Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity

Structure

Volumn 24, Issue 6, 2016, Pages 862-873

  Lambert, Abigail R ^a   Hallinan, Jazmine P ^a   Shen, Betty W ^a   Chik, Jennifer K ^a   Bolduc, Jill M ^a   Kulshina, Nadia ^a   Robins, Lori I ^b   Kaiser, Brett K ^c   Jarjour, Jordan ^d   Havens, Kyle ^d   Scharenberg, Andrew M ^e   Stoddard, Barry L ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

^b UNIVERSITY OF WASHINGTON BOTHELL   (United States)

^c SEATTLE UNIVERSITY   (United States)

^d BLUEBIRD BIO   (United States)

^e SEATTLE CHILDREN S RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENDONUCLEASE; FUNGAL DNA; NUCLEASE; DEOXYRIBONUCLEASE; DNA;

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DNA BINDING; DNA CLEAVAGE; DNA CLEAVAGE ASSAY; DNA CONFORMATION; DNA SEQUENCE; DNA STRUCTURE; ENZYME ACTIVITY; ENZYME STRUCTURE; GENE IDENTIFICATION; GENE TARGETING; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; BINDING SITE; CHEMISTRY; CONFORMATION; ENZYME SPECIFICITY; METABOLISM; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; PROTEIN CONFORMATION;

BASE SEQUENCE; BINDING SITES; DEOXYRIBONUCLEASES; DNA; DNA CLEAVAGE; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; SUBSTRATE SPECIFICITY;

EID: 84964618101     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2016.03.024     Document Type: Article

References (41)

