Purity Analysis and Impurities Determination by Reversed- Phase High-Performance Liquid Chromatography

Handbook of Analysis of Oligonucleotides and Related Products

Volumn , Issue , 2011, Pages 1-46

  Cramer, Hagen ^a   Finn, Kevin J ^a   Herzberg, Eric ^a  

^a Girindus America Inc ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84555198948     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/b10714-6     Document Type: Chapter

References (90)

1. Cunliffe, J. M., and T. D. Maloney. 2007. Fused-core particle technology as an alternative to sub-2- microm particles to achieve high separation efficiency with low backpressure. Journal of Separation Science 30: 3104-3109.
2. Destefano, J. J., T. J. Langlois, and J. J. Kirkland. 2008. Characteristics of superficially-porous silica particles for fast HPLC: some performance comparisons with sub-2-microm particles. Journal of Chromatographic Science 46: 254-260.
3. Kirkland, J. J. 2000. Ultrafast reversed-phase high-performance liquid chromatographic separations: an overview. Journal of Chromatographic Science 38: 535-544.
4. Kirkland, J. J., F. A. Truszkowski, and R. D. Ricker. 2002. Atypical silica-based column packings for high-performance liquid chromatography. J. Chromatography A 965: 25-34.
5. Svec, F. 2008. What is “hot” in column technologies for liquid chromatography. American Laboratory 40: 13-17.
6. Majors, R. E. 2006. Fast and ultrafast HPLC on sub-2 um porous particles-where do we go from here? LC-GC Europe 19: 352-362.
7. Kirkland, J. J. 2004. Development of some stationary phases for reversed-phase high-performance liquid chromatography. Journal of Chromatography A 1060: 9-21.
8. O’Gara, J. E., B. A. Alden, T. H. Walter, J. S. Peterson, C. L. Niederländer, and U. D. Neue. 1995. Simple preparation of a CS HPLC stationary phase with an internal polar functional group. Analytical Chemistry 67: 3809-3814.
9. O’Gara, J. E., and K. D. Wyndham. 2006. Porous hybrid organic-inorganic particles in reversed-phase liquid chromatography. Journal of Liquid Chromatography and Related Technologies 29: 1025-1045.
10. Kirkland, J. J., F. A. Truszkowski, C. H. Dilks, Jr., and G. S. Engel. 2000. Superficially porous silica microspheres for fast high-performance liquid chromatography of macromolecules. Journal of Chromatography A 890: 3-13.
11. Abrahim, A., M. Al-Sayah, P. Skrdla, Y. Bereznitski, Y. Chen, and N. Wu. 2010. Practical comparison of 2.7 microm fused-core silica particles and porous sub-2 microm particles for fast separations in pharmaceutical process development. Journal of Pharmaceutical and Biomedical Analysis 51: 131-137.
12. Gilar, M., K. J. Fountain, Y. Budman, et al. 2002. Ion-pair reversed-phase high-performance liquid chromatography analysis of oligonucleotides: retention prediction. Journal of Chromatography A 958: 167-182.
13. Van Deemter, J. J., F. J. Zuiderweg, and A. Klinkenberg. 1956. Longitudinal diffusion and resistance to mass transfer as causes of nonideality in chromatography. Chemical Engineering Science 5: 271-290.
14. Arghavani, M. B., and L. J. Romano. 1995. A method for the purification of oligonucleotides containing strong intra- or intermolecular interactions by reversed-phase high-performance liquid chromatography. Analytical Biochemistry 231: 201-209.
15. Germann, M. W., R. T. Pon, and J. H. van de Sande. 1987. A general method for the purification of synthetic oligodeoxyribonucleotides containing strong secondary structure by reversed-phase high-performance liquid chromatography on PRP-1 resin. Analytical Biochemistry 165: 399-405.
16. Swiderski, P. M., E. L. Bertrand, and B. E. Kaplan. 1994. Polystyrene reverse-phase ion-pair chromatography of chimeric ribozymes. Analytical Biochemistry 216: 83-88.
17. Johnson, J. L., W. Guo, J. Zang, et al. 2005. Quantification of raf antisense oligonucleotide (rafAON) in biological matrices by LC-MS/MS to support pharmacokinetics of a liposome-entrapped rafAON formulation. Biomedical Chromatography 19: 272-278.
