A native chromatin extraction method based on salicylic acid coated magnetic nanoparticles and characterization of chromatin

Analyst

Volumn 140, Issue 3, 2015, Pages 938-944

  Zhou, Zhongwu ^a   Irudayaraj, Joseph ^a  

^a PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATIN; DNA BINDING PROTEIN; MAGNETITE NANOPARTICLE; SALICYLIC ACID;

ATOMIC FORCE MICROSCOPY; CELL CULTURE; CHEMISTRY; CHROMATIN; CONFOCAL MICROSCOPY; FEMALE; HUMAN; ISOLATION AND PURIFICATION; MAMMARY GLAND; METABOLISM; TRANSMISSION ELECTRON MICROSCOPY; WESTERN BLOTTING;

BLOTTING, WESTERN; CELLS, CULTURED; CHROMATIN; DNA-BINDING PROTEINS; FEMALE; HUMANS; MAGNETITE NANOPARTICLES; MAMMARY GLANDS, HUMAN; MICROSCOPY, ATOMIC FORCE; MICROSCOPY, CONFOCAL; MICROSCOPY, ELECTRON, TRANSMISSION; SALICYLIC ACID;

EID: 84921528992     PISSN: 00032654     EISSN: 13645528     Source Type: Journal    
DOI: 10.1039/c4an01897d     Document Type: Article

References (37)

