Liquid chromatographic separation of oligonucleotides

Abstract Synthetic oligonucleotides have become increasingly important molecules as a part of new developments in the use of aptamers, antisense, and small interfering ribonucleic acid (siRNA) for the treatment of different human diseases. The development of chromatographic separation methods for the quantitative and sensitive analysis of oligonucleotides is a critical part for the advancement of this research area. A typical therapeutic oligonucleotide sample is a short ribonucleic acid (RNA) molecule with about 19–21 nucleotide length (~ 7–8 kDa), or a 21-mer base pair length in double-stranded siRNA (~ 16 kDa). Due to their relatively large sizes and multiple negative charges compared with typical, small molecule pharmaceutical compounds, oligonucleotides can be difficult to analyze with conventional reversed-phase liquid chromatography (RPLC) methods. In this chapter, we provide an overview of liquid chromatographic (LC) separation of oligonucleotides, including anion-exchange, ion-pair reversed-phase, and mixed-mode LC.

[1]  Ronald R. Breaker,et al.  Natural and engineered nucleic acids as tools to explore biology , 2004, Nature.

[2]  Martin Gilar,et al.  Ion-pair reversed-phase high-performance liquid chromatography analysis of oligonucleotides: retention prediction. , 2002, Journal of chromatography. A.

[3]  D. Hornby,et al.  Studying the mechanism of RNA separations using RNA chromatography and its application in the analysis of ribosomal RNA and RNA:RNA interactions. , 2009, Journal of chromatography. A.

[4]  A. Pingoud,et al.  Comparison of several high-performance liquid chromatography techniques for the separation of oligodeoxynucleotides according to their chain lengths , 1983 .

[5]  V. Wacheck,et al.  Short interfering RNA (siRNA): tool or therapeutic? , 2006, Clinical science.

[6]  J. Watts,et al.  Chemically modified siRNA: tools and applications. , 2008, Drug discovery today.

[7]  B. Buszewski,et al.  The Effects of Stationary Phases on Retention and Selectivity of Oligonucleotides in IP-RP-HPLC , 2014, Chromatographia.

[8]  M. Staehelin.  Studies on nucleotide sequences in ribonucleic acids: I. Separation of oligonucleotides on DEAE-cellulose , 1961 .

[9]  Xiaoyan Chen,et al.  Bioanalysis of an oligonucleotide and its metabolites by liquid chromatography-tandem mass spectrometry. , 2010, Journal of pharmaceutical and biomedical analysis.

[10]  C. Horváth,et al.  Enhancement of retention by ion-pair formation in liquid chromatography with nonpolar stationary phases , 1977 .

[11]  Jennifer A. Lockridge,et al.  Liquid chromatography electrospray ionization mass spectrometry analysis of the ocular metabolites from a short interfering RNA duplex. , 2006, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[12]  M. Beverly.  Applications of mass spectrometry to the study of siRNA. , 2011, Mass spectrometry reviews.

[13]  Alberto Cavazzini,et al.  Synthetic oligonucleotide separations by mixed-mode reversed-phase/weak anion-exchange liquid chromatography. , 2014, Journal of chromatography. A.

[14]  Lisa Jarvis.  DELIVERING THE PROMISE , 2009 .

[15]  P. Gilham,et al.  Separation of oligonucleotides, nucleotides, and nucleosides on columns of polystyrene anion-exchangers with solvent systems containing ethanol. , 1976, Analytical biochemistry.

[16]  E. Volkin,et al.  On the structure of ribonucleic acids. II. The products of ribonuclease action. , 1953, The Journal of biological chemistry.

[17]  T. Raglione,et al.  Mixed-mode hydrophobic ion exchange for the separation of oligonucleotides and DNA fragments using HPLC. , 1986, Analytical biochemistry.

[18]  Buyun Chen,et al.  Chromatographic methods for the determination of therapeutic oligonucleotides. , 2012, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[19]  W. Parson,et al.  Preparation and evaluation of packed capillary columns for the separation of nucleic acids by ion-pair reversed-phase high-performance liquid chromatography. , 2000, Journal of chromatography. A.

[20]  van Ma Marion Straten,et al.  Effect of buffers on silica-based column stability in reversed-phase high-performance liquid chromatography , 1996 .

[21]  Rainer Bischoff,et al.  Chemically synthesized hydrophobic anion-exchange high-performance liquid chromatography supports used for oligonucleotide resolution by mixed mode chromatography , 1983 .

[22]  A. Klippel,et al.  Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells. , 2003, Nucleic acids research.

