DNA/RNA Oligonucleotide Separations

Addressing Challenges in LC and LC-MS Based Analyses

Reversed-phase and ion-exchange chromatography for the analysis of synthetic oligonucleotides and related DNA/RNA species is well documented in their ability to purify and analyze these heterogeneous entities (e.g., full-length oligonucleotide product from undesired shorter and longer length sequences). With increased use of MS detection, Waters introduced the XTerra C18 family of "hybrid particles" that are MS compatible with increased high pH tolerance based on various application needs. Waters second-generation of XBridge C18 hybrid columns were introduced to expand performance characteristics.

Scalable offering in 1.7 μm UPLC particles, 2.5 μm HPLC/UHPLC particles, and 5 µm lab-scale preparative particles in various column dimensions.
Increased confidence in results: MaxPeak Premier Columns with MaxPeak HPS are available for those who have more challenging samples that are prone to metal affinity; providing improved sensitivity, recovery, reproducibility, and less time-consuming column conditioning. ACQUITY Premier and XBridge Premier Oligonucleotide Columns are available in 1.7 µm and 2.5 µm particle sizes.
Exceptional sample resolution and superior column life.
Confidence in results: All columns are QC tested with relevant application standards to help ensure consistent batch-to-batch and column-to-column performance.

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ACQUITY Premier Columns for oligonucleotides

Reduced Column Conditioning for More Reliable Results

Oligonucleotide analysis comes with many unique challenges related to non-specific adsorption (NSA) as oligos may react with metal surfaces in stainless steel columns. The MaxPeak Premier Oligonucleotide Columns with MaxPeak High Performance Surfaces (HPS) reduce these interactions, saving time-consuming column conditioning and enabling scientists to generate results, faster. In addition, a reduction in metal interactions leads to greater reproducibility and enhanced confidence in analytical results. These MaxPeak Premier Columns also provide increased sensitivity for oligonucleotides prone to NSA due to metal interactions, improving limits of detection and data quality.

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Exceptional Resolution of Synthetic Oligonucleotide Mixtures

Chromatography of synthetic oligonucleotides and DNA/RNA species of less than approximately 12,000 base pairs can be performed using reversed-phase or ion-exchange gradient techniques capable of resolving sample components based on minor changes in size (i.e., charge). ACQUITY UPLC Oligonucleotide C18, 1.7 μm Columns (designed for use with an ACQUITY UPLC System) and XBridge Oligonucleotide C18, 2.5 μm Columns are well suited for the analysis of detritylated oligonucleotides using ion-pair, reversed-phase chromatography.

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Separation of 15-60 mer deoxythymidine ladder

zoom	Outstanding Column Lifetime Oligonucleotide columns packed with BEH Technology particles show remarkable column longevity under these demanding separation conditions, while maintaining outstanding separation performance.

Scaleable Column Offerings from Analytical to Lab-Scale Prep

The availability of 1.7 μm UPLC particles or 2.5 μm HPLC/UHPLC particles in various column dimensions provides flexibility to meet various lab-scale isolation or analysis needs, and delivers exceptional sample resolution and superior column life.

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Impact of sorbent particle size on oligonucleotide ladder separations

Benchmarking Oligonucleotides with a Relevant Standard

In addition to column offerings for oligonucleotide analysis, the pre-packaged MassPREP Oligonucleotide Standard is available and designed for benchmarking HPLC/UPLC separations and assessing column performance for synthetic oligonucleotide analyses.

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Oligonucleotide Desalting by Solid-Phase Extraction

Desalting of synthetic oligonucleotides is essential for MS analysis (QC, genotyping applications, and SNP analysis). The Oasis μElution Plate combines a patented plate design, proven Oasis chemistries, and generic protocols enabling elution volumes as low as 25 μL. You can perform SPE clean-up and concentration of small sample volumes. The Oasis hydrophilic-lipophilic-balanced (HLB) sample extraction products incorporate a patented copolymer made from a balanced ratio of two monomers: lipophilic divinylbenzene and hydrophilic N-vinylpyrolodone.