18. Lee, D. P. 1988. Chromatographic evaluation of large-pore and non-porous polymeric reversed phases. Journal of Chromatography 443: 143-153.
19. Huber, C. G., P. J. Oefner, and G. K. Bonn. 1992. High-performance liquid chromatographic separation of detritylated oligonucleotides on highly cross-linked poly-(styrene-divinylbenzene) particles. Journal of Chromatography 599: 113-118.
20. Huber, C. G., P. J. Oefner, and G. K. Bonn. 1993. High-resolution liquid chromatography of oligonucleotides on nonporous alkylated styrene-divinylbenzene copolymers. Analytical Biochemistry 212: 351-358.
21. Gelhaus, S. L., and W. R. LaCourse. 2005. Separation of modified 2'-deoxyoligonucleotides using ion-pairing reversed-phase HPLC. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences 820: 157-163.
22. Lloyd, L. L., M. I. Millichip, and K. J. Mapp. 2003. Rigid polymerics: the future of oligonucleotide analysis and purification. Journal of Chromatography A 1009: 223-230.
23. Unger, K. K., ed. 1990. Packings and Stationary Phases in Chromatographic Techniques. New York: Marcel Dekker.
24. Petro, M., F. Svec, and J. M. Frechet. 1996. Molded continuous poly(styrene-co-divinylbenzene) rod as a separation medium for the very fast separation of polymers. Comparison of the chromatographic properties of the monolithic rod with columns packed with porous and non-porous beads in high-performance liquid chromatography of polystyrenes. Journal of Chromatography A 752: 59-66.
25. Afeyan, N. B., N. F. Gordon, I. Mazsaroff, et al. 1990. Flow-through particles for the high-performance liquid chromatographic separation of biomolecules: perfusion chromatography. Journal of Chromatography 519: 1-29.
26. Svec, F., and J. M. J. Frechet. 1992. Continuous rods of macroporous polymer as high-performance liquid chromatography separation media. Analytical Chemistry 64: 820-822.
27. Svec, F., and J. M. J. Frechet. 1995. Temperature, a simple and efficient tool for the control of pore size distribution in macroporous polymers. Macromolecules 28: 7580-7582.
28. Mayr, B., G. Holzl, K. Eder, M. R. Buchmeiser, and C. G. Huber. 2002. Hydrophobic, pellicular, monolithic capillary columns based on cross-linked polynorbornene for biopolymer separations. Analytical Chemistry 74: 6080-6087.
29. Oberacher, H., B. Wellenzohn, and C. G. Huber. 2002. Comparative sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry. Analytical Chemistry 74: 211-218.
30. Premstaller, A., H. Oberacher, W. Walcher, et al. 2001. High-performance liquid chromatography-electrospray ionization mass spectrometry using monolithic capillary columns for proteomic studies. Analytical Chemistry 73: 2390-2396.
31. Huber, C. G., P. J. Oefner, and G. K. Bonn. 1993. High-resolution liquid chromatography of oligonucleotides on nonporous alkylated styrene-divinylbenzene copolymers. Analytical Biochemistry 212: 351-358.
32. Huber, C. G., P. J. Oefner, and G. K. Bonn. 1992. High-performance liquid chromatographic separation of detritylated oligonucleotides on highly cross-linked poly-(styrene-divinylbenzene) particles. Journal of Chromatography 599: 113-118.
33. Oberacher, H., A. Premstaller, and C. G. Huber. 2004. Characterization of some physical and chromatographic properties of monolithic poly(styrene-co-divinylbenzene) columns. Journal of Chromatography A 1030: 201-208.
34. Premstaller, A., H. Oberacher, and C. G. Huber. 2000. High-performance liquid chromatography-electrospray ionization mass spectrometry of single- and double-stranded nucleic acids using monolithic capillary columns. Analytical Chemistry 72: 4386-4393.
35. Bisjak, C. P., L. Trojer, S. H. Lubbad, W. Wieder, and G. K. Bonn. 2007. Influence of different polymerisation parameters on the separation efficiency of monolithic poly(phenyl acrylate-co-1, 4-phenylene diacrylate) capillary columns. Journal of Chromatography A 1154: 269-276.
