<h3><strong>A Practical Guide to Oligonucleotide Production – From Concept to Final Product</strong></h3><p><strong>In 2020, an internal innovation at KNAUER significantly reshaped our perspective on nucleic acid technologies. The development of Impingement Jets Mixing (IJM) for lipid nanoparticle (LNP) generation—originally driven by the urgent need for mRNA-based COVID-19 vaccines—sparked a deeper engagement with DNA and RNA-based therapeutics. Although mRNA vaccines were the first application, it soon became clear that the same platform could support a broad range of oligonucleotides, including short DNA and RNA sequences.</strong></p><p>This realization naturally expanded our focus beyond formulation alone. Purification strategies, analytical control, and scalable manufacturing of oligonucleotides became equally compelling challenges. Today, simplifying and optimizing oligonucleotide production workflows is a central pillar of KNAUER’s technology roadmap.</p><h4><strong>Technologies for LNP Manufacturing</strong></h4><ul><li><strong>NanoScaler</strong></li><li><strong>Customized NanoProducer</strong></li></ul><p>These systems provide flexible solutions for research and production-scale LNP generation, supporting nucleic acid delivery applications.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Systems_for_LNP_production_Middle_Nano_Scaler_Right_Customized_Nano_Producer_1cf4727f38.jpg" alt="KNAUER: Systems for LNP production. Middle - NanoScaler, Right - Customized NanoProducer" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Systems_for_LNP_production_Middle_Nano_Scaler_Right_Customized_Nano_Producer_1cf4727f38.jpg 245w," sizes="100vw" width="1547" height="524"></p><h4><strong>What Is Required to Manufacture Oligonucleotides?</strong></h4><p>Whether producing oligonucleotides for internal use or as a CDMO, establishing a dedicated oligo production laboratory requires a sequence of well-defined steps. This introductory article outlines a mid-scale production workflow (from approximately 1 µmol up to several hundred mmol). Each operation is introduced here and will be explored in greater depth in future articles, with particular attention to purification and quality control. But before assessing purity, the oligonucleotide itself must first be synthesized.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Typical_workflow_for_oligonucleotide_production_a52b1aabd0.jpg" alt="KNAUER: Typical workflow for oligonucleotide production" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Typical_workflow_for_oligonucleotide_production_a52b1aabd0.jpg 245w," sizes="100vw" width="1593" height="510"></p><h4><strong>Typical Oligonucleotide Production Workflow</strong></h4><h5><strong>Step 1: Solid-Phase Oligonucleotide Synthesis</strong></h5><p>Oligonucleotide assembly begins on a solid support, most commonly controlled pore glass (CPG) or polystyrene resin. Individual nucleotides are sequentially added through a cyclic series of reactions:</p><ul><li><strong>Detritylation</strong> – removal of temporary protecting groups</li><li><strong>Coupling</strong> – attachment of the next nucleotide</li><li><strong>Oxidation or thiolation</strong> – stabilization of the phosphate backbone</li><li><strong>Capping</strong> – deactivation of unreacted chains</li></ul><p>These repetitive steps involve precise reagent delivery, washing, and activation, and are typically performed on automated synthesizers. KNAUER’s own oligonucleotide synthesizer is currently approaching completion.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Solid_phase_synthesis_5d16092ede.jpg" alt="KNAUER: Solid-phase synthesis" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Solid_phase_synthesis_5d16092ede.jpg 203w," sizes="100vw" width="809" height="622"></p><h5><strong>Step 2: Cleavage and Deprotection</strong></h5><p>Once synthesis is complete, the crude oligonucleotide must be released from the solid support. This is commonly achieved using ammonia-based reagents. Subsequent treatment with heated ammonium hydroxide removes remaining protecting groups. After filtration to remove the solid matrix, the solution is neutralized and prepared for initial analytical evaluation.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Flow_scheme_KNAUER_Synthesizer_a4212a41a2.jpg" alt="KNAUER: Flow scheme KNAUER Synthesizer​" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Flow_scheme_KNAUER_Synthesizer_a4212a41a2.jpg 245w," sizes="100vw" width="834" height="506"></p><h5><strong>Step 3: Chromatographic Analysis and Purification</strong></h5><p>Chromatography plays a central role in both the characterization and purification of oligonucleotides. Commonly used techniques include:</p><ul><li><strong>Anion-Exchange Chromatography (AEX)</strong><br>Separation based on charge; cost-efficient but generates high salt loads requiring downstream removal.