Single-nucleotide resolution of RNAs up to 59 nucleotides by high-performance liquid chromatography

Analytical Biochemistry

Volumn 435, Issue 1, 2013, Pages 35-43

  Huang, Zhen ^a   Jayaseelan, Sabarinath ^a   Hebert, Jeffrey ^a   Seo, Hyojung ^a   Niu, Li ^a  

^a STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

HPLC; PAGE column; RNA purification and separation; Single nucleotide resolution

Indexed keywords

DRUG PRODUCTS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; IONS; MASS SPECTROMETRY; RNA; SEPARATION;

HPLC; ION-PAIRING AGENTS; MAGNESIUM CONCENTRATIONS; MOBILE PHASIS; OPTIMAL CONDITIONS; REVERSE PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; REVERSE PHASE HPLC; SINGLE NUCLEOTIDES;

NUCLEOTIDES;

APTAMER; BUFFER; MAGNESIUM; NUCLEOTIDE; SOLVENT;

ARTICLE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PRIORITY JOURNAL; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; RNA CONFORMATION; RNA STRUCTURE;

EID: 84873047596     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2012.12.011     Document Type: Article

References (46)

1. M. Fotin-Mleczek, K.M. Duchardt, C. Lorenz, R. Pfeiffer, S. Ojkic-Zrna, J. Probst, and K.J. Kallen Messenger RNA-based vaccines with dual activity induce balanced TLR-7 dependent adaptive immune responses and provide antitumor activity J. Immunother. 34 2011 1 15
2. M.J. Fedor, and J.R. Williamson The catalytic diversity of RNAs Nat. Rev. Mol. Cell Biol. 6 2005 399 412 (Pubitemid 40637857)
3. T.R. Cech, A.J. Zaug, and P.J. Grabowski In vitro splicing of the ribosomal RNA precursor of Tetrahymena: involvement of a guanosine nucleotide in the excision of the intervening sequence Cell 27 1981 487 496 (Pubitemid 12200785)
4. C. Guerrier-Takada, K. Gardiner, T. Marsh, N. Pace, and S. Altman The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme Cell 35 1983 849 857 (Pubitemid 14168384)
5. 13C labeling of nucleotides for large RNA NMR spectroscopy using an E. coli strain disabled in the TCA cycle J. Biomol. NMR 48 2010 179 192
6. P.S. Pallan, and M. Egli Selenium modification of nucleic acids: preparation of oligonucleotides with incorporated 2′-SeMe-uridine for crystallographic phasing of nucleic acid structures Nat. Protoc. 2 2007 647 651 (Pubitemid 47040025)
7. S.S. Sastry, and B.M. Ross Nuclease activity of T7 RNA polymerase and the heterogeneity of transcription elongation complexes J. Biol. Chem. 272 1997 8644 8652 (Pubitemid 27147831)
8. J.F. Milligan, D.R. Groebe, G.W. Witherell, and O.C. Uhlenbeck Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates Nucleic Acids Res. 15 1987 8783 8798
9. S.A. Scaringe, F.E. Wincott, and M.H. Caruthers Novel RNA synthesis method using 5′-O-silyl-2′-O-orthoester protecting groups J. Am. Chem. Soc. 120 1998 11820 11821 (Pubitemid 28543605)
10. D.P. Bartel MicroRNAs: genomics, biogenesis, mechanism, and function Cell 116 2004 281 297
11. L.S. Waters, and G. Storz Regulatory RNAs in bacteria Cell 136 2009 615 628
12. J.T. Cuperus, A. Carbonell, N. Fahlgren, H. Garcia-Ruiz, R.T. Burke, A. Takeda, C.M. Sullivan, S.D. Gilbert, T.A. Montgomery, and J.C. Carrington Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis Nat. Struct. Mol. Biol. 17 2010 997 1003
13. P.A. Manavella, D. Koenig, and D. Weigel Plant secondary siRNA production determined by microRNA-duplex structure Proc. Natl. Acad. Sci. USA 109 2012 2461 2466
14. Z. Huang, W. Pei, Y. Han, S. Jayaseelan, A. Shekhtman, H. Shi, and L. Niu One RNA aptamer sequence, two structures: a collaborating pair that inhibits AMPA receptors Nucleic Acids Res. 37 2009 4022 4032
15. S.V. Solomatin, M. Greenfeld, S. Chu, and D. Herschlag Multiple native states reveal persistent ruggedness of an RNA folding landscape Nature 463 2010 681 684
16. X. Zhuang, H. Kim, M.J. Pereira, H.P. Babcock, N.G. Walter, and S. Chu Correlating structural dynamics and function in single ribozyme molecules Science 296 2002 1473 1476 (Pubitemid 34553093)
17. W.A. Kibbe OligoCalc: an online oligonucleotide properties calculator Nucleic Acids Res. 35 2007 W43 W46
18. P. Schuster, W. Fontana, P.F. Stadler, and I.L. Hofacker From sequences to shapes and back: a case study in RNA secondary structures Proc. Biol. Sci. 255 1994 279 284 (Pubitemid 24102288)
19. P.T. Li, J. Vieregg, and I. Tinoco Jr. How RNA unfolds and refolds Annu. Rev. Biochem. 77 2008 77 100
20. S.P. Waghmare, P. Pousinis, D.P. Hornby, and M.J. Dickman Studying the mechanism of RNA separations using RNA chromatography and its application in the analysis of ribosomal RNA and RNA:RNA interactions J. Chromatogr. A 1216 2009 1377 1382
21. D.C. Rio, M. Ares Jr., G.J. Hannon, and T.W. Nilsen Polyacrylamide gel electrophoresis of RNA Cold Spring Harb. Protoc. 2010 http://cshprotocols.cshlp. org/content/2010/6/pdb.prot5444.long