36. Wieder, W., C. P. Bisjak, C. W. Huck, R. Bakry, and G. K. Bonn. 2006. Monolithic poly(glycidyl methacrylate-co-divinylbenzene) capillary columns functionalized to strong anion exchangers for nucleotide and oligonucleotide separation. Journal of Separation Science 29: 2478-2484.
37. Greiderer, A., S. C. Ligon, Jr., C. W. Huck, and G. K. Bonn. 2009. Monolithic poly(1, 2-bis(p-vinylphenyl)ethane) capillary columns for simultaneous separation of low- and high-molecular-weight compounds. Journal of Separation Science 32: 2510-2520.
38. Bakry, R., C. W. Huck, and G. K. Bonn. 2009. Recent applications of organic monoliths in capillary liquid chromatographic separation of biomolecules. Journal of Chromatography Science 47: 418-431.
39. Wieder, W., S. H. Lubbad, L. Trojer, C. P. Bisjak, and G. K. Bonn. 2008. Novel monolithic poly(p-methylstyrene-co-bis(p-vinylbenzyl)dimethylsilane) capillary columns for biopolymer separation. Journal of Chromatography A 1191: 253-262.
40. Trojer, L., S. H. Lubbad, C. P. Bisjak, W. Wieder, and G. K. Bonn. 2007. Comparison between monolithic conventional size, microbore and capillary poly(p-methylstyrene-co-1, 2-bis(p-vinylphenyl)ethane) high-performance liquid chromatography columns synthesis, application, long-term stability and reproducibility. Journal of Chromatography A 1146: 216-224.
41. Holdsvendova, P., J. Suchankova, M. Buncek, V. Backovska, and P. Coufal. 2007. Hydroxymethyl methacrylate-based monolithic columns designed for separation of oligonucleotides in hydrophilic-interaction capillary liquid chromatography. Journal of Biochemical and Biophysical Methods 70: 23-29.
42. Xiong, W., J. Glick, Y. Lin, and P. Vouros. 2007. Separation and sequencing of isomeric oligonucleotide adducts using monolithic columns by ion-pair reversed-phase nano-HPLC coupled to ion trap mass spectrometry. Analytical Chemistry 79: 5312-5321.
43. Sturm, M., S. Quinten, C. G. Huber, and O. Kohlbacher. 2007. A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data. Nucleic Acids Research 35: 4195-4202.
44. Kohlbacher, O., S. Quinten, M. Sturm, B. M. Mayr, and C. G. Huber. 2006. Structure-activity relationships in chromatography: retention prediction of oligonucleotides with support vector regression. Angewwandte Chemie (International Edition in English) 45: 7009-7012.
45. Przybyciel, M., and R. E. Majors. 2002. Phase collapse in reversed-phase LC. LC-GC Europe 15: 652-657.
46. Agrawal, S., J. Y. Tang, and D. M. Brown. 1990. Analytical study of phosphorothioate analogues of oligodeoxynucleotides using high-performance liquid chromatography. Journal of Chromatography 509: 396-399.
47. Gilar, M., A. Belenky, and A. S. Cohen. 2000. Polymer solutions as a pseudostationary phase for capillary electrochromatographic separation of DNA diastereomers. Electrophoresis 21: 2999-3009.
48. Metelev, V., and S. Agrawal. 1992. Ion-exchange high-performance liquid chromatography analysis of oligodeoxyribonucleotide phosphorothioates. Analytical Biochemistry 200: 342-346.
49. Huber, C. G. 1998. Micropellicular stationary phases for high-performance liquid chromatography of double-stranded DNA. Journal of Chromatography A 806: 3-30.
50. Gilar, M. 2001. Analysis and purification of synthetic oligonucleotides by reversed-phase high-performance liquid chromatography with photodiode array and mass spectrometry detection. Analytical Biochemistry 298: 196-206.
51. Snyder, L. R., J. W. Dolan, and P. W. Carr. 2004. The hydrophobic-subtraction model of reversed-phase column selectivity. Journal of Chromatography A 1060: 77-116.
