENCE ANALYSIS; GEL ELECTROPHORESIS; LIMIT OF DETECTION; MOLECULAR BEACON; PRIORITY JOURNAL; PROTEIN CLEAVAGE; REACTION TIME; SENSITIVITY AND SPECIFICITY; ANTAGONISTS AND INHIBITORS; ENTEROBACTERIA PHAGE T4; ENZYMOLOGY; METABOLISM; NUCLEOTIDE SEQUENCE; PROCEDURES; SPECTROFLUOROMETRY;

BACTERIOPHAGE T4; BASE SEQUENCE; DNA PRIMERS; LIMIT OF DETECTION; POLYNUCLEOTIDE 5'-HYDROXYL-KINASE; SPECTROMETRY, FLUORESCENCE;

EID: 84906730050     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2014.07.008     Document Type: Article

References (32)

1. C.J. Whitehouse, R.M. Taylor, A. Thistlethwaite, H. Zhang, F. Karimi-Busheri, D.D. Lasko, M. Weinfeld, and K.W. Caldecott XRCC1 stimulates human polynucleotide kinase activity at damaged DNA termini and accelerates DNA single-strand break repair Cell 104 2001 107 117 (Pubitemid 32144976)
2. L.K. Wang, C.D. Lima, and S. Shuman Structure and mechanism of T4 polynucleotide kinase: an RNA repair enzyme EMBO J. 21 2002 3873 3880 (Pubitemid 34787059)
3. N. Tahbaz, S. Subedi, and M. Weinfeld Role of polynucleotide kinase/phosphatase in mitochondrial DNA repair Nucleic Acids Res. 40 2012 3484 3495
4. F. Karimi-Busheri, A. Rasouli-Nia, J. AIlalunis-Turner, and M. Weinfeld Human polynucleotide kinase participates in repair of DNA double-strand breaks by nonhomologous end joining but not homologous recombination Cancer Res. 67 2007 6619 6625 (Pubitemid 47105507)
5. J.W. Lown, and L.W. McLaughlin Nitrosourea-induced DNA single-strand breaks Biochem. Pharmacol. 28 1979 1631 1638 (Pubitemid 9194005)
6. W. Henner, L. Rodriguez, S. Hecht, and W. Haseltine γ-ray induced deoxyribonucleic acid strand breaks: 3′ Glycolate termini J. Biol. Chem. 258 1983 711 713
7. M. Meijer, F. Karimi-Busheri, T.Y. Huang, M. Weinfeld, and D. Young Pnk1, a DNA kinase/phosphatase required for normal response to DNA damage by γ-radiation or camptothecin in Schizosaccharomyces pombe J. Biol. Chem. 277 2002 4050 4055 (Pubitemid 34968661)
8. M. Amitsur, R. Levitz, and G. Kaufmann Bacteriophage T4 anticodon nuclease, polynucleotide kinase, and RNA ligase reprocess the host lysine tRNA EMBO J. 6 1987 2499 2503
9. F. Karimi-Busheri, G. Daly, P. Robins, B. Canas, D.J. Pappin, J. Sgouros, G.G. Miller, H. Fakhrai, E.M. Davis, and M.M. LeBeau Molecular characterization of a human DNA kinase J. Biol. Chem. 274 1999 24187 24194
10. Z. Tang, K. Wang, W. Tan, C. Ma, J. Li, L. Liu, Q. Guo, and X. Meng Real-time investigation of nucleic acids phosphorylation process using molecular beacons Nucleic Acids Res. 33 2005 e97
11. C. Song, and M. Zhao Real-time monitoring of the activity and kinetics of T4 polynucleotide kinase by a singly labeled DNA-hairpin smart probe coupled with λ exonuclease cleavage Anal. Chem. 81 2009 1383 1388
12. L. Lin, Y. Liu, X. Zhao, and J. Li Sensitive and rapid screening of T4 polynucleotide kinase activity and inhibition based on coupled exonuclease reaction and graphene oxide platform Anal. Chem. 83 2011 8396 8402
13. W. Wu, H. Hu, F. Li, L. Wang, J. Gao, J. Lu, and C. Fan A graphene oxide-based nano-beacon for DNA phosphorylation analysis Chem. Commun. 47 2011 1201 1203
14. Y. Huang, J. Chen, M. Shi, S. Zhao, Z.-F. Chen, and H. Liang A gold nanoparticle-enhanced fluorescence polarization biosensor for amplified detection of T4 polynucleotide kinase activity and inhibition J. Mater. Chem. B 1 2013 2018 2021
