Synthetic Oligonucleotide Analysis Tools and Solutions

Overview

A resurgence in oligonucleotide therapeutic development has led to a rapidly expanding preclinical/clinical pipeline. Working at the level of gene transcription and translation, these short-chain nucleic acid drugs hold great promise for many inherited disorders and common ailments alike.

For more than a decade, Waters has been leading the development of advanced tools and techniques for synthetic oligonucleotide characterization, purification and bioanalysis. With passion, dedication and focus, we remain committed to helping our customers solve their most difficult analytical challenges. From our innovative high-performance chromatography columns and sample prep consumables, to our suite of LC, MS and Light Scattering instruments, to our compliance-ready software and application-based workflows, to our unrivaled service and support, we stand ready to help you succeed with your synthetic oligonucleotide development goals.

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Applications

Characterization
Impurities Analysis
Bioanalysis
Particle Count and Identification
Purification

With oligonucleotide therapeutics, the sequence and location of modified nucleotides are of critical importance to their function, stability, and efficacy. LC-MS/MS fragmentation is a key technique that can provide this level of sequence confirmation, and automated data analysis and reporting tools make the process fast and easy.

With oligonucleotide therapeutics, the sequence and location of modified nucleotides are of critical importance to their function, stability, and efficacy. LC-MS/MS fragmentation is a key technique that can provide this level of sequence confirmation, and automated data analysis and reporting tools make the process fast and easy.

Application Notes

Synthetic oligonucleotides contain many process and product related impurities, including truncated n-X failure sequences, oxidized (e.g., PS to PO conversions) and deaminated variants, and for dsRNA species (e.g., siRNA) single stranded components are considered impurities. For regulatory filings, these impurities must be identified and quantified down to as little as 0.01% of the full length product.

Synthetic oligonucleotides contain many process and product related impurities, including truncated n-X failure sequences, oxidized (e.g., PS to PO conversions) and deaminated variants, and for dsRNA species (e.g., siRNA) single stranded components are considered impurities. For regulatory filings, these impurities must be identified and quantified down to as little as 0.01% of the full length product.

Application Notes

Quantitative analysis of oligonucleotides from biofluids requires effective, sample preparation approaches to achieve maximum recovery, reproducibility, and lower limits of detection. Waters sample preparation, liquid chromatography, and mass spectrometry tools are designed to deliver the sensitivity, repeatability, and productivity needed for your oligonucleotide bioanalysis projects.

Quantitative analysis of oligonucleotides from biofluids requires effective, sample preparation approaches to achieve maximum recovery, reproducibility, and lower limits of detection. Waters sample preparation, liquid chromatography, and mass spectrometry tools are designed to deliver the sensitivity, repeatability, and productivity needed for your oligonucleotide bioanalysis projects.

Application Notes

Subvisible and visible particles in synthetic oligonucleotides can compromise patient safety and trigger costly FDA recalls. With backgrounded membrane imaging (BMI) and fluorescence membrane microscopy (FMM), you can count and identify particles at high throughput using just 5 µL of sample—helping you mitigate risks early, ensure compliance, and make confident decisions.

Subvisible and visible particles in synthetic oligonucleotides can compromise patient safety and trigger costly FDA recalls. With backgrounded membrane imaging (BMI) and fluorescence membrane microscopy (FMM), you can count and identify particles at high throughput using just 5 µL of sample—helping you mitigate risks early, ensure compliance, and make confident decisions.

Application Notes

Discover how Waters oligonucleotide lab-scale preparative columns and consumables enable direct scale-up, high recovery, and high throughput purifications. Built with industry-leading pH and temperature stability, each batch of sorbent is QC tested and selected using Waters oligonucleotide standards to ensure lot-to-lot performance and reproducibility.

Discover how Waters oligonucleotide lab-scale preparative columns and consumables enable direct scale-up, high recovery, and high throughput purifications. Built with industry-leading pH and temperature stability, each batch of sorbent is QC tested and selected using Waters oligonucleotide standards to ensure lot-to-lot performance and reproducibility.

Application Notes

Solutions

Waters LC and LC-MS systems offer leading separations performance and sensitivity for synthetic oligonucleotide analysis.

MaxPeak Premier Soultions-illustrated coulum with System

Ultra-low non-specific adsorption for maximum sensitivity and reproducibility

MaxPeak Premier Solutions

MaxPeak Premier columns and systems eliminate the unpredictability of analyte losses due to metal interactions, which can be especially pronounced with negatively charged oligonucleotides.

Streamlined, simplified LC-MS analysis for every laboratory

A compliance-ready LC-MS solution built for ease-of-use and deployment across development and manufacturing labs

BioAccord LC-MS System

Simplify high-performance LC-MS oligonucleotide analysis for all levels of expertise with the Waters BioAccord LC-MS Solution that integrates an ACQUITY Premier LC with an ACQUITY RDa high-resolution MS detector, and runs on the compliance-ready waters_connect Platform.

