Artificial restriction DNA cutter for site-selective scission of double-stranded DNA with tunable scission site and specificity

Nature Protocols

Volumn 3, Issue 4, 2008, Pages 655-662

  Komiyama, Makoto ^a   Aiba, Yuichiro ^a   Yamamoto, Yoji ^a   Sumaoka, Jun ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CERIUM; DOUBLE STRANDED DNA; EDETIC ACID; PEPTIDE NUCLEIC ACID; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; RESTRICTION ENDONUCLEASE;

ANIMAL CELL; ARTICLE; ARTIFICIAL RESTRICTION DNA CUTTER; CATALYSIS; CLINICAL PROTOCOL; COMPLEX FORMATION; CONTROLLED STUDY; GENETIC ENGINEERING; HYDROLYSIS; NONHUMAN; NUCLEIC ACID SYNTHESIS; PRIORITY JOURNAL; PURIFICATION;

CERIUM; DNA; DNA, BACTERIAL; EDETIC ACID; ESCHERICHIA COLI; PEPTIDE NUCLEIC ACIDS;

EID: 42049106385     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2008.7     Document Type: Article

References (41)

1. Komiyama, M. & Sumaoka, J. Progress towards synthetic enzymes for phosphoester hydrolysis. Curr. Opin. Chem. Biol. 2, 751-757 (1998).
2. Hegg, E.L. & Burstyn, J.N. Toward the development of metal-based synthetic nucleases and peptidases: A rationale and progress report in applying the principles of coordination chemistry. Coord. Chem. Rev. 173, 133-165 (1998).
3. Blasko, A. & Bruice, T.C. Recent studies of nucleophilic, general-acid, and metal ion catalysis of phosphate diester hydrolysis. Acc. Chem. Res. 32, 475-484 (1999).
4. Williams, N.H., Takasaki, B., Wall, M. & Chin, J. Structure and nuclease activity of simple dinuclear metal complexes: Quantitative dissection of the role of metal ions. Acc. Chem. Res. 32, 485-493 (1999).
5. Ott, R. & Krämer, R. DNA hydrolysis by inorganic catalysts. Appl. Microbiol. Biotechnol. 52, 761-767 (1999).
6. Bashkin, J.K. Hydrolysis of phosphates, esters and related substrates by models of biological catalysts. Curr. Opin. Chem. Biol. 3, 752-758 (1999).
7. Sreedhara, A. & Cowan, J.A. Catalytic hydrolysis of DNA by metal ions and complexes. J. Biol. Inorg. Chem. 6, 337-347 (2001).
8. Franklin, S.J. Lanthanide-mediated DNA hydrolysis. Curr. Opin. Chem. Biol. 5, 201-208 (2001).
9. Suh, J. Synthetic artificial peptidases and nucleases using macromolecular catalytic systems. Acc. Chem. Res. 36, 562-570 (2003).
10. Liu, C., Wang, M., Zhang, T. & Sun, H. DNA hydrolysis promoted by di- and multinuclear metal complexes. Coord. Chem. Rev. 248, 147-168 (2004).
11. Mancin, F., Scrimin, P., Tecilla, P. & Tonellato, U. Artificial metallonucleases. Chem. Commun. 2540-2548 (2005).
12. Mancin, F. & Tecilla, P. Zinc(II) complexes as hydrolytic catalysts of phosphate diester cleavage: From model substrates to nucleic acids. New J. Chem. 31, 800-817 (2007).
13. Strobel, S.A. & Dervan, P.B. Single-site enzymatic cleavage of yeast genomic DNA mediated by triple helix formation. Nature 350, 172-174 (1991).
14. Ferrin, L.J. & Cameriniotero, R.D. Selective cleavage of human DNA: RecA-assisted restriction endonuclease (RARE) cleavage. Science 254, 1494-1497 (1991).
15. Veselkov, A.G., Demidov, U., Frank-Kamenetskii, M.D. & Nielsen, P.E. PNA as a fare genome-cutter. Nature 379, 214 (1996).
16. Veselkov, A.G., Demidov, U., Nielsen, P.E. & Frank-Kamenetskii, M.D. A new class of genome rare cutters. Nucleic Acids Res. 24, 2483-2487 (1996).
17. Arimondo, P.B. et al. Recognition and cleavage of DNA by rebeccamycin- or benzopyndoquinoxaline conjugated of triple hellix-forming oligonucleotides. Bioorg. Med. Chem. 8, 777-784 (2000).
18. Izvolsky, K.I., Demidov, V.V., Nielsen, P.E. & Frank-Kamenetskii, M.D. Sequence-specific protection of duplex DNA against restriction and methylation enzymes by pseudocomplementary PNAs. Biochemistry 39, 10908-10913 (2000).