[23]  Y. Yu,et al.  Ultra-performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) and UPLC/MS(E) analysis of RNA oligonucleotides. , 2010, Rapid communications in mass spectrometry : RCM.

[24]  T. Murotsu,et al.  Separation of oligonucleotides by high-performance ion-exchange chromatography on a non-porous ion exchanger. , 1988, Journal of chromatography.

[25]  D. Guyer,et al.  Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease , 2006, Nature Reviews Drug Discovery.

[26]  H. Vornlocher,et al.  Characterization of small interfering RNA by non-denaturing ion-pair reversed-phase liquid chromatography. , 2011, Journal of chromatography. A.

[27]  B. Silvestrini,et al.  Sertoli cell synthesizes and secretes a protease inhibitor, alpha 2-macroglobulin. , 1990, Biochemistry.

[28]  F. Regnier,et al.  High-performance anion-exchange chromatography of oligonucleotides. , 1985, Analytical biochemistry.

[29]  G. Srivatsa,et al.  Handbook of Analysis of Oligonucleotides and Related Products , 2011 .

[30]  Matthias John,et al.  RNAi-mediated gene silencing in non-human primates , 2006, Nature.

[31]  R. Hartwick,et al.  High-performance liquid chromatographic separation of oligonucleotides and other nucleic acid constituents on multifunctional stationary phases , 1983 .

[32]  J. Thayer,et al.  Advantages of ion-exchange chromatography for oligonucleotide analysis. , 2011, Bioanalysis.

[33]  T. Tuschl,et al.  RNA Interference and Small Interfering RNAs , 2001, Chembiochem : a European journal of chemical biology.

[34]  R. Bischoff,et al.  Isolation of specific tRNAs using an ionic-hydrophobic mixed-mode chromatographic matrix. , 1985, Analytical biochemistry.

[35]  Akhmad Sabarudin,et al.  Preparation of methacrylate-based anion-exchange monolithic microbore column for chromatographic separation of DNA fragments and oligonucleotides. , 2012, Analytica chimica acta.

[36]  J. J. Kirkland.  Superficially porous silica microspheres for the fast high-performance liquid chromatography of macromolecules , 1992 .

[37]  J. H. Spencer,et al.  Nucleotide clusters in deoxyribonucleic acids. Separation of oligo-nucleotides released by deoxyribonuclease I. , 1970, Biochemistry.

[38]  H. Radilová,et al.  Retention Behavior of Oligonucleotides on a Glycidyl Methacrylate-Based DEAE-Modified Sorbent , 2005 .

[39]  J. Kirkland,et al.  Superficially porous silica microspheres for fast high-performance liquid chromatography of macromolecules. , 2000, Journal of chromatography. A.

[40]  F. Regnier,et al.  High-performance anion-exchange chromatography of oligonucleotides , 1983 .

[41]  W S Hancock,et al.  Analysis of Oligonucleotides by HPLC-Electrospray Ionization Mass Spectrometry. , 1997, Analytical chemistry.

[42]  J. H. Boom,et al.  Sequence analysis of synthetic oligonucleotides by high-performance liquid anion-exchange chromatography. , 1977 .

[43]  Sheila A Doggrell,et al.  Pegaptanib: the first antiangiogenic agent approved for neovascular macular degeneration , 2005, Expert opinion on pharmacotherapy.

[44]  E. Southern,et al.  Measurement of DNA length by gel electrophoresis. , 1979, Analytical biochemistry.

[45]  M. Manoharan,et al.  RNAi therapeutics: a potential new class of pharmaceutical drugs , 2006, Nature chemical biology.

[46]  S. Takenaka,et al.  A reversed-phase intercalator column for high performance liquid chromatographic separation of oligonucleotides. , 1988 .

[47]  C. Pohl,et al.  Control of oligonucleotide retention on a pH-stabilized strong anion exchange column. , 2005, Analytical biochemistry.

[48]  A. Fire,et al.  Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.

[49]  L. Baratova,et al.  Use of an amino-silica column for the high-performance liquid chromatographic analysis of synthetic oligodeoxy-nucleotides. , 1977, Journal of chromatography.

[50]  M. Dickman,et al.  Nucleic acid separations using superficially porous silica particles , 2016, Journal of chromatography. A.

[51]  J. Gebler,et al.  Reversed-phase ion-pair liquid chromatography analysis and purification of small interfering RNA. , 2009, Analytical biochemistry.

[52]  R. V. Tomlinson,et al.  THE EFFECT OF UREA, FORMAMIDE, AND GLYCOLS ON THE SECONDARY BINDING FORCES IN THE ION-EXCHANGE CHROMATOGRAPHY OF POLYNUCLEOTIDES OF DEAE-CELLULOSE. , 1963, Biochemistry.

