Exonuclease III action on microarrays: Observation of DNA degradation by fluorescence correlation spectroscopy

Analytical Biochemistry

Volumn 399, Issue 2, 2010, Pages 251-256

  Ehrlich, Nicky ^a   Anhalt, Katrin ^b   Hübner, Christian ^a   Brakmann, Susanne ^b  

^a UNIVERSITY OF LÜBECK   (Germany)

^b TU DORTMUND UNIVERSITY   (Germany)

Author keywords

DNA; Exonuclease; Fluorescence labeling; Fluorescence spectroscopy; Single molecule studies

Indexed keywords

FLUORESCENCE; FLUORESCENCE SPECTROSCOPY; SPECTROSCOPIC ANALYSIS;

DNA DEGRADATION; DOWNSTREAM-PROCESSING; EXONUCLEASE; EXONUCLEASE III; FLUORESCENCE CORRELATION SPECTROSCOPY; FLUORESCENCE LABELING; SINGLE MOLECULE; SINGLE-MOLECULE STUDIES;

DNA;

DOUBLE STRANDED DNA; EXODEOXYRIBONUCLEASE III;

ANALYTIC METHOD; ARTICLE; CHEMICAL LABELING; CONTROLLED STUDY; DNA BINDING; DNA DEGRADATION; DNA MICROARRAY; ENZYMATIC DEGRADATION; FLUORESCENCE CORRELATION SPECTROSCOPY; FLUOROSCOPY; HYDROLYSIS; PRIORITY JOURNAL;

EID: 77049099770     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2009.12.004     Document Type: Article

References (32)