52. Bidlingmeyer, B. A., S. N. Deming, W. P. Price, Jr., B. Sachok, and M. Petrusek. 1979. Retention mechanism for reversed-phase ion-pair liquid chromatography. Journal of Chromatography 186: 419-445.
53. Melander, W. R., and C. Horvath. 1980. Mechanistic study on ion-pair reversed-phase chromatography. Journal of Chromatography 201: 211-224.
54. Cecchi, T. 2008. Ion pairing chromatography. Critical Reviews in Analytical Chemistry 38: 161-214.
55. Jost, W., K. Unger, and G. Schill. 1982. Reverse-phase ion-pair chromatography of polyvalent ions using oligonucleotides as model substances. Analytical Biochemistry 119: 214-224.
56. Snyder, L. R., J. J. Kirkland, and J. W. Dolan. 2010. Introduction to Modern Liquid Chromatography. 3rd ed. Hoboken, N.J.: John Wiley.
57. Andrus, A., and R. G. Kuimelis. 2001. Analysis and purification of synthetic nucleic acids using HPLC. Current Protocols in Nucleic Acid Chemistry Chapter 10: Unit 10.5.
58. Haupt, W. P., and A. Pingoud. 1983. Comparison of several high-performance liquid chromatography techniques for the separation of oligodeoxynucleotides according to their chain lengths. Journal of Chromatography 260: 419-428.
59. Hoffman, N. E., and J. C. Liao. 1977. Reversed phase high performance liquid chromatographic separations of nucleotides in the presence of solvophobic ions. Analytical Chemistry 49: 2231-2234.
60. Crowther, J. B., R. Jones, and R. A. Hartwick. 1981. High-performance liquid chromatography of the oligonucleotides. Journal of Chromatography 217: 479-490.
61. Makino, K., H. Ozaki, T. Matsumoto, H. Imaishia, T. Takeuchi, and T. Fukui. 1987. Reversed-phase ion-pair chromatography of oligodeoxyribonucleotides. Journal of Chromatography A 400: 271-277.
62. McKeown, A. P., P. N. Shaw, and D. A. Barrett. 2002. Retention behaviour of an homologous series of oligodeoxythymidilic acids using reversed-phase ion-pair chromatography. Chromatographia 55: 271-277.
63. Kurata, C., D. C. Capaldi, Z. Wang, N. Luu, and H. Gaus. 2006. Methods for detection, identification and quantification of impurities. US Patent 2009/0095896, filed on Mar. 31, 2006.
64. Ikuta, S., R. Chattopadhyaya, and R. E. Dickerson. 1984. Reverse-phase polystyrene column for purification and analysis of DNA oligomers. Analytical Chemistry 56: 2253-2257.
65. McCarthy, S. M., and M. Gilar. 2010. Hexylammonium acetate as an ion-pairing agent for IP-RP LC analysis of oligonucleotides. Waters Application Note 720003361EN.
66. Gjerde, D. T., L. Hoang, and D. Hornby. 2009. RNA Purification and Analysis: Sample Preparation, Extraction, Chromatography. Weinheim: Wiley-VCH.
67. McCarthy, S. M., M. Gilar, and J. Gebler. 2009. Reversed-phase ion-pair liquid chromatography analysis and purification of small interfering RNA. Analytical Biochemistry 390: 181-188.
68. Apffel, A., J. A. Chakel, S. Fischer, K. Lichtenwalter, and W. S. Hancock. 1997. New procedure for the use of high-performance liquid chromatography-electrospray ionization mass spectrometry for the analysis of nucleotides and oligonucleotides. Journal of Chromatography A 777: 3-21.
69. Apffel, A., J. A. Chakel, S. Fischer, K. Lichtenwalter, and W. S. Hancock. 1997. Analysis of oligonucleotides by HPLC-electrospray ionization mass spectrometry. Analytical Chemistry 69: 1320-1325.
70. Gilar, M., K. J. Fountain, Y. Budman, J. L. Holyoke, H. Davoudi, and J. C. Gebler. 2003. Characterization of therapeutic oligonucleotides using liquid chromatography with on-line mass spectrometry detection. Oligonucleotides 13: 229-243.
71. Gilar, M., and U. D. Neue. 2007. Peak capacity in gradient reversed-phase liquid chromatography of biopolymers. Theoretical and practical implications for the separation of oligonucleotides. Journal of Chromatography A 1169: 139-150.