[53]  M. D. Garilhe,et al.  Séparation des oligonucléotides du DNA apurinique par chromatographie bidimensionnelle sur couches minces de gel de silice , 1967 .

[54]  H. Ozaki,et al.  A RPLC C30 Column for the Separation of Oligonucleotides , 1987 .

[55]  Shengqi Wang,et al.  An Improved Ion-Pair Reversed Phase LC Method for Analysis of Major Impurities of Phosphorothioate Oligonucleotide Cantide , 2010 .

[56]  M. Gilar.  Analysis and purification of synthetic oligonucleotides by reversed-phase high-performance liquid chromatography with photodiode array and mass spectrometry detection. , 2001, Analytical biochemistry.

[57]  T. Kitamura,et al.  High-performance ion-exchange chromatography of proteins on non-porous ion exchangers. , 1987, Journal of chromatography.

[58]  A. Andrus.  Oligonucleotide analysis by gel capillary electrophoresis , 1992 .

[59]  M. Caruthers,et al.  Deoxynucleoside phosphoramidites—A new class of key intermediates for deoxypolynucleotide synthesis , 1981 .

[60]  van Ma Marion Straten,et al.  Stability of silica-based, endcapped columns with pH 7 and 11 mobile phases for reversed-phase high-performance liquid chromatography. , 1997, Journal of chromatography. A.

[61]  C. McNeff,et al.  High-performance anion-exchange chromatography of oligonucleotides and oligodeoxynucleotides on quaternized polyethylenimine-coated zirconia. , 1995, Analytical chemistry.

[62]  S. Crooke,et al.  An overview of progress in antisense therapeutics. , 1998, Antisense & nucleic acid drug development.

[63]  J. Gebler,et al.  Analysis of native and chemically modified oligonucleotides by tandem ion-pair reversed-phase high-performance liquid chromatography/electrospray ionization mass spectrometry. , 2003, Rapid communications in mass spectrometry : RCM.

[64]  Beverly L. Davidson,et al.  Current prospects for RNA interference-based therapies , 2011, Nature Reviews Genetics.

[65]  R. Scott,et al.  Some aspects of ion-exchange chromatography employing adsobed ion exchangers on reversed-phase columns , 1979 .

[66]  P. Oefner.  Allelic discrimination by denaturing high-performance liquid chromatography. , 2000, Journal of chromatography. B, Biomedical sciences and applications.

[67]  Mirlinda Biba,et al.  Factors influencing the separation of oligonucleotides using reversed-phase/ion-exchange mixed-mode high performance liquid chromatography columns. , 2013, Journal of chromatography. A.

[68]  S. Crooke.  Vitravene--another piece in the mosaic. , 1998, Antisense & nucleic acid drug development.

[69]  L. McLaughlin.  Mixed-mode chromatography of nucleic acids , 1989 .

[70]  H. Khorana,et al.  Studies on Polynucleotides. II.1 The Synthesis and Characterization of Linear and Cyclic Thymidine Oligonucleotides2 , 1958 .

[71]  F. Regnier,et al.  Separation of synthetic oligonucleotides on columns of microparticulate silica coated with crosslinked polyethylene imine. , 1983, Analytical biochemistry.

[72]  B. Egan.  Separation of oligonucleotides by reversed-phase chromatography. , 1973, Biochimica et biophysica acta.

[73]  Rebecca A. Arvary,et al.  Evaluation of core-shell particle columns for ion-pair reversed-phase liquid chromatography analysis of oligonucleotides. , 2013, Journal of pharmaceutical and biomedical analysis.

[74]  Weili Wei,et al.  Recent advances in materials for stationary phases of mixed-mode high-performance liquid chromatography , 2016 .

[75]  C. Welch,et al.  Investigation of a new core-shell particle column for ion-pair reversed-phase liquid chromatography analysis of oligonucleotides. , 2014, Journal of pharmaceutical and biomedical analysis.

[76]  M. Manoharan.  RNA interference and chemically modified small interfering RNAs. , 2004, Current opinion in chemical biology.

[77]  H. Gassen,et al.  Application of a weakly basic dimethylamino-modified silica ion exchanger to the separation of oligonucleotides , 1979 .

[78]  K. Draper,et al.  Quality Aspects of Oligonucleotide Drug Development: Specifications for Active Pharmaceutical Ingredients , 2012 .

[79]  P. Oefner,et al.  High-resolution liquid chromatography of oligonucleotides on nonporous alkylated styrene-divinylbenzene copolymers. , 1993, Analytical biochemistry.