Robust high-resolution coverage for confident characterization

Xevo G3 QTof

Accelerate characterization of synthetic oligonucleotides with the Xevo G3 QTof high-performance HRMS benchtop system that delivers accurate qualitative and quantitative results.

An incredibly compact, more sustainable tandem quadrupole mass spectrometer, the Waters Xevo TQ Absolute XR enables your lab to achieve and maintain high performance and productivity.

Exquisite sensitivity for quantification analyses

Xevo TQ Absolute XR Triple Quadrupole Mass Spectrometry

Expand the scope of ultimate sensitivity analysis with the new Waters Xevo TQ Absolute XR Triple Quadrupole Mass Spectrometer that delivers unprecedented levels of sensitivity and robustness for your oligonucleotide bioanalytical applications.

Exceptional performance, without compromise for RNA attribute characterization and monitoring Xexo MRT Mass Spectrometer Confidently identify and monitor RNA quality attributes using the Xevo MRT on waters_connect. Sub-ppm mass accuracy, efficient fragmentation, high mass resolution, and powerful quantitative capabilities enhance both accuracy and lab productivity.

Exceptional performance for oligonucleotide characterization and impurity analyses

Xevo MRT Mass Spectrometer

The powerfully advanced Xevo MRT mass spectrometer delivers low- to sub-ppm mass accuracy coupled with high levels of sensitivity and dynamic range for in-depth oligonucleotide characterization, including confident detection of multiple product-related synthetic impurities and detection of subtle differences and modifications.

Analyze antibody-oligo-conjugates (AOCs) in their native state

DAWN and Optilab-dRI Detectors for MALS Analysis

LC-MALS methods enable routine analysis of AOCs, including determining average oligonucleotide to antibody ratios (OARs), and aggregation/high molecular weight species (HMWS) in all aqueous mobile phases, including formulation buffers.

The Waters Analytical-Scale Purification System is a fully automated solution designed for labs that require more efficient purification solutions on smaller prep scales.

Bring your analytical purification performance to the next level

Analytical Scale Purification System

The Analytical Scale Purification System is a fully automated purification solution designed for purification labs that need more efficient purification on a smaller scale. It offers high-capacity sample processing, low-volume fraction collection, and high-pressure capabilities.

Waters software streamlines data acquisition, processing, and reporting oligonucleotide analysis results.

waters_connect supports deployment of compliance-ready LC-MS workflows throughout development and into production and QC lab environments.

Streamline data analysis and processing

waters_connect for biopharmaceuticals

Accelerate the journey from sample analysis to decision-making with waters_connect for biopharmaceutical analysis. This compliance-ready, networkable data acquisition, analysis and reporting platform supports the deployment of LC-MS methods across development and manufacturing labs, and offers built-in apps for intact mass analysis, sequence confirmation of oligonucleotides & mRNA, process monitoring, quantitative analysis, and more.

Operate more efficiently and securely with the flexible capabilities of Empower Chromatography Data System (CDS).

Match MS spectral peaks with Empower CDS libraries

Empower Chromatography Data System (CDS)

Users can build MS spectral libraries in Empower CDS for matching spectral peaks from samples that were collected in different projects and under different conditions. Filtering options increase the spectral matching accuracy.

Oligonucleotide columns, standards and sample prep tools purposely designed to deliver maximum performance and productivity.

Enhanced sensitivity with unmatched pH and temperature stability

Oligonucleotide Reversed-Phase Columns

With silica-based particles providing unrivaled pH & temperature tolerance, and MaxPeak Premier surface technology providing ultra-low non-specific adsorption, these columns deliver exceptional ion pair reversed phase (IP-RP) resolution, sensitivity, and stability for oligonucleotide analysis. Every batch of sorbent is QC-tested with our Waters MassPREP Oligonucleotide Standard to ensure excellent lot-to-lot reproducibility.

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High recovery extractions for LC-MS bioanalysis

OligoWorks SPE Kits & Components

OligoWorks SPE Kits deliver high recoveries via a detergent-free, MS-compatible, automation-friendly workflow —saving time, reducing method development, and improving lab efficiency with reliable, QC-tested performance.

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Benchmark column and system performance with confidence

Oligonucleotide/Nucleic Acid Standards and Enzymes

Eliminate the need to prepare complex mixtures with Waters prepackaged, lot-certified oligonucleotide standards that deliver ease-of-use and peace-of-mind when running oligonucleotide separations.

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Achieve ultra-low adduct formation for greater MS sensitivity

IonHance HFIP

Achieve ultra- low sodium and potassium adduct formation with Waters MS-grade IonHance HFIP: a high-purity, LC-MS compatible reagent that delivers the performance and confidence needed for oligonucleotide IP-RP LC-MS analysis. Now available in 10 and 100ml.