72. Gaus, H. J., S. R. Owens, M. Winniman, S. Cooper, and L. L. Cummins. 1997. On-line HPLC electrospray mass spectrometry of phosphorothioate oligonucleotide metabolites. Analytical Chemistry 69: 313-319.
73. Griffey, R. H., M. J. Greig, H. J. Gaus, et al. 1997. Characterization of oligonucleotide metabolism in vivo via liquid chromatography/electrospray tandem mass spectrometry with a quadrupole ion trap mass spectrometer. Journal of Mass Spectrometry 32: 305-313.
74. Bidlingmeyer, B., and Q. Wang. 2006. Additives for reversed-phase HPLC mobile phases. US Patent 7125492, filed July 17, 2003 and issued Jan. 2005.
75. McCarthy, S. M., W. J. Warren, A. Dubey, and M. Gilar. 2008. Ion-pairing systems for reversed-phase chromatography separation of oligonucleotides, paper presented at TIDES Conference in Las Vegas, Nevada.
76. Bartha, Á., and J. Ståhlberg. 1994. Electrostatic retention model of reversed-phase ion-pair chromatography. Journal of Chromatography A 668: 255-284.
77. Cruz, E., M. R. Euerby, C. M. Johnson, and C. A. Hackett. 1997. Chromatographic classification of commercially available reverse-phase HPLC columns. Chromatographia 44: 151-161.
78. Bidlingmeyer, B. A. 1980. Separation of ionic compounds by reversed-phase liquid chromatography: an update of ion-pairing techniques. J. Chromatogr. Sci. 18: 525-539.
79. Cantor, C. R., and P. R. Schimmel. 1980. The Conformation of Biological Macromolecules. Part 1. Their Biophysical Chemistry. San Francisco: W. H. Freeman.
80. Nawrocki, J. 1997. The silanol group and its role in liquid chromatography. Journal of Chromatography A 779: 29-71.
81. Daignault, L. G., and D. P. Rillema. 1992. Ion-interaction chromatography: a study of the distribution of n-alkylammonium ions on an ODS-2 column. Journal of Chromatography A 602: 3-8.
82. Zou, Y., P. Tiller, I. W. Chen, M. Beverly, and J. Hochman. 2008. Metabolite identification of small interfering RNA duplex by high-resolution accurate mass spectrometry. Rapid Communications in Mass Spectrometry 22: 1871-1881.
83. Beverly, M., K. Hartsough, and L. Machemer. 2005. Liquid chromatography/electrospray mass spectrometric analysis of metabolites from an inhibitory RNA duplex. Rapid Communications in Mass Spectrometry 19: 1675-1682.
84. Lei, B., S. Li, L. Xi, J. Li, H. Liu, and X. Yao. 2009. Novel approaches for retention time prediction of oligonucleotides in ion-pair reversed-phase high-performance liquid chromatography. Journal of Chromatography A 1216: 4434-4439.
85. Gelhaus, S. L., W. R. LaCourse, N. A. Hagan, G. K. Amarasinghe, and D. Fabris. 2003. Rapid purification of RNA secondary structures. Nucleic Acids Research 31: e135.
86. Tan, L. C., P. W. Carr, and M. H. Abraham. 1996. Study of retention in reversed-phase liquid chromatography using linear solvation energy relationships I. The stationary phase. Journal of Chromatography A 752: 1-18.
87. Katritzky, A. R., S. Perumal, R. Petrukhin, and E. Kleinpeter. 2001. Codessa-based theoretical QSPR model for hydantoin HPLC-RT lipophilicities. Journal of Chemical Information Computer Sciences 41: 569-574.
88. Uhlmann, E., and A. Peyman. 1990. Antisense oligonucleotides: a new therapeutic principle. Chemical Reviews 90: 543-584.
89. Dias, N., and C. A. Stein. 2002. Antisense oligonucleotides: basic concepts and mechanisms. Molecular Cancer Therapeutics 1: 347-355.
90. Kreuzian, T. B. 2009. Analysis of duplexes. Paper presented at EuroTides Conference, Dec. 2-3, in Amsterdam, Netherlands.