1. M.S. Antunes, J.J. Smith, D. Jantz, and J.I. Medford Targeted DNA excision in Arabidopsis by a re-engineered homing endonuclease BMC Biotechnol. 12 2012 86
2. S. Arnould, C. Perez, J.-P. Cabaniols, J. Smith, A. Gouble, S. Grizot, J.-C. Epinat, A. Duclert, P. Duchateau, and F. Paques Engineered I-CreI derivatives cleaving sequences from the human XPC gene can induce highly efficient gene correction in mammalian cells J. Mol. Biol. 371 2007 49 65
3. A.C. Babic, E.J. Little, V.M. Manohar, J. Bitinaite, and N.C. Horton DNA distortion and specificity in a sequence-specific endonuclease J. Mol. Biol. 383 2008 186 204
4. S. Baxter, A.R. Lambert, R. Kuhar, J. Jarjour, N. Kulshina, F. Parmeggiani, P. Danaher, J. Gano, D. Baker, B.L. Stoddard, and et al. Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases Nucleic Acids Res. 40 2012 7985 8000
5. C.W. Bock, A.K. Katz, G.D. Markham, and J.P. Glusker Manganese as a replacement for magnesium and Zinc: functional comparison of the divalent ions J. Am. Chem. Soc. 121 1999 7360 7372
6. S.J. Boissel, J. Jarjour, A. Astrakhan, A. Adey, A. Gouble, P. Duchateau, J. Shendure, B.L. Stoddard, M. Certo, D. Baker, and A.M. Scharenberg MegaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering Nucleic Acids Res. 42 2014 2591 2601
7. Y.S. Chan, R. Takeuchi, J. Jarjour, D.S. Huen, B.L. Stoddard, and S. Russell The design and in vivo evaluation of engineered I-OnuI-Based enzymes for HEG gene drive PLoS One 8 2013 e74254
8. G. Chao, W.L. Lau, B.J. Hackel, S.L. Sazinsky, S.M. Lippow, and K.D. Wittrup Isolating and engineering human antibodies using yeast surface display Nat. Protoc. 1 2006 755 768
9. B. Chevalier, M. Turmel, C. Lemieux, R.J. Monnat, and B.L. Stoddard Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI J. Mol. Biol. 329 2003 253 269
10. J. Curuksu, M. Zacharias, R. Lavery, and K. Zakrzewska Local and global effects of strong DNA bending induced during molecular dynamics simulations Nucleic Acids Res. 37 2009 3766 3773
11. K. D'Halluin, C. Vanderstraeten, J. Van Hulle, J. Rosolowska, I. Van Den Brande, A. Pennewaert, K. D'Hont, M. Bossut, D. Jantz, R. Ruiter, and et al. Targeted molecular trait stacking in cotton through targeted double-strand break induction Plant Biotechnol. J. 11 2013 933 941
12. V. Djukanovic, J. Smith, K. Lowe, M. Yang, H. Gao, S. Jones, M.G. Nicholson, A. West, J. Lape, D. Bidney, and et al. Male-sterile maize plants produced by targeted mutagenesis of the cytochrome P450-like gene (MS26) using a re-designed I-CreI homing endonuclease Plant J. 76 2013 888 899
13. H. Gao, J. Smith, M. Yang, S. Jones, V. Djukanovic, M.G. Nicholson, A. West, D. Bidney, S.C. Falco, D. Jantz, and et al. Heritable targeted mutagenesis in maize using a designed endonuclease Plant J. 61 2010 176 187
14. R.D. Gietz, and R.H. Schiestl FrozFrozen competent yeast cells that can be transformed with high efficiency using the LiAc/SS carrier DNA/PEG methoden competent yeast cells that can be transformed with high efficiency using the LiAc/SS carrier DNA/PEG method Nat. Protoc. 2 2007 1 4
15. R.D. Gietz, and R.H. Schiestl High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method Nat. Protoc. 2 2007 31 34
16. A. Izmiryan, O. Danos, and A. Hovnanian Meganuclease-mediated COL7A1 gene correction for recessive dystrophic epidermolysis bullosa J. Invest. Dermatol. 136 2016 872 875
17. J. Jarjour, H. West-Foyle, M.T. Certo, C.G. Hubert, L. Doyle, M.M. Getz, B.L. Stoddard, and A.M. Scharenberg High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display Nucleic Acids Res. 37 2009 6871 6880
18. H.K. Joshi, C. Etzkorn, L. Chatwell, J. Bitinaite, and N.C. Horton Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism J. Biol. Chem. 281 2006 23852 23869
19. A.N.-S. Mak, A.R. Lambert, and B.L. Stoddard Folding, DNA recognition, and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI Structure 18 2010 1 11
20. A.N. Mak, P. Bradley, A.J. Bogdanove, and B.L. Stoddard TAL effectors: function, structure, engineering and applications Curr. Opin. Struct. Biol. 23 2013 93 99
21. A.M. Martin, M.D. Sam, N.O. Reich, and J.J. Perona Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease Nat. Struct. Biol. 6 1999 269 277
22. S. Menoret, S. Fontaniere, D. Jantz, L. Tesson, R. Thinard, S. Remy, C. Usal, L.H. Ouisse, A. Fraichard, and I. Anegon Generation of Rag1-knockout immunodeficient rats and mice using engineered meganucleases FASEB J. 27 2013 703 711
23. M.J. Osborn, B.R. Webber, F. Knipping, C.L. Lonetree, N. Tennis, A.P. DeFeo, A.N. McElroy, C.G. Starker, C. Lee, S. Merkel, and et al. Evaluation of TCR gene editing achieved by TALENs, CRISPR/Cas9, and megaTAL nucleases Mol. Ther. 24 2015 570 581
24. F. Paques, and P. Duchateau Meganucleases and DNA double-strand break-induced recombination: perspectives for gene therapy Curr. Gene Ther. 7 2007 49 66
25. E. Pennisi The CRISPR craze Science 341 2013 833 836
26. E. Protozanova, P. Yakovchuk, and M.D. Frank-Kamenetskii Stacked-unstacked equilibrium at the nick site of DNA J. Mol. Biol. 342 2004 775 785
27. F.A. Ran, P.D. Hsu, C.Y. Lin, J.S. Gootenberg, S. Konermann, A.E. Trevino, D.A. Scott, A. Inoue, S. Matoba, Y. Zhang, and et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity Cell 154 2013 1380 1389
28. B.D. Sather, G.S. Romano Ibarra, K. Sommer, G. Curinga, M. Hale, I.F. Khan, S. Singh, Y. Song, K. Gwiazda, J. Sahni, and et al. Efficient modification of CCR5 in primary human hematopoietic cells using a megaTAL nuclease and AAV donor template Sci. Transl. Med. 7 2015 307ra156
29. M. Scalley-Kim, A. McConnell-Smith, and B.L. Stoddard Coevolution of homing endonuclease specificity and its host target sequence J. Mol. Biol. 372 2007 1305 1319
30. D.J. Segal, and J.F. Meckler Genome engineering at the dawn of the golden age Annu. Rev. Genomics Hum. Genet. 14 2013 135 158
31. J. Sethuraman, A. Majer, N.C. Friedrich, D.R. Edgell, and G. Hausner Genes within genes: multiple LAGLIDADG homing endonucleases target the ribosomal protein S3 gene encoded within an rnl group I intron of Ophiostoma and related taxa Mol. Biol. Evol. 26 2009 2299 2315
32. B.W. Shen, A. Lambert, B.C. Walker, B.L. Stoddard, and B.K. Kaiser The structural basis of asymmetry in DNA binding and cleavage as exhibited by the I-SmaMI LAGLIDADG meganuclease J. Mol. Biol. 428 2016 206 220
33. T. Shrader, and D. Crothers Artificial nucleosome positioning sequences Proc. Natl. Acad. Sci. USA 86 1989 7418 7422
34. B.L. Stoddard Homing endonucleases from mobile group I introns: discovery to genome engineering Mob. DNA 5 2014 1 15
35. R. Takeuchi, A. Lambert, A. Mak, K. Jacoby, R. Dickson, G. Gloor, A. Scharenberg, D. Edgell, and B. Stoddard Tapping natural reservoirs of homing endonucleases for targeted gene modification Proc. Natl. Acad. Sci. USA 108 2011 13077 13082
36. R. Takeuchi, M. Choi, and B.L. Stoddard Efficient engineering of meganucleases and MegaTALs using bioinformatics and in vitro compartmentalization for targeted gene modification Proc. Natl. Acad. Sci. USA 111 2014 4061 4066
37. S.B. Thyme, J. Jarjour, R. Takeuchi, J.J. Havranek, J. Ashworth, A.M. Scharenberg, B.L. Stoddard, and D. Baker Exploitation of binding energy for catalysis and design Nature 461 2009 1300 1304
38. Y. Wang, I.F. Khan, S. Boissel, J. Jarjour, J. Pangallo, S. Thyme, D. Baker, A.M. Scharenberg, and D.J. Rawlings Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus Nucleic Acids Res. 42 2014 6463 6475
39. P. Yakovchuk, E. Protozanova, and M.D. Frank-Kamenetskii Base-stacking and base-pairing contributions into thermal stability of the DNA double helix Nucleic Acids Res. 34 2006 564 574
40. K. Zakrzewska DNA deformation energetic and protein binding Biopolymers 70 2003 414 423
41. G. Zheng, X.-J. Lu, and W.K. Olson Web 3DNA - a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures Nucleic Acids Res. 37 2009 W240 W246