High-performance affinity chromatography of oligonucleotides on nucleic acid analogue immobilized silica gel columns

The role of fluoroalcohols as counter anions for ion-pairing reversed-phase liquid chromatography/high-resolution electrospray ionization mass spectrometry analysis of oligonucleotides

RATIONALE

Hexafluoroisopropanol (HFIP) has been widely used as a counter anion in the mobile phase for ion-pairing reversed-phase liquid chromatography/mass spectrometry (IP-RP-LC/MS) analysis of oligonucleotides. However, researchers are still searching for improvements to counter anions for LC/MS analysis of oligonucleotides. This study aimed to find alternatives to HFIP for analyzing oligonucleotides.

METHODS

The study was performed using an Agilent 1290 ultra-high-performance liquid chromatography (UHPLC) system coupled to an Agilent 6540 mass spectrometer by using an oligonucleotide BEH C18 column (100 × 2.1 mm, 1.7 μm). Buffer systems containing ion-pairing reagents (triethylamine, tripropylamine, hexylamine, dimethylbutylamine, diisopropylethylamine, N,N-dimethylcyclohexylamine, and octylamine) and fluoroalcohols (HFIP and hexafluoro-2-methyl-2-propanol (HFTP)) were compared chromatographically and mass spectrometrically.

RESULTS

Results showed that HFTP has better desalting ability than HFIP, but both HFIP and HFTP have comparable effects on the separation of oligonucleotides sized from 10mer to 40mer for most of ion-pairing reagents, with the exception of triethylamine and N,N-dimethylcyclohexylamine, where HFIP performed better than HFTP.

CONCLUSIONS

The choice of fluoroalcohols in IP-RP-LC/MS analysis of oligonucleotides depends on the type of ion-pairing reagents used in the mobile phase. As a guideline, we would recommend to use either HA-HFIP or HA-HFTP for small oligonucleotides, but TPA-HFTP for large oligonucleotides for IP-RP-LC/MS analysis of synthetic oligonucleotides.

Base-specific separation of oligodeoxynucleotides by capillary affinity gel electrophoresis

Capillary affinity gel electrophoresis was applied to sequence-specific and base composition-specific recognition of oligodeoxynucleotides, utilizing the formation of heteroduplexes between a nucleic acid analogue immobilized into the capillary gel and soluble oligodeoxynucleotides with different sequences. Capillary affinity gel electrophoresis using capillaries filled with a conjugated gel of polyacrylamide and a synthetic nucleic acid analogue [poly(9-vinyladenine)] was effective for the selective separation of hexathymidylic acid from a mixture of four homopolymers of A6, C6, G6, and T6 and for the complete resolution of five heteropolymers of hexadeoxynucleotides (TAAAAA, TTAAAA, TTTAAA, TTTTAA, TTTTTA). We also demonstrated that capillary affinity gel electrophoresis was useful for the selective and the sensitive sequence-specific recognition of sequence isomers of DNA (TTTTAA, TTTTAAT, TTTATA, and TTTTAA).

Chromatography in analytical biotechnology

Recent advances in biochromatography have focused on improvements in the design of stationary supports for liquid chromatography. During the past year, the innovative use of columns packed with small non-porous particles has significantly improved the efficiency of chromatographic separations. Bioseparations that previously took hours are now possible in only a few minutes.

Affinity gel electrophoresis of nucleic acids. Nucleobase-selective separation of DNA and RNA on agarose-poly(9-vinyladenine) conjugated gel

Poly(9-vinyladenine) (PVAd) was immobilized within an agarose gel matrix to produce a novel affinity gel for the base-specific separation of nucleic acids by electrophoresis. The shape (single- or double-stranded) and base content of nucleic acids were specifically recognized by the affinity gel. Only single stranded DNA, of which the sequence is not regular enough to form a stable duplex hairpin structure, was selectively absorbed over double-stranded DNA. Among five polynucleotides having different bases such as poly(A), poly(G), poly(C), poly(U) and poly(I), poly(U) and poly(I) were base-specifically adsorbed by PVAd, probably by hydrogen bond formation. The effect of the molecular mass and size of poly(9-vinyladenine) was also examined.

Affinity gel electrophoresis of nucleic acids. Specific base- and shape-selective separation of DNA and RNA on polyacrylamide-nucleobase conjugated gel

Two types of affinity gels consisting of cross-linked polyacrylamide and affinity ligands possessing nucleic acid bases were prepared. One type of gel was polyacrylamide-poly(vinylnucleobase) conjugated gel, where the poly(vinylnucleobase) such as poly(9-vinyladenine) (PVAd) bearing a nucleobase in the side-chain was entrapped in the gel matrix. The other type of gel, in which a nucleobase such as adenine is chemically bonded to polyacrylamide gel, was prepared by copolymerization of acrylamide, cross-linker and 9-vinyladenine. These affinity gels, especially the former, demonstrated characteristic nucleobase- and shape-selective separation of nucleic acids. The gels showed high affinity for single-stranded DNA and both single- and double-stranded polynucleotides and could separate a double-stranded DNA in mixtures of double-stranded DNA and polynucleotides. The electrophoretic mobilities of poly(uridylic acid) and poly(inosinic acid) were selectively retarded even in the presence of 7 M urea. The electrophoretic behaviours of nucleic acids on the polyacrylamide-PVAd conjugated gels were compared with those on the agarose-PVAd conjugated gel. The effects of urea, temperature and concentration of PVAd were also examined. The polyacrylamide-PVAd conjugated gel served to elucidate interactions between PVAd and nucleic acids that could not be detected by usual spectroscopic methods.

Effect of urea concentration on the base-specific separation of oligodeoxynucleotides in capillary affinity gel electrophoresis

Base-specific separations of oligodeoxynucleotides were achieved with high resolution by electrophoresis, using a urea-gel capillary, in which poly(9-vinyladenine) (PVAd) was utilized as an affinity ligand. The migration behaviour and the plate number of oligodeoxynucleotides were investigated as a function of urea concentration between 2 and 10 M in capillary gel electrophoresis (CGE) as well as capillary affinity gel electrophoresis (CAGE). The migration time in CGE separation increases as urea concentration increases. An increase in the viscosity of the gel buffer medium as well as a change in the conformation of oligodeoxynucleotides is found to be a predominant factor for an increase in the migration time. The migration time and the plate number of oligothymidylic acids, which interact with PVAd in CAGE, is manipulated by differing urea concentration, which leads to the change in the dissociation process of a specific hydrogen bonding between oligothymidylic acids and PVAd. The migration time of oligodeoxyadenylic acids, which do not interact with PVAd in CAGE, increases with an increase in urea concentration as in CGE separation. The plate number of oligodeoxyadenylic acid was not affected by the urea concentration.

Affinity chromatography with nucleic acid polymers

Column chromatography utilizing polynucleotides immobilized on solid support is reviewed. This form of affinity chromatography is used for the isolation of polynucleotides and polynucleotide binding proteins, and to a lesser extent for analysis. Several specific applications within these categories have been widely used in the biomedical sciences. Poly(A) mRNA is routinely isolated using oligo(dT) or oligo(dU) supports. Many DNA binding proteins, including transcription factors, restriction endonucleases, and proteins involved in DNA repair, replication, recombination, and transposition have been purified using DNA affinity chromatography. Recently, DNA supports suitable for use in high-performance liquid chromatography have been described and utilized. The current usage of DNA affinity chromatography is reviewed and potential future uses for this technology are speculated upon.