Histidine affinity chromatography-based methodology for the simultaneous isolation of Escherichia coli small and ribosomal RNA

Biomedical Chromatography

Volumn 26, Issue 7, 2012, Pages 781-788

  Martins, Rita ^a   Queiroz, João António ^a   Sousa, Fani ^a  

^a UNIVERSITY OF BEIRA INTERIOR   (Portugal)

Author keywords

Affinity chromatography; Histidine; Ribosomal RNA; RNA extraction; Small RNA

Indexed keywords

AMINO ACIDS; ESCHERICHIA COLI; NITROGEN COMPOUNDS; RNA; SULFUR COMPOUNDS;

AMMONIUM SULFATE PRECIPITATION; BIOLOGICAL DISCOVERIES; CELL LYSIS; GUANIDINIUM; HISTIDINE; RIBOSOMAL RNA; RNA EXTRACTION; RNA MOLECULES; SMALL RNA; THERAPEUTIC TARGETS;

AFFINITY CHROMATOGRAPHY;

BACTERIAL PROTEIN; BACTERIAL RNA; GENOMIC DNA; GUANIDINE; HISTIDINE; RIBOSOME RNA; SMALL RNA; TRANSFER RNA; UNCLASSIFIED DRUG;

AFFINITY CHROMATOGRAPHY; ARTICLE; CELL FUNCTION; CYTOLYSIS; ESCHERICHIA COLI; HISTIDINE AFFINITY CHROMATOGRAPHY; MEDICAL TECHNOLOGY; NONHUMAN; PROTEIN STRUCTURE; RNA ISOLATION;

ESCHERICHIA COLI;

EID: 84862202716     PISSN: 02693879     EISSN: 10990801     Source Type: Journal    
DOI: 10.1002/bmc.1729     Document Type: Article

References (41)