</li><li><strong>Ion-Pair Reversed-Phase Chromatography (IP-RP)</strong><br>Offers excellent resolution and typically simplifies downstream processing due to volatile buffers, though at higher operating costs.</li><li><strong>Hydrophilic Interaction Liquid Chromatography (HILIC)</strong><br>An increasingly popular analytical tool, particularly suitable for short or chemically modified oligos, without ion-pairing reagents. Its primary strength lies in analysis rather than large-scale purification.</li></ul><h5><strong>Step 3a: In-Process Quality Control</strong></h5><p>Throughout production, oligonucleotides must be monitored for purity, sequence fidelity, and structural modifications. Liquid chromatography remains the primary analytical technique for these assessments, commonly using IP-RP, AEX, or HILIC methods. This is an area where KNAUER’s analytical expertise and HPLC platforms play a key role.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Representative_KNAUER_analytical_HPLC_system_and_Chromatogram_of_Oligonucleotide_Analysis_26f4619c5b.jpg" alt="KNAUER: Representative KNAUER analytical HPLC system  and Chromatogram of Oligonucleotide Analysis" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Representative_KNAUER_analytical_HPLC_system_and_Chromatogram_of_Oligonucleotide_Analysis_26f4619c5b.jpg 245w," sizes="100vw" width="1342" height="674"></p><h5><strong>Step 3b: Preparative Chromatographic Purification</strong></h5><p>Following analytical assessment, purification removes synthesis-related impurities such as truncated sequences or residual protecting groups. AEX and IP-RP are the most frequently applied methods. Process development teams often evaluate both approaches at small scale before selecting the optimal strategy. Notably, both modes can be implemented on the same preparative system, such as the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=41&amp;manufacturerItems=503&amp;search=lab"><strong>AZURA® Lab </strong></a>or <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=41&amp;manufacturerItems=503&amp;search=pilot"><strong>Pilot Prep HPLC platforms.</strong></a></p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Representative_KNAUER_preparative_LC_System_and_Chromatogram_of_Oligonucleotide_Purification_19415a7614.jpg" alt="KNAUER: Representative KNAUER preparative LC System and  Chromatogram of Oligonucleotide Purification" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Representative_KNAUER_preparative_LC_System_and_Chromatogram_of_Oligonucleotide_Purification_19415a7614.jpg 245w," sizes="100vw" width="1335" height="673"></p><h5><strong>Step 4: Desalting or Solvent Exchange via Tangential Flow Filtration (TFF)</strong></h5><p>After chromatographic purification, oligonucleotides remain in matrices containing salts or organic solvents. Tangential flow filtration enables gentle and scalable buffer exchange. Low-molecular-weight components pass through the membrane, while oligonucleotides are retained. This step prepares the product for formulation or further processing. KNAUER is currently developing a modular TFF solution tailored to this application.</p><h5><strong>Step 5: Endotoxin Reduction</strong></h5><p>For therapeutic applications, endotoxin levels must be rigorously controlled. Lipopolysaccharides from bacterial sources can be efficiently reduced using an additional TFF step. By selecting appropriate membranes, multiple diafiltration cycles can lower endotoxin concentrations by several orders of magnitude, supporting regulatory compliance depending on dose and administration route.</p><h5><strong>Step 6: Lyophilization</strong></h5><p>For preclinical and early-stage batches, freeze-drying is the standard finishing step. The oligonucleotide solution is frozen below –40 °C and subjected to vacuum sublimation, producing a dry, stable product that can be stored at ambient temperature and rapidly reconstituted when needed.</p><h4><strong>Connecting the Workflow with KNAUER Technology</strong></h4><p>KNAUER provides a cohesive portfolio supporting oligonucleotide production from synthesis to final formulation. <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=37&amp;manufacturerItems=503&amp;search=azura"><strong>AZURA® (U)HPLC systems</strong></a> and dedicated columns such as <strong>Sepapure® oliGO</strong> enable robust analytical control and efficient purification. Preparative LC platforms are optimized for oligo workflows, while new solutions—including an in-house oligonucleotide synthesizer and a modular TFF system—are being developed to streamline desalting and endotoxin removal.</p><p>Together, these technologies allow laboratories to build scalable, integrated oligonucleotide production environments without relying on fragmented, multi-vendor solutions.</p>