22. J. Sambrook, and D.W. Russell Isolation of DNA fragments from polyacrylamide gels by the crush and soak method Cold Spring Harb. Protoc. 2006 http://cshprotocols.cshlp.org/content/2006/1/pdb.prot2936.full
23. A. Azarani, and K.H. Hecker RNA analysis by ion-pair reversed-phase high performance liquid chromatography Nucleic Acids Res. 29 2001 E7
24. B. Noll, S. Seiffert, H.P. Vornlocher, and I. Roehl Characterization of small interfering RNA by non-denaturing ion-pair reversed-phase liquid chromatography J. Chromatogr. A 1218 2011 5609 5617
25. D.S. Levin, B.T. Shepperd, and C.J. Gruenloh Combining ion pairing agents for enhanced analysis of oligonucleotide therapeutics by reversed phase-ion pairing ultra performance liquid chromatography (UPLC) J. Chromatogr. B 879 2011 1587 1595
26. V. Murugaiah, W. Zedalis, G. Lavine, K. Charisse, and M. Manoharan Reversed-phase high-performance liquid chromatography method for simultaneous analysis of two liposome-formulated short interfering RNA duplexes Anal. Biochem. 401 2010 61 67
27. K. Kariko, H. Muramatsu, J. Ludwig, and D. Weissman Generating the optimal mRNA for therapy: HPLC purification eliminates immune activation and improves translation of nucleoside-modified, protein-encoding mRNA Nucleic Acids Res. 39 2011 e142
28. M.J. Dickman, and D.P. Hornby Enrichment and analysis of RNA centered on ion pair reverse phase methodology RNA 12 2006 691 696
29. F. Wincott, A. DiRenzo, C. Shaffer, S. Grimm, D. Tracz, C. Workman, D. Sweedler, C. Gonzalez, S. Scaringe, and N. Usman Synthesis, deprotection, analysis, and purification of RNA and ribozymes Nucleic Acids Res. 23 1995 2677 2684
30. A.C. Anderson, S.A. Scaringe, B.E. Earp, and C.A. Frederick HPLC purification of RNA for crystallography and NMR RNA 2 1996 110 117 (Pubitemid 26371300)
31. M.J. Dickman, M.J. Conroy, J.A. Grasby, and D.P. Hornby RNA footprinting analysis using ion pair reverse phase liquid chromatography RNA 8 2002 247 251 (Pubitemid 34288911)
32. S. Garcia, and J.P. Liautard Behaviour of macromolecular RNA in reversed-phase HPLC J. Chromatogr. Sci. 21 1983 398 404 (Pubitemid 14452171)
33. M. Gilar, K.J. Fountain, Y. Budman, U.D. Neue, K.R. Yardley, P.D. Rainville, R.J. Russell 2nd, and J.C. Gebler Ion-pair reversed-phase high-performance liquid chromatography analysis of oligonucleotides: retention prediction J. Chromatogr. A 958 2002 167 182 (Pubitemid 34556947)
34. W.C. Winkler, A. Nahvi, A. Roth, J.A. Collins, and R.R. Breaker Control of gene expression by a natural metabolite-responsive ribozyme Nature 428 2004 281 286 (Pubitemid 38418792)
35. C.Z. Chuang, F.A. Ragan, and C. Prasad Use of triethylamine as an ion-pairing reagent J. Liquid Chromatogr. 17 1994 2383 2394 (Pubitemid 24234624)
36. S.L. Beaucage Solid-phase synthesis of siRNA oligonucleotides Curr. Opin. Drug Discov. Dev. 11 2008 203 216 (Pubitemid 351281060)
37. V.K. Misra, and D.E. Draper The linkage between magnesium binding and RNA folding J. Mol. Biol. 317 2002 507 521 (Pubitemid 34722166)
38. M.J. Serra, J.D. Baird, T. Dale, B.L. Fey, K. Retatagos, and E. Westhof Effects of magnesium ions on the stabilization of RNA oligomers of defined structures RNA 8 2002 307 323 (Pubitemid 34311181)
39. R.A. Cox Conformation of nucleic acids and the analysis of the hypochromic effect Biochem. J. 120 1970 539 547
40. R.A. Friedman, and B. Honig A free energy analysis of nucleic acid base stacking in aqueous solution Biophys. J. 69 1995 1528 1535
41. B. Noll, S. Seiffert, F. Hertel, H. Debelak, P. Hadwiger, H.P. Vornlocher, and I. Roehl Purification of small interfering RNA using nondenaturing anion-exchange chromatography Nucleic Acid Ther. 21 2011 383 393
42. A.D. Keefe, S. Pai, and A. Ellington Aptamers as therapeutics Nat. Rev. Drug Discov. 9 2010 537 550
43. A. Apffel, J.A. Chakel, S. Fischer, K. Lichtenwalter, and W.S. Hancock Analysis of oligonucleotides by HPLC-electrospray ionization mass spectrometry Anal. Chem. 69 1997 1320 1325
44. A. Apffel, J.A. Chakel, S. Fischer, K. Lichtenwalter, and W.S. Hancock New procedure for the use of high-performance liquid chromatography-electrospray ionization mass spectrometry for the analysis of nucleotides and oligonucleotides J. Chromatogr. A 777 1997 3 21 (Pubitemid 27353323)
45. T.H. Nguyen, L.A. Cunningham, K.M. Hammond, and Y. Lu High-resolution preparative-scale purification of RNA using the Prep Cell Anal. Biochem. 269 1999 216 218 (Pubitemid 29174289)
46. Z. Chen, and D.E. Ruffner Modified crush-and-soak method for recovering oligodeoxynucleotides from polyacrylamide gel Biotechniques 21 1996 820 822 (Pubitemid 26380347)