19. Nomura, A. & Sugiura, Y. Sequence-selective and hydrolytic cleavage of DNA by zinc finger mutants. J. Am. Chem. Soc. 126, 15374-15375 (2004).
20. Eisenschmidt, K. et al. Developing a programmed restriction endonuclease for highly specific DNA cleavage. Nucleic Acids Res. 33, 7039-7047 (2005).
21. Nakatsukasa, T. et al. Site-specific DNA cleavage by artificial zinc finger-type nuclease with cerium-binding peptide. Biochem. Biophys. Res. Commun. 330, 247-252 (2005).
22. Miller, J.C. et al. An improved zinc-finger nuclease architecture for highly specific genome editing. Nat. Biotechnol. 25, 778-785 (2007).
23. Yamamoto, Y. & Komiyama, M. Site-selective scission of double-stranded DNA by combining peptide nucleic acids and Ce(IV)EDTA. Chem. Lett. 33, 920-921 (2004).
24. Yamamoto, Y., Uehara, A., Tomita, T. & Komiyama, M. Site-selective and hydrolytic two-strand scission of double-stranded DNA using Ce(IV/ EDTA and pseudo-complementary PNA. Nucleic Acids Res. 32, e153 (2004).
25. Yamamoto, Y. et al. Chemical-reaction-based site-selective DNA cutter for PCR-free gene manipulation. Chembiochem 7, 673-677 (2006).
26. Yamamoto, Y., Miura, K. & Komiyama, M. Site-specific scission of lambda phage genomic DNA by Ce(IV)/EDTA-based artificial restriction DNA cutter. Chem. Lett. 35, 594-595 (2006).
27. Sumaoka, J., Yamamoto, Y., Kitamura, Y. & Komiyama, M. Artificial restriction DNA cutters (ARCUT) for future biotechnology. Curr. Org. Chem. 11, 463-475 (2007).
28. IV/EDTA. Chem. Lett. 36, 780-781 (2007).
29. Yamamoto, Y. et al. Chemical modification of Ce(IV)/EDTA-based artificial restriction DNA cutter for versatile manipulation of double-stranded DNA. Nucleic Acids Res. 35, e53 (2007).
30. Sumaoka, J., Azuma, Y. & Kumiyama, M. Enzymatic manipulation of the fragments obtained by cerium (IV)-induced DNA scission: Characterization of hydrolytic termini. Chem. Eur. J. 4, 205-209 (1998).
31. Kitamura, Y. et al. Recombination of the GFP gene to the BFP gene using a man-made site-selective DNA cutler. J. Biol. Inorg. Chem. 11, 13-16 (2006).
32. Nielsen, P.E., Egholm, M., Berg, R.H. & Buchardt, O. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 254, 1497-1500 (1991).
33. Egholm, M. et al. PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature 365, 566-568 (1993).
34. Haaima, G., Hansen, H.F., Christensen, L., Dahl, O. & Nielsen, P.E. Increased DNA binding and sequence discrimination of PNA oligomers containing 2,6-diaminopurine. Nucleic Acids Res. 25, 4639-4643 (1997).
35. Lohse, J., Dahl, O. & Nielsen, P.E. Double duplex invasion by peptide nucleic acid: A general principle for sequence-specific targeting of double-stranded DNA. Proc. Natl. Acad. Sci. USA 96, 11804-11808 (1999).
36. Komiyama, M., Aiba, Y., Ishizuka, T. & Sumaoka, J. Solid-phase synthesis of pseudo-complementary peptide nucleic acids. Nat. Protoc. 3 646-654 (2008).
37. Komiyama, M., Takeda, N. & Shigekawa, H. Hydrolysis of DNA and RNA by Lanthanide ions: Mechanistic studies leading to new applications. Chem. Commun. 1443-1451 (1999).
38. Kitamura, Y. & Komiyama, M. Preferential hydrolysis of gap and bulge sites in DNA by Ce(IV)/EDTA complex. Nucleic Acids Res. 30, e102 (2002).
39. Christensen, L. et al. Solid-phase synthesis of peptide nucleic acids. J. Peptide Sci. 1, 175-183 (1995).
40. Chen, W. et al. Site-selective DNA hydrolysis by combining Ce(IV)/ EDTA with monophosphate-bearing oligonucleotides and enzymatic ligation of the scission fragments. J. Am. Chem. Soc. 126, 10285-10291 (2004).
41. Sambrook, J. & Russell, D.W. Molecular Cloning: A Laboratory Manual 3rd edn. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2001).