Oligos Made Easy - Part 1: Overview

<h3><strong>Charged for Action: The Hidden Secrets of AEX Oligonucleotide Analysis</strong></h3><p><strong>Oligonucleotides—short, well-defined fragments of DNA or RNA—have become indispensable tools in modern life sciences. They underpin cutting-edge applications in molecular diagnostics, gene therapy, and pharmaceutical development. Before oligonucleotides can be confidently used in research or clinical settings, however, their quality must be rigorously assessed. Purity, sequence integrity, length distribution, and chemical modifications all play a decisive role in their performance.</strong></p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Oligos_Made_Easy_Part_2_AEX_2_45eee54fa0.jpg" alt="KNAUER: Oligos Made Easy - Part 2: AEX" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Oligos_Made_Easy_Part_2_AEX_2_45eee54fa0.jpg 245w," sizes="100vw" width="1534" height="711"></p><p>Among the analytical techniques available today, <strong>anion exchange chromatography (AEX)</strong> stands out as a robust and highly informative method for characterizing oligonucleotides. By exploiting their intrinsic negative charge, AEX provides detailed insight into product composition and impurity profiles that are difficult to obtain by other approaches.</p><blockquote><p><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6808"><strong>Part 1 of the Oligos series: A Practical Guide to Oligonucleotide Production – From Concept to Final Product</strong></a></p></blockquote><h4><strong>How Scientists Read Oligonucleotides Using Charge</strong></h4><p>At the core of AEX lies a simple but powerful principle: oligonucleotides carry a negatively charged phosphate backbone. This charge increases in a predictable way with strand length and, to a lesser extent, sequence composition. Anion exchange chromatography uses this property to separate oligonucleotides based on differences in charge strength and interaction with a positively charged stationary phase.</p><p>As a result, AEX has become one of the most widely used analytical tools for evaluating oligonucleotide quality. It allows scientists to distinguish full-length products from truncated species, degradation products, or closely related variants—often with single-nucleotide resolution.</p><h4><strong>Why Ion Exchange Works: Binding, Retention, and Release</strong></h4><p>Ion exchange chromatography (IEX) relies on electrostatic interactions between analytes and a charged stationary phase. In the case of oligonucleotides, <strong>anion exchange</strong> is used, where negatively charged molecules interact with positively charged functional groups on the resin—most commonly quaternary amines.</p><p>The system consists of two main components:</p><ul><li><strong>Stationary phase:</strong> A positively charged resin that binds anionic analytes.</li><li><strong>Mobile phase:</strong> An aqueous buffer system, typically combined with a salt gradient, that controls both pH and elution strength.</li></ul><p>Retention in AEX is governed primarily by charge. Molecules with weaker overall charge interact less strongly with the stationary phase and elute earlier, while more highly charged oligonucleotides bind more tightly and require stronger elution conditions.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_1_IEX_overview_including_elution_order_dependency_on_analyte_charge_3419ad3075.jpg" alt="KNAUER: Oligos Made Easy - Part 2 AEX: Figure 1 IEX overview including elution order dependency on analyte charge." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_1_IEX_overview_including_elution_order_dependency_on_analyte_charge_3419ad3075.jpg 245w," sizes="100vw" width="1583" height="654"></p><h4><strong>The Five-Step Workflow of Ion Exchange Chromatography</strong></h4><p>AEX separations generally follow a well-established sequence of steps:</p><ol><li><strong>Column equilibration</strong><br>The column is conditioned with the starting buffer until the baseline and pH are stable. This ensures that all charged sites on the resin are ready for interaction.