1. Sobek J., Bartscherer K., Jacob A., Hoheisel J.D., and Angenendt P. Microarray technology as a universal tool for high-throughput analysis of biological systems. Comb. Chem. High-Throughput Screen. 9 (2006) 365-380
2. Astier Y., Braha O., and Bayley H. Toward single molecule DNA sequencing: direct identification of ribonucleoside and deoxyribonucleoside 5′-monophosphates by using an engineered protein nanopore equipped with a molecular adapter. J. Am. Chem. Soc. 128 (2006) 1705-1710
3. Chan E.Y. Advances in sequencing technology. Mutat. Res. 573 (2005) 13-40
4. Deamer D.W., and Akeson M. Nanopores and nucleic acids: prospects for ultrarapid sequencing. Trends Biotechnol. 18 (2000) 147-151
5. Dear P.H. One by one: single molecule tools for genomics. Brief. Funct. Genomic. Proteomic. 1 (2003) 397-416
6. Greenleaf W.J., and Block S.M. Single-molecule, motion-based DNA sequencing using RNA polymerase. Science 313 (2006) 801
7. Kasianowicz J.J., Brandin E., Branton D., and Deamer D.W. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. USA 93 (1996) 13770-13773
8. Shendure J., Mitra R.D., Varma C., and Church G.M. Advanced sequencing technologies: methods and goals. Nat. Rev. Genet. 5 (2004) 335-344
9. Voulgarakis N.K., Redondo A., Bishop A.R., and Rasmussen K.O. Sequencing DNA by dynamic force spectroscopy: limitations and prospects. Nano Lett. 6 (2006) 1483-1486
10. Davis L.M., Fairfield F.R., Hahn J.H., Harger C.A., Jett J.H., Keller R.A., Krakowski L.A., Marrone B.L., Martin J.C., Nutter H.L., Ratliff R.L., Shera E.B., Simpson D.J., and Soper S.A. Rapid DNA sequencing based upon single molecule detection. Genet. Anal. Biomol. Eng. 8 (1991) 1-7
11. Dörre K., Brakmann S., Brinkmeier M., Han K.T., Riebeseel K., Schwille P., Stephan J., Wetzel T., Lapczyna M., Stuke M., Bader R., Hinz M., Seliger H., Holm J., Eigen M., and Rigler R. Techniques for single molecule sequencing. Bioimaging 5 (1997) 139-152
12. Puapaiboon U., Jai-Nhuknan J., and Cowan J.A. Rapid and direct sequencing of double-stranded DNA using exonuclease III and MALDI-TOF MS. Anal. Chem. 72 (2000) 3338-3341
13. Stephan J., Dörre K., Brakmann S., Winkler T., Wetzel T., Lapczyna M., Stuke M., Angerer B., Ankenbauer W., Földes-Papp Z., Rigler R., and Eigen M. Towards a general procedure for sequencing single DNA molecules. J. Biotechnol. 86 (2001) 255-267
14. Werner J.H., Cai H., Jett J.H., Reha-Krantz L., Keller R.A., and Goodwin P.M. Progress towards single-molecule DNA sequencing: a one color demonstration. J. Biotechnol. 102 (2003) 1-14
15. Brakmann S. Optimal enzymes for single-molecule sequencing. Curr. Pharm. Biotechnol. 5 (2004) 119-126
16. Brakmann S. High-density labeling of DNA for single molecule sequencing. In: Niemeyer C.M. (Ed). Bioconjugation Protocols (2004), Humana, Totowa, NJ 137-144
17. Richardson C.C., and Kornberg A. A deoxyribonucleic acid phosphatase-exonuclease from Escherichia coli: I. Purification of the enzyme and characterization of the phosphatase activity. J. Biol. Chem. 239 (1964) 242-250
18. Richardson C.C., Lehman I.R., and Kornberg A. A deoxyribonucleic acid phosphatase-exonuclease from Escherichia coli: II. Characterization of the exonuclease activity. J. Biol. Chem. 139 (1964) 251-258
19. Linxweiler W., and Hörz W. Sequence specificity of exonuclease III from E. coli. Nucleic Acids Res. 10 (1982) 4845-4858
20. Thomas K.R., and Olivera B.M. Processivity of DNA exonucleases. J. Biol. Chem. 253 (1978) 424-429
21. Hoheisel J.D. On the activities of Escherichia coli exonuclease III. Anal. Biochem. 209 (1993) 238-246
22. Brakmann S., and Löbermann S. A further step towards single-molecule sequencing: Escherichia coli exonuclease III degrades DNA that is fluorescently labeled at each base pair. Angew. Chem., Int. Ed. 41 (2002) 3215-3217
23. Davanloo P., Rosenberg A.H., Dunn J.J., and Studier F.W. Cloning and expression of the gene for bacteriophage T7 RNA polymerase. Proc. Natl. Acad. Sci. USA 81 (1984) 2035-2039
24. Brakmann S., and Löbermann S. High-density labeling of DNA: preparation and characterization of the target material for single-molecule sequencing. Angew. Chem., Int. Ed. 40 (2001) 1427-1429
25. Földes-Papp Z., Angerer B., Thyberg P., Hinz M., Wennmalm S., Ankenbauer W., Seliger H., Holmgren A., and Rigler R. Fluorescently labeled model DNA sequences for exonucleolytic sequencing. J. Biotechnol. 86 (2001) 203-224
26. Kusnezow W., Jacob A., Walijew A., Diehl F., and Hoheisel J.D. Antibody microarrays: an evaluation of production parameters. Proteomics 3 (2003) 254-264
27. Pirrung M.C. How to make a DNA chip. Angew. Chem., Int. Ed. 41 (2002) 1276-1289
28. Zammatteo N., Jeanmart L., Hamels S., Courtois S., Louette P., Hevesi L., and Remacle J. Comparison between different strategies of covalent attachment of DNA to glass surfaces to build DNA microarrays. Anal. Biochem. 280 (2000) 143-150
29. Lee H.J., Li Y., Wark A.W., and Corn R.M. Enzymatically amplified surface plasmon resonance imaging detection of DNA by exonuclease III digestion of DNA microarrays. Anal. Chem. 77 (2005) 5096-5100
30. Matsuura S., Komatsu J., Hirano K., Yasuda H., Takashima K., Katsura S., and Mizuno A. Real-time observation of a single DNA digestion by lambda exonuclease under a fluorescence microscope field. Nucleic Acids Res. 29 (2001) e79
31. Mol C.D., Kuo C.H., Thayer M.M., Cunningham R.P., and Tainer J.A. Structure and function of the multifunctional DNA-repair enzyme exonuclease III. Nature 374 (1995) 381-386
32. Goodrich T.T., Lee H.J., and Corn R.M. Enzymatically amplified surface plasmon resonance imaging method using RNase H and RNA microarrays for the ultrasensitive detection of nucleic acids. J. Am. Chem. Soc. 126 (2004) 4086-4087