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Orthogonal selectivity with ion-pairing-free Chromatography

Gene-Based Therapeutics (GTx) HILIC Columns

Hydrophilic interaction chromatography (HILIC) offers orthogonal selectivity and an ion pairing free LC option for oligonucleotide analysis.

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Achieve higher purity fractions and higher yields

Oligonucleotide Purification Columns

Waters oligonucleotide preparative columns support direct scale-up from analytical scale columns and enable high-throughput purifications with high recovery. Each batch of sorbent undergoes QC testing and selection using Waters oligonucleotide standards to ensure consistent performance and reproducibility. For maximum flexibility, columns are available in MaxPeak Premier and stainless-steel hardware.

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Gain efficiency and walk away time with verified lab automation solutions

Kairos Amino Acid Kit is a fully automated LC-MS-based amino acid kit that gets you results in record time with unprecedented accuracy and precision.

Enhance sample prep efficiency and throughput

Laboratory Automation and Equipment

Streamline the extraction of oligonucleotides from biofluids for quantitative LC-MS analyses with verified workflows that help minimize variability, improve traceability, and simplify method transfer.

Your success is just a click away

Waters Global Services

Optimize your laboratory's productivity and success with Waters Global Services. Maintain peak system performance, minimize down time, address application challenges and support stringent compliance requirements.

Make science more accessible with Waters Capital

Payment Solutions

Maximize resources and minimize risk with payment options from Waters Capital, including upgrading aging equipment, getting customized support and bundling services into one monthly payment.

Webinars and Resources

Oligonucleotide Analysis Solutions: Streamlined Decisions for Consistent Quality Flyer

Download

Oligonucleotides Applications Notebook

Download

Adding Cost Effective Mass Detection for Improved Productivity in Oligonucleotide Screening Assays

Download

Simplify Bioanalysis of Oligotherapeutics

Download

The Art of RNA Purification: Method Considerations for Improving Scalability & Yield with Long Modified Oligonucleotides

Download

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Synthetic Oligonucleotide Analysis

Overview

Applications

Application Notes

Application Notes

Application Notes

Application Notes

Application Notes

Learn how BioSpring leveraged compliance-ready Waters BioAccord LC-MS System and Vion IMS QTof with waters_connect to ensure data integrity, support shorter turnaround times, and meet regulatory requirements as it expanded its oligonucleotide manufacturing and analysis services.

Solutions

Systems .st0{fill:none;stroke:#000;stroke-linecap:round;stroke-linejoin:round} .st0{fill:none;stroke:#000;stroke-linecap:round;stroke-linejoin:round}

Waters LC and LC-MS systems offer leading separations performance and sensitivity for synthetic oligonucleotide analysis.

Ultra-low non-specific adsorption for maximum sensitivity and reproducibility

A compliance-ready LC-MS solution built for ease-of-use and deployment across development and manufacturing labs

Robust high-resolution coverage for confident characterization

Exquisite sensitivity for quantification analyses

Exceptional performance for oligonucleotide characterization and impurity analyses

Analyze antibody-oligo-conjugates (AOCs) in their native state

Bring your analytical purification performance to the next level

Software .st0{fill:none;stroke:#000;stroke-linecap:round;stroke-linejoin:round} .st0{fill:none;stroke:#000;stroke-linecap:round;stroke-linejoin:round}

Waters software streamlines data acquisition, processing, and reporting oligonucleotide analysis results.

Streamline data analysis and processing

Match MS spectral peaks with Empower CDS libraries

Columns and Consumables .st0{fill:none;stroke:#000;stroke-linecap:round;stroke-linejoin:round} .st0{fill:none;stroke:#000;stroke-linecap:round;stroke-linejoin:round}

Oligonucleotide columns, standards and sample prep tools purposely designed to deliver maximum performance and productivity.

Enhanced sensitivity with unmatched pH and temperature stability

High recovery extractions for LC-MS bioanalysis

Benchmark column and system performance with confidence

Achieve ultra-low adduct formation for greater MS sensitivity

Orthogonal selectivity with ion-pairing-free Chromatography

Achieve higher purity fractions and higher yields

Lab Automation .st0{fill:none;stroke:#000;stroke-linecap:round;stroke-linejoin:round} .st0{fill:none;stroke:#000;stroke-linecap:round;stroke-linejoin:round}

Gain efficiency and walk away time with verified lab automation solutions

Enhance sample prep efficiency and throughput

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Your success is just a click away

Make science more accessible with Waters Capital

The data speaks for itself

Webinars and Resources

Quantifying Oligonucleotides Brochure

Characterizing Oligonucleotides eBook

Purifying Oligonucleotides eBook

Oligonucleotide Analysis Solutions: Streamlined Decisions for Consistent Quality Flyer

Oligonucleotides Applications Notebook

Adding Cost Effective Mass Detection for Improved Productivity in Oligonucleotide Screening Assays

Simplify Bioanalysis of Oligotherapeutics

The Art of RNA Purification: Method Considerations for Improving Scalability & Yield with Long Modified Oligonucleotides

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