</li><li><strong>Sample loading</strong><br>Samples, prepared in the starting buffer, are introduced under conditions that promote binding of the target oligonucleotides while minimizing retention of unwanted impurities.</li><li><strong>Washing</strong><br>The column is washed with the starting buffer to remove uncharged or weakly interacting components. The baseline stabilizes as these species are flushed away.</li><li><strong>Elution</strong><br>Bound oligonucleotides are released using a salt or pH gradient. Increasing ionic strength introduces competing ions that displace the analytes from the resin. Weakly bound species elute first; strongly charged oligonucleotides elute later.</li><li><strong>Regeneration and re-equilibration</strong><br>A high-salt buffer removes any remaining bound material. The column is then returned to starting conditions in preparation for the next analysis.</li></ol><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_2_Five_steps_of_IEX_procedure_in_blue_outlined_using_an_example_chromatogram_in_red_38dd70b1b1.jpg" alt="KNAUER: Oligos Made Easy - Part 2 AEX: Figure 2  Five steps of IEX procedure (in blue), outlined using an example chromatogram (in red)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_2_Five_steps_of_IEX_procedure_in_blue_outlined_using_an_example_chromatogram_in_red_38dd70b1b1.jpg 245w," sizes="100vw" width="1583" height="674"></p><h4><strong>Why AEX Is Especially Effective for Oligonucleotides</strong></h4><p>The repeating phosphate backbone of oligonucleotides gives rise to a strong and uniform anionic character across a wide pH range (typically pH 7–9). This makes oligonucleotides exceptionally well suited for anion exchange separations.</p><p>Key factors influencing AEX behavior include:</p><ul><li><strong>Charge density:</strong> Longer oligonucleotides carry more negative charges and therefore exhibit stronger retention.</li><li><strong>Resin chemistry:</strong> Strong and weak anion exchangers differ in functional groups and pH stability, influencing selectivity and robustness.</li><li><strong>Buffer composition:</strong> The choice of buffering ions and salt gradients directly affects elution strength and resolution.</li></ul><p>Salt gradients—commonly based on chloride ions—compete with the oligonucleotide backbone for binding sites on the resin. By carefully tuning gradient slope and composition, analysts can achieve highly reproducible and finely resolved separations.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_3_Ionic_interactions_and_p_H_influence_on_Anion_Exchange_Chromatography_AEX_612e231ba4.jpg" alt="KNAUER: Oligos Made Easy - Part 2 AEX: Figure 3 Ionic interactions and pH influence on Anion Exchange Chromatography (AEX)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_3_Ionic_interactions_and_p_H_influence_on_Anion_Exchange_Chromatography_AEX_612e231ba4.jpg 245w," sizes="100vw" width="1547" height="593"></p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_4_AEX_buffer_selection_and_gradient_strategy_chromatogram_with_red_buffer_gradient_curve_53fd1bb11b.jpg" alt="KNAUER: Oligos Made Easy - Part 2 AEX: Figure 4 AEX buffer selection and gradient strategy (chromatogram with red buffer gradient curve)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_4_AEX_buffer_selection_and_gradient_strategy_chromatogram_with_red_buffer_gradient_curve_53fd1bb11b.jpg 245w," sizes="100vw" width="1600" height="327"></p><h4><strong>AEX as the Gold Standard for Oligonucleotide Separation</strong></h4><p>Anion exchange chromatography has become the method of choice for both analytical and preparative oligonucleotide workflows. Its advantages include:</p><ul><li><strong>High resolving power:</strong> Closely related impurities, including n–1 or n–2 species, can often be separated and quantified.</li><li><strong>Predictable retention behavior:</strong> In many cases, retention time correlates linearly with oligonucleotide length, simplifying identification.</li><li><strong>Compatibility with modified oligonucleotides:</strong> Even chemically modified sequences retain their anionic nature, allowing AEX to resolve both products and related impurities.</li><li><strong>Excellent control via gradient elution:</strong> Salt gradients provide precise tuning of selectivity and resolution.</li></ul><p>Typically, shorter or degraded oligonucleotides elute at lower ionic strength, while full-length products with higher charge density appear later in the chromatogram.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_5_AEX_Advantages_and_Challenges_7835521e34.jpg" alt="KNAUER: Oligos Made Easy - Part 2 AEX: Figure 5 AEX Advantages and Challenges." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_5_AEX_Advantages_and_Challenges_7835521e34.jpg 245w," sizes="100vw" width="1535" height="707"></p><h4><strong>Final Perspective: Mastering AEX with Confidence</strong></h4><p>Anion exchange chromatography may appear complex at first, but with thoughtful optimization of pH, buffer composition, and gradient conditions, it becomes a highly precise and reliable tool for oligonucleotide analysis. When properly applied, AEX delivers sharp peaks, excellent resolution, and robust performance—even for challenging sequences and modifications.</p><p>For laboratories developing or refining oligonucleotide workflows, AEX offers both analytical depth and operational confidence.</p><blockquote><p>If you would like to discuss AEX method development or optimization for oligonucleotides, feel free to contact us at <strong>sales@knauer.net</strong>. More insights into practical oligonucleotide analysis will follow in our <i>“Oligos Made Easy”</i> series.</p><p>For technical questions or in-depth discussion, the author can be reached at <strong>kindler@knauer.net</strong></p></blockquote>

Oligos Made Easy - Part 2: AEX

<h3><strong>Mastering Ion-Pair Reversed-Phase Chromatography for Oligonucleotide Analysis</strong></h3><h4><strong>Why Purity Is Critical in the Oligonucleotide Era</strong></h4><p>Oligonucleotides — short, synthetic strands of DNA or RNA — are central to modern biotechnology. They power gene therapies, advanced diagnostics, and cutting-edge molecular research. However, before these molecules can be used in clinical or research settings, their purity and structural integrity must be thoroughly verified. High-resolution chromatographic analysis plays a crucial role in ensuring quality and safety.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_1_Separation_Example_of_Oligonucleotides_5577514561.jpg" alt="KNAUER: Figure 1 - Separation Example of Oligonucleotides." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_1_Separation_Example_of_Oligonucleotides_5577514561.jpg 245w," sizes="100vw" width="1024" height="368"></p><h4><strong>Understanding Ion-Pair Reversed-Phase (IP-RP) Chromatography</strong></h4><p>For scientists involved in oligonucleotide synthesis and characterization, Ion-Pair Reversed-Phase Chromatography (IP-RP) is one of the most effective analytical tools available.</p><p>Unlike separation techniques that rely solely on charge differences, IP-RP combines:</p><ul><li>Ionic interactions</li><li>Hydrophobic interactions</li></ul><p>This dual retention mechanism enables exceptional resolution — even for oligonucleotides that differ by only a single nucleotide or subtle chemical modification. Whether assessing synthesis efficiency or purifying therapeutic-grade material, IP-RP provides reliable, reproducible separations.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_2_Overview_of_IP_RP_Mode_prinicple_ecd54b6e9c.jpg" alt="KNAUER: Figure 2 - Overview of IP-RP Mode prinicple." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_2_Overview_of_IP_RP_Mode_prinicple_ecd54b6e9c.jpg 245w," sizes="100vw" width="1024" height="456"></p><h4><strong>The Principle Behind Ion-Pairing</strong></h4><p>Oligonucleotides possess a highly negatively charged phosphate backbone. In a traditional reversed-phase system, such hydrophilic, charged molecules would show little retention.</p><p>IP-RP overcomes this limitation by introducing a positively charged ion-pairing reagent into the mobile phase. The cation associates with the negatively charged oligonucleotide, forming a transient ion pair with increased hydrophobic character. This modified complex can now interact with the hydrophobic stationary phase.</p><p>Retention strength depends on:</p><ul><li>The hydrophobicity of the ion-pair reagent</li><li>The strength of ionic interaction</li><li>The applied organic gradient</li></ul><p>During gradient elution (commonly using acetonitrile), analytes are released in a controlled manner according to size, sequence, and chemical modifications.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_3_Ion_Pair_Reversed_Phase_Principle_9a4fcd12f2.jpg" alt="KNAUER: Figure 3 - Ion-Pair Reversed Phase Principle." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_3_Ion_Pair_Reversed_Phase_Principle_9a4fcd12f2.jpg 245w," sizes="100vw" width="1024" height="393"></p><h4><strong>Choosing the Right Ion-Pair Reagent</strong></h4><p>Successful IP-RP separation depends heavily on selecting an appropriate ion-pair reagent. Two key factors determine retention behavior:</p><ol><li>Alkyl chain length</li><li>Charge density</li></ol><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_4_Ion_Pair_Classification_eaad172a4e.jpg" alt="KNAUER: Figure 4 - Ion-Pair Classification." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_4_Ion_Pair_Classification_eaad172a4e.jpg 245w," sizes="100vw" width="1024" height="398"></p><h4><strong>Strong Cationic Ion-Pair Reagents</strong></h4><p>Ion-pair reagents with longer alkyl chains provide stronger hydrophobic interactions and increased retention. A widely used example is tetrabutylammonium (TBA⁺), frequently applied for strongly retained anionic analytes.</p><p>These reagents are particularly useful when high retention strength is required.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Table_1_Strong_Cationic_Ion_Pair_Reagents_8dbf00c57e.jpg" alt="KNAUER: Table 1 - Strong Cationic Ion-Pair Reagents." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Table_1_Strong_Cationic_Ion_Pair_Reagents_8dbf00c57e.jpg 245w," sizes="100vw" width="1024" height="396"></p><h4><strong>Volatile (Weaker) Ion-Pair Reagents</strong></h4><p>Short-chain ion-pair reagents generate weaker retention but offer a significant advantage: compatibility with LC–MS detection.</p><p>Triethylammonium (TEA⁺) is among the most commonly used reagents for oligonucleotide analysis, particularly when mass spectrometric detection is involved. Other options, such as diisopropylethylammonium (DIEA⁺), are also widely applied, often combined with HFIP to enhance MS performance.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Table_2_Weak_Cationic_Ion_Pair_Reagents_6332a4975e.jpg" alt="KNAUER: Table 2 - Weak Cationic Ion-Pair Reagents." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Table_2_Weak_Cationic_Ion_Pair_Reagents_6332a4975e.jpg 245w," sizes="100vw" width="1024" height="283"></p><h4><strong>Building an IP-RP Method for Oligonucleotides</strong></h4><p>Developing a robust IP-RP method follows a logical sequence:</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Table_3_IP_RP_Method_Step_Procedure_for_Oligos_c2216c24a0.jpg" alt="KNAUER: Table 3 - IP-RP Method Step Procedure for Oligos." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Table_3_IP_RP_Method_Step_Procedure_for_Oligos_c2216c24a0.jpg 245w," sizes="100vw" width="1024" height="304"></p><h5><strong>1. Characterize the Analyte</strong></h5><p>Oligonucleotides typically contain 10–50+ nucleotides and exhibit high negative charge density. This necessitates a suitable cationic partner such as TEA⁺ or DIEA⁺.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_5_Cationic_Ion_Pair_Principle_for_Oligonucleotides_cb2dfb7457.jpg" alt="KNAUER: Figure 5 - Cationic Ion-Pair Principle for Oligonucleotides." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_5_Cationic_Ion_Pair_Principle_for_Oligonucleotides_cb2dfb7457.jpg 245w," sizes="100vw" width="512" height="320"></p><h5><strong>2. Select the Column</strong></h5><p>Use a reversed-phase column with:</p><ul><li>Large pore size (≈300 Å)</li><li>Appropriate internal diameter</li></ul><p>These parameters support the so-called “ON–OFF” retention mechanism — a bind-and-elute behavior where analytes are strongly retained until the gradient triggers rapid elution.</p><h5><strong>3. Optimize the Mobile Phase</strong></h5><p>A typical starting condition includes:</p><ul><li>10 mM TEA buffer at pH ~7</li><li>Acetonitrile as organic modifier</li></ul><p>Gradient programs from approximately 5% to 50% organic solvent over 15–30 minutes are commonly effective for complex oligonucleotide mixtures.</p><h5><strong>4. Adjust Retention Strength if Needed</strong></h5><p>To increase retention:</p><ul><li>Raise ion-pair concentration (up to ~100 mM if required)</li><li>Select a more hydrophobic ion-pair reagent</li></ul><h5><strong>5. Validate the Method</strong></h5><p>Ensure robustness, sensitivity, and reproducibility by carefully evaluating:</p><ul><li>UV chromatograms</li><li>MS traces</li><li>Peak shape and resolution</li></ul><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_6_UV_MS_traces_of_IP_RP_Oligonucleotide_Analysis_81faf4e9f0.jpg" alt="KNAUER: Figure 6 - UV-MS traces of IP-RP Oligonucleotide Analysis." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_6_UV_MS_traces_of_IP_RP_Oligonucleotide_Analysis_81faf4e9f0.jpg 245w," sizes="100vw" width="1024" height="365"></p><h4><strong>Why IP-RP Is Considered the Gold Standard</strong></h4><p>Ion-Pair Reversed-Phase Chromatography uniquely combines the resolving power of reversed-phase LC with the ability to retain highly polar, charged biomolecules.