1. J. Watson and F. Crick, A structure for deoxyribose nucleic acid, Nature, 1953, 421, 397-3988.
2. K. Luger, A. W. Mader, R. K. Richmond, D. F. Sargent and T. J. Richmond, Crystal structure of the nucleosome core particle at 2.8 A˚ resolution, Nature, 1997, 389, 251-260.
3. C. L. Woodcock and R. A. Horowitz, Chromatin organization re-viewed, Trends Cell Biol., 1995, 5, 272-277.
4. F. Song, P. Chen, D. Sun, M. Wang, L. Dong, D. Liang, R.-M. Xu, P. Zhu and G. Li, Cryo-EM Study of the Chromatin Fiber Reveals a Double Helix Twisted by Tetranucleosomal Units, Science, 2014, 344, 376-380.
5. M. Eltsov, K. M. MacLellan, K. Maeshima, A. S. Frangakis and J. Dubochet, Analysis of cryo-electron microscopy images does not support the existence of 30 nm chromatin fibers in mitotic chromosomes in situ, Proc. Natl. Acad. Sci. U. S. A., 2008, 105, 19732-19737.
6. R. A. Horowitz-Scherer and C. L. Woodcock, Organization of interphase chromatin, Chromosoma , 2006, 115, 1-14.
7. P. J. Giannasca, R. A. Horowitz and C. L. Woodcock, Transitions between in situ and isolated chromatin, J. Cell Sci. , 1993, 105(2), 551-561.
8. J. S. Bhorjee and T. Pederson, Chromatin. Its isolation from cultured mammalian cells with particular reference to contamination by nuclear ribonucleoprotein particles, Biochemistry , 1973, 12, 2766-2773.
9. R. Harlow and J. Wells, Preparation of membrane-free chromatin bodies from avian erythroid cells and analysis of chromatin acidic proteins, Biochemistry, 1975, 14, 2665-2674.
10. J. J. Monahan and R. H. Hall, Preparation of chromatin from tissue culture cells-A convenient method, Anal. Biochem., 1975, 65, 187-203.
11. T. Pederson, Isolation and characterization of chromatin from the cellular slime mold, Dictyostelium discoideum, Biochemistry, 1977, 16, 2771-2777.
12. R. D. Kornberg; J. W. Lapointe and Y. Lorch, Preparation of nucleosomes and chromatin, in Methods in Enzymology , ed. M. W. Paul and D. K. Roger, Academic Press, 1989, vol. 170, pp. 3-14.
13. X. Jiang, X. Jiang, S. Feng, R. Tian, M. Ye and H. Zou, Development of Efficient Protein Extraction Methods for Shotgun Proteome Analysis of Formalin-Fixed Tissues, J. Proteome Res., 2007, 6, 1038-1047.
14. Y. Zhang, Z. Hu, H. Qin, X. Wei, K. Cheng, F. Liu, R. a. Wu and H. Zou, Highly Efficient Extraction of Cellular Nucleic Acid Associated Proteins in Vitro with Magnetic Oxidized Carbon Nanotubes, Anal. Chem., 2012, 84, 10454-10462.
15. J. S. Bhorjee and L. Adler, Nuclear shearing and chromatin structure, Cell Biol. Int. Rep., 1982, 6, 1065-1076.
16. C. L. Woodcock, H. E. Sweetman and L. L. Frado, Structural repeating units in chromatin. II. Their isolation and partial characterization, Exp. Cell Res., 1976, 97, 111-119.
17. P. C. Abad, J. Lewis, I. S. Mian, D. W. Knowles, J. Sturgis, S. Badve, J. Xie and S. A. Lelíevre, NuMA influences higher order chromatin organization in human mammary epithelium, Mol. Biol. Cell, 2007, 18, 348-361.
18. B. Unal, Z. Durmus, H. Kavas, A. Baykal and M. S. Toprak, Synthesis, conductivity and dielectric characterization of salicylic acid-Fe3O4 nanocomposite, Mater. Chem. Phys., 2010, 123, 184-190.
19. Z. Zhou, U. S. Kadam and J. Irudayaraj, One-stop genomic DNA extraction by salicylic acid-coated magnetic nanoparticles, Anal. Biochem., 2013, 442, 249-252.
20. J. S. Beveridge, J. R. Stephens and M. E. Williams, The use of magnetic nanoparticles in analytical chemistry, Annu. Rev. Anal. Chem. , 2011, 4, 251-273.
21. Z. Shan, Q. Wu, X. Wang, Z. Zhou, K. D. Oakes, X. Zhang, Q. Huang and W. Yang, Bacteria capture, lysate clearance, and plasmid DNA extraction using pH-sensitive multifunctional magnetic nanoparticles, Anal. Biochem., 2010, 398, 120-122.
22. Z. Shan, Z. Zhou, H. Chen, Z. Zhang, Y. Zhou, A. Wen, K. D. Oakes and M. R. Servos, PCR-ready human DNA extraction from urine samples using magnetic nanoparticles, J. Chromatogr. B , 2012, 881, 63-68.
23. Z. Zhou, U. S. Kadam and J. Irudayaraj, One-stop genomic DNA extraction by salicylic acid-coated magnetic nanoparticles, Anal. Biochem., 2013, 442, 249-252.
24. Z. Shan, Y. Jiang, M. Guo, J. C. Bennett, X. Li, H. Tian, K. Oakes, X. Zhang, Y. Zhou, Q. Huang and H. Chen, Promoting DNA loading on magnetic nanoparticles using a DNA condensation strategy, Colloids Surf. B: Biointerfaces, 2014, DOI: 10.1016/j.colsurfb.2014.10.036.
25. T. L. Hawkins, T. O'Connor-Morin, A. Roy and C. Santillan, DNA purification and isolation using a solid-phase, Nucleic Acids Res., 1994, 22, 4543.
26. M. M. DeAngelis, D. G. Wang and T. L. Hawkins, Solid-phase reversible immobilization for the isolation of PCR products, Nucleic Acids Res. , 1995, 23, 4742-4743.
27. C. L. Woodcock and S. Dimitrov, Higher-order structure of chromatin and chromosomes, Curr. Opin. Genet. Dev., 2001, 11, 130-135.
28. J. Bednar, R. A. Horowitz, J. Dubochet and C. L. Woodcock, Chromatin conformation and salt-induced compaction: three-dimensional structural information from cryoelectron microscopy, J. Cell Biol., 1995, 131, 1365-1376.
29. J. Bednar, R. A. Horowitz, S. A. Grigoryev, L. M. Carruthers, J. C. Hansen, A. J. Koster and C. L. Woodcock, Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin, Proc. Natl. Acad. Sci. U. S. A., 1998, 95, 14173-14178.
30. L. M. Carruthers, J. Bednar, C. L. Woodcock and J. C. Hansen, Linker histones stabilize the intrinsic salt-dependent folding of nucleosomal arrays: mechanistic ramifications for higher-order chromatin folding, Biochemistry, 1998, 37, 14776-14787.
31. S. Cuddapah, A. Barski, K. Cui, D. E. Schones, Z. Wang, G. Wei and K. Zhao, Native Chromatin Preparation and Illumina/Solexa Library Construction, Cold Spring Harbor Protocols, 2009, 2009.
32. M. C. Cardoso, K. Schneider, R. M. Martin and H. Leonhardt, Structure, function and dynamics of nuclear subcompartments, Curr. Opin. Cell Biol., 2012, 24, 79-85.
33. R. Lucchini, R. E. Wellinger and J. M. Sogo, Nucleosome positioning at the replication fork, EMBO J., 2001, 20, 7294-7302.
34. A. Groth, W. Rocha, A. Verreault and G. Almouzni, Chromatin Challenges during DNA Replication and Repair, Cell , 2007, 128, 721-733.
35. S. L. McKnight and O. L. Miller Jr, Electron microscopic analysis of chromatin replication in the cellular blastoderm drosophila melanogaster embryo, Cell, 1977, 12, 795-804.
36. T. Nikitina and C. L. Woodcock, Closed chromatin loops at the ends of chromosomes, J. Cell Biol., 2004, 166, 161-165.
37. C. L. Woodcock and R. P. Ghosh, Chromatin higher-order structure and dynamics, Cold Spring Harbor Perspect. Biol., 2010, 2, a000596.