1. Boom R, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM and van der Noordaa J. Rapid and simple method for purification of nucleic acids. Journal of Clinical Microbiology 1990; 28(3): 495-503.
2. Chatterjee A, Mirer PL, Zaldivar Santamaria E, Klapperich C, Sharon A and Sauer-Budge AF. RNA isolation from mammalian cells using porous polymer monoliths: an approach for high-throughput automation. Analytical Chemistry 2010; 82(11): 4344-4356.
3. Chen P, Jager G and Zheng B. Transfer RNA modifications and genes for modifying enzymes in Arabidopsis thaliana. BMC Plant Biology 2010; 10(1): 201.
4. Chomczynski P and Sacchi N. The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: twenty-something years on. Nature Protocols 2006; 1: 581-585.
5. Cristóvão AC, Choi D-H, Baltazar G, Beal MF and Kim Y-S. The role of NADPH oxidase 1-derived reactive oxygen species in paraquat-mediated dopaminergic cell death. Antioxidants & Redox Signaling 2009; 11(9): 2105-2118.
6. Cruz C, Cabrita EJ and Queiroz JA. Analysis of nucleotides binding to chromatography supports provided by nuclear magnetic resonance spectroscopy. Journal of Chromatography. A 2011; 1218(22): 3559-3564.
7. David-Eden H, Mankin AS and Mandel-Gutfreund Y. Structural signatures of antibiotic binding sites on the ribosome. Nucleic Acids Research 2010; 38(18): 5982-5994.
8. Doudna JA. Structural genomics of RNA. Nature Structural Biology 2000; 7(suppl.): 954-956.
9. Elkon R, Rashi-Elkeles S, Lerenthal Y, Linhart C, Tenne T, Amariglio N, Rechavi G, Shamir R and Shiloh Y. Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis. Genome Biology 2005; 6(5): R43.
10. Farrell RE. RNA Methodologies, 3rd edn. Academic Press: New York, 2005.
11. Fischer SE. Small RNA-mediated gene silencing pathways in C. elegans. The International Journal of Biochemistry & Cell Biology 2010; 42(8): 1306-1315.
12. Foloppe N, Matassova N and Aboul-ela F. Towards the discovery of drug-like RNA ligands? Drug Discovery Today 2006; 11(21-22): 1019-1027.
13. Gottesman S. The small RNA regulators of Escherichia coli: roles and mechanisms. Annual Review of Microbiology 2004; 58: 303-328.
14. Guarino H, Goyal SM and Murtaugh MP. Comparison of four RNA extraction methods for the detection of porcine reproductive and respiratory syndrome virus by RT-PCR. The New Microbiologica 1997; 20: 319-324.
15. Hoffman MM, Khrapov MA, Cox JC, Yao J, Tong L and Ellington AD. AANT: the Amino Acid-Nucleotide Interaction Database. Nucleic Acids Research 2004; 32: 174-181.
16. Jeong E, Kim H, Lee SW and Han K. Discovering the interaction propensities of amino acids and nucleotides from protein-RNA complexes. Molecules and Cells 2003; 16: 161-167.
17. Jin ZB, Hirokawa G, Gui L, Takahashi R, Osakada F, Hiura Y, Takahashi M, Yasuhara O and Iwai N. Targeted deletion of miR-182, an abundant retinal microRNA. Molecular Vision 2009; 15: 523-533.
18. Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub C, Kai C, Kawai J, Yasuda J, Carninci P and Hayashizaki Y. Hidden layers of human small RNAs. BMC Genomics 2008; 9(1): 157.
19. Kim VN. Small RNAs: classification, biogenesis, and function. Molecules and Cells 2005; 19(1): 1-15.
20. Lagos-Quintana M, Rauhut R, Lendeckel W and Tuschl T. Identification of novel genes coding for small expressed RNAs. Science 2001; 294(5543): 853-858.
21. Madabusi LV, Latham GJ and Andruss BF. RNA extraction for arrays. In Methods in Enzymology, Alan K and Brian O (eds). Academic Press: San Diego, CA, 2006; 1-14.
22. Maia C, Socorro S, Schmitt F and Santos C. STEAP1 is over-expressed in breast cancer and down-regulated by 17β-estradiol in MCF-7 cells and in the rat mammary gland. Endocrine 2008; 34(1): 108-116.
23. Martinho A, Gonçalves I, Cardoso I, Almeida MR, Quintela T, Saraiva MJ and Santos CRA. Human metallothioneins 2 and 3 differentially affect amyloid-beta binding by transthyretin. FEBS Journal 2010; 277(16): 3427-3436.
24. Martins R, Queiroz JA and Sousa F. A new affinity approach to isolate Escherichia coli 6S RNA with histidine-chromatography. Journal of Molecular Recognition 2010; 23(6): 519-524.
25. Morozova N, Allers J, Myers J and Shamoo Y. Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures. Bioinformatics 2006; 22: 2746-2752.
26. Özkara S, Yavuz H, Patr S, Arca MY and Denizli A. Separation of human-immunoglobulin-G from human plasma with l-histidine immobilized pseudo-specific bioaffinity adsorbents. Separation Science and Technolology 2002; 37: 717-731.
27. Pitiot O and Vijayalakshmi MA, Immobilized histidine ligand affinity chromatography. In Biochromatography: Theory and Practice, Vijayalakshmi MA (ed.). Taylor & Francis: New York, 2002; 301-324.
28. Sambrook J, Fritsch EF and Maniatis T. Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor Laboratory Press: New York, 2001.
29. Sousa F and Queiroz JA. Supercoiled plasmid quality assessment by analytical arginine-affinity chromatography. Journal of Chromatography. A 2011; 1218(1): 124-129.
30. Sousa F, Tomaz CT, Prazeres DM and Queiroz JA. Separation of supercoiled and open circular plasmid DNA isoforms by chromatography with a histidine-agarose support. Analytical Biochemistry 2005; 343: 183-185.
31. Sousa F, Freitas S, Azzoni AR, Prazeres DM and Queiroz JA. Selective purification of supercoiled plasmid DNA from clarified cell lysates with a single histidine-agarose chromatography step. Biotechnology and Applied Biochemistry 2006; 45: 131-140.
32. Sousa F, Prazeres DM and Queiroz JA. Affinity chromatography approaches to overcome the challenges of purifying plasmid DNA. Trends in Biotechnology 2008; 26(9): 518-525.
33. Sousa A, Sousa F and Queiroz JA. Biorecognition of supercoiled plasmid DNA isoform in lysine-affinity chromatography. Journal of Chromatography B 2009a; 877(27): 3257-3260.
34. Sousa A, Sousa F, Prazeres DM and Queiroz JA. Histidine affinity chromatography of homo-oligonucleotides. Role of multiple interactions on retention. Biomedical Chromatography 2009b; 23: 745-753.
35. Sousa A, Sousa F and Queiroz JA. Differential interactions of plasmid DNA, RNA and genomic DNA with amino acid-based affinity matrices. Journal of Separation Science 2010; 33(17-18): 2610-2618.
36. Sousa F, Prazeres DMF and Queiroz JA. Improvement of transfection efficiency by using supercoiled plasmid DNA purified with arginine affinity chromatography. The Journal of Gene Medicine 2009c; 11(1): 79-88.
37. Stellrecht CM and Gandhi V. Concurrent isolation of ribosomal, messenger, and low molecular weight RNA. Biotechniques 2002; 33(5): 1122-1124.
38. Tan SC and Yiap BC. DNA, RNA, and protein extraction: the past and the present. Journal of Biomedicine and Biotechnology 2009; 2009: 1-10.
39. Tenson T and Mankin A. Antibiotics and the ribosome. Molecular Microbiology 2006; 59(6): 1664-1677.
40. Vomelova I, Vanickova Z and Sedo A. Methods of RNA purification. All ways (should) lead to Rome. Folia Biologica (Praha) 2009; 55(6): 243-251.
41. Wassarman KM, Zhang A and Storz G. Small RNAs in Escherichia coli. Trends in Microbiology 1999; 7(1): 37-45.