</p><p>Its advantages include:</p><ul><li>Tunable selectivity</li><li>Compatibility with UV and MS detection</li><li>Scalability from analytical to preparative workflows</li><li>Applicability from research to pharmaceutical production</li></ul><p>By transforming highly charged oligonucleotides into hydrophobic ion-pair complexes, IP-RP enables precise and reproducible separations that would otherwise be impossible in conventional reversed-phase systems.</p><p>For these reasons, IP-RP is widely regarded as the benchmark technique for oligonucleotide analysis.</p><h4><strong>Final Thoughts</strong></h4><p>Mastering IP-RP is less intimidating than it may seem. A successful method comes down to:</p><ul><li>Selecting the right ion-pair reagent</li><li>Choosing a suitable column</li><li>Optimizing gradient conditions</li><li>Fine-tuning temperature and concentration parameters</li></ul><p>With thoughtful method development, IP-RP delivers sharp peaks, clean separations, and reliable performance — fully compatible with modern mass spectrometry workflows and ready to meet the demands of advanced oligonucleotide analysis.</p>

Oligos Made Easy - Part 3: IP-RP

<h4><strong>Why Consider HILIC in Modern Oligonucleotide Analysis?</strong></h4><p>Oligonucleotides play a central role in gene therapies, molecular diagnostics, and cutting-edge biomedical research. Before these molecules reach application, however, they must be carefully characterized to confirm purity, identity, and performance.</p><p>Analyzing therapeutic oligonucleotides is far from straightforward. Their polarity, structural diversity, and modifications demand highly selective and MS-compatible separation methods. Although ion-pair reversed-phase LC (IP-RP-LC) remains the established standard for LC-MS workflows, hydrophilic interaction liquid chromatography (HILIC) is rapidly emerging as a powerful complementary technique.</p><p>When IP-RP approaches reach practical or performance limits, HILIC offers an attractive alternative, delivering strong retention and efficient separation of highly polar oligonucleotides — without relying on ion-pairing reagents.</p><h4><strong>How Does HILIC Separate Oligonucleotides?</strong></h4><p>HILIC essentially reverses conventional reversed-phase logic. It combines:</p><ul><li>A <strong>polar stationary phase</strong></li><li>An <strong>organic-rich mobile phase</strong></li></ul><p>In this configuration, the stationary phase retains a thin, water-enriched layer on its surface. Polar analytes — such as oligonucleotides — partition into this aqueous layer while the acetonitrile-rich mobile phase passes through.</p><p>This mechanism allows:</p><ul><li>Retention of short or highly polar oligonucleotides</li><li>Separation of modified sequences</li><li>LC-MS compatibility without ion-pairing reagents</li></ul><p>The key to performance lies in carefully tuning the parameters that govern HILIC selectivity and retention.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_1_Key_Parameter_of_HILIC_Mode_fb364c9a8b.webp" alt="KNAUER: Figure 1 - Key Parameter of HILIC Mode." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_1_Key_Parameter_of_HILIC_Mode_fb364c9a8b.webp 245w," sizes="100vw" width="945" height="433"></p><h4><strong>What Controls Retention in HILIC?</strong></h4><p>Several interaction mechanisms contribute to analyte behavior in HILIC:</p><h5><strong>Hydrophilic Partitioning – The Primary Mechanism</strong></h5><p>Polar molecules distribute into the thin water layer formed on the stationary phase surface. The greater the polarity of the analyte, the stronger its affinity for this layer, leading to increased retention.</p><h5><strong>Hydrogen Bonding – Fine-Tuning Effects</strong></h5><p>Functional groups such as –OH, –NH₂, and –COOH can form hydrogen bonds with the stationary phase, subtly influencing retention time and selectivity.</p><h5><strong>Electrostatic Contributions – The Role of Charge</strong></h5><p>Some HILIC materials (e.g., bare silica) exhibit surface charges. Depending on mobile phase pH and buffer composition, electrostatic interactions can either enhance or suppress analyte retention.</p><h5><strong>Dipole and Ion–Dipole Interactions – Added Selectivity</strong></h5><p>Highly polar or zwitterionic compounds — including phosphorylated species and sugars — may engage in dipole–dipole or ion–dipole interactions, further refining separation behavior.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_2_Hydrophilic_Partitioning_on_Water_enriched_Layer_41ab9ac902.webp" alt="KNAUER: Figure 2 - Hydrophilic Partitioning on Water-enriched Layer." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_2_Hydrophilic_Partitioning_on_Water_enriched_Layer_41ab9ac902.webp 245w," sizes="100vw" width="945" height="409"></p><h4><strong>How to Develop a HILIC Method for Oligonucleotides</strong></h4><p>Like any chromatographic method, successful HILIC development follows a structured approach:</p><h5><strong>Step 1: Define the Analytes</strong></h5><p>Understand oligonucleotide length, polarity, charge, and modifications.</p><h5><strong>Step 2: Select a Suitable Column</strong></h5><p>Choose a polar stationary phase (e.g., amide or zwitterionic) appropriate for the oligonucleotide’s chemical properties.</p><h5><strong>Step 3: Optimize the Mobile Phase</strong></h5><ul><li>Start with <strong>70–95% acetonitrile</strong></li><li>Use a <strong>volatile buffer</strong> (e.g., ammonium formate or ammonium acetate, typically 5–20 mM)</li><li>Adjust pH (commonly between 6–8, with testing up to pH 9 if column stability allows)</li></ul><p>Small pH shifts can significantly alter selectivity and MS response.</p><h5><strong>Step 4: Design the Gradient</strong></h5><p>Employ a gradient that increases water content to modulate retention and separate oligonucleotides by size or chemical modification.</p><h5><strong>Step 5: Match Injection Conditions</strong></h5><p>Samples should be injected in a solvent similar to the starting mobile phase (high organic content) to prevent peak distortion.</p><h5><strong>Step 6: Evaluate Performance</strong></h5><p>Assess:</p><ul><li>Resolution</li><li>Retention time stability</li><li>Peak shape</li><li>Reproducibility</li></ul><p>Balancing separation performance with MS ionization efficiency is essential.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Table_1_HILIC_Method_Step_Procedure_for_Oligos_f3b9ea6b08.webp" alt="KNAUER: Table 1 - HILIC Method Step Procedure for Oligos." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Table_1_HILIC_Method_Step_Procedure_for_Oligos_f3b9ea6b08.webp 245w," sizes="100vw" width="945" height="357"></p><h4><strong>Practical Tips for High-Performance HILIC</strong></h4><h5><strong>Maintain a Stable Water Layer</strong></h5><p>A minimum of ~5% water is necessary at the start of the run. Too little water can eliminate retention entirely. Adjust water content carefully to fine-tune retention.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_3_Water_Adjustment_Principle_for_HILIC_c0d8616f20.webp" alt="KNAUER: Figure 3 - Water Adjustment Principle for HILIC." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_3_Water_Adjustment_Principle_for_HILIC_c0d8616f20.webp 245w," sizes="100vw" width="951" height="374"></p><h5><strong>Use High Organic Content</strong></h5><p>HILIC typically operates best with 70–95% acetonitrile. Polar analytes are retained more effectively under these conditions.</p><h5><strong>Include a Volatile Buffer</strong></h5><p>Use low concentrations (5–20 mM) of ammonium formate or acetate to:</p><ul><li>Stabilize pH</li><li>Reduce peak tailing</li><li>Maintain MS compatibility</li></ul><h5><strong>Control Injection Solvent</strong></h5><p>Avoid high-water sample solvents. They disrupt the partitioning mechanism and distort peaks.</p><h5><strong>Allow Proper Column Equilibration</strong></h5><p>HILIC columns require longer equilibration times than reversed-phase columns — typically 10–20 column volumes after major gradient or solvent changes.</p><h5><strong>Consider Temperature</strong></h5><p>Operating at 30–50 °C can:</p><ul><li>Improve peak shape</li><li>Reduce mobile phase viscosity</li><li>Stabilize retention behavior</li></ul><h4><strong>From Alternative to Essential? Final Perspective</strong></h4><p>HILIC-MS is steadily advancing as a strong, ion-pair-free option for oligonucleotide analysis. While IP-RP-LC still dominates in sensitivity for many applications, HILIC is closing the gap and offering valuable flexibility — particularly for highly polar or challenging sequences.</p><p>Although HILIC follows different chromatographic principles than reversed-phase separations, once optimized, it can deliver robust and highly selective results.</p><p>Rather than being a niche method, HILIC is becoming a strategic tool in modern oligonucleotide workflows — especially when MS compatibility and method versatility are priorities.</p><p>If you are developing or refining an oligonucleotide LC-MS method, HILIC may be worth integrating into your analytical toolbox.</p><blockquote><ul><li>For additional information or discussion, feel free to contact: <a><strong>sales@knauer.net</strong><span><strong><svg><use></use></svg></strong></span></a></li><li>For direct scientific inquiries, reach out to the author at: <