15. R.D. Morgan, C. Calvet, M. Demeter, R. Agra, and H. Kong Characterization of the specific DNA nicking activity of restriction endonuclease N.BstNBI Biol. Chem. 381 2000 1123 1125 (Pubitemid 32000808)
16. L.S. Higgins, C. Besnier, and H. Kong The nicking endonuclease N: BstNBI is closely related to type IIs restriction endonucleases MlyI and PleI Nucleic Acids Res. 29 2001 2492 2501 (Pubitemid 32600304)
17. H. Wang, and J.B. Hays Preparation of DNA substrates for in vitro mismatch repair Mol. Biotechnol. 15 2000 97 104 (Pubitemid 30618631)
18. R.G. Higuchi, and H. Ochman Production of single-stranded DNA templates by exonuclease digestion following the polymerase chain reaction Nucleic Acids Res. 17 1989 5865 (Pubitemid 19187145)
19. J.W. Little An exonuclease induced by bacteriophage λ II: nature of the enzymatic reaction J. Biol. Chem. 242 1967 679 686
20. T. Hou, X. Wang, X. Liu, T. Lu, S. Liu, and F. Li Amplified detection of T4 polynucleotide kinase activity by the coupled λ exonuclease cleavage reaction and catalytic assembly of bimolecular beacons Anal. Chem. 86 2014 884 890
21. K. Subramanian, W. Rutvisuttinunt, W. Scott, and R.S. Myers The enzymatic basis of processivity in λ exonuclease Nucleic Acids Res. 31 2003 1585 1596
22. S. Sharma, K. Doherty, and R. Brosh Mechanisms of RecQ helicases in pathways of DNA metabolism and maintenance of genomic stability Biochem. J. 398 2006 319 337 (Pubitemid 44453376)
23. S. Liu, J. Ming, Y. Lin, C. Wang, T. Liu, C. Cheng, and F. Li Amplified detection of T4 polynucleotide kinase activity based on a λ-exonuclease cleavage-induced DNAzyme releasing strategy Sens. Actuators B 192 2014 157 163
24. S. Liu, J. Ming, Y. Lin, C. Wang, C. Wang, C. Cheng, T. Liu, and L. Wang Highly sensitive detection of T4 polynucleotide kinase activity by coupling split DNAzyme and ligation-triggered DNAzyme cascade amplification Biosens. Bioelectron. 55 2014 225 230
25. L. Zhang, J. Zhao, H. Zhang, J. Jiang, and R. Yu Double strand DNA-templated copper nanoparticle as a novel fluorescence indicator for label-free detection of polynucleotide kinase activity Biosens. Bioelectron. 44 2013 6 9
26. J.H. Hoeijmakers Genome maintenance mechanisms for preventing cancer Nature 411 2001 366 374 (Pubitemid 32467046)
27. K.L. Berkner, and W.R. Folk Polynucleotide kinase exchange reaction: quantitative assay for restriction endonuclease-generated 5′-phosphoroyl termini in DNA J. Biol. Chem. 252 1977 3176 3184 (Pubitemid 8111165)
28. J.R. Lillehaug, R.K. Kleppe, and K. Kleppe Phosphorylation of double-stranded DNAs by T4 polynucleotide kinase Biochemistry 15 1976 1858 1865
29. J.R. Lillehaug, and K. Kleppe Effect of salts and polyamines on T4 polynucleotide kinase Biochemistry 14 1975 1225 1229
30. S. Chen, and M.P. Zhao Real-time monitoring of the activity and kinetics of T4 polynucleotide kinase by a singly labeled DNA-hairpin smart probe coupled with λ exonuclease cleavage Anal. Chem. 81 2009 1383 1388
31. Z.W. Tang, K.M. Wang, W.H. Tan, C.B. Ma, J. Li, L.F. Liu, Q.P. Guo, and X.X. Meng Real-time investigation of nucleic acids phosphorylation process using molecular beacons Nucleic Acids Res. 33 2005 e97
32. V. Houten, V. Denkers, F. van Dijk, M. van den Brekel, and M. Brakenhoff Labeling efficiency of oligonucleotides by T4 polynucleotide kinase depends on 5′-nucleotide Anal. Biochem. 265 1998 386 389 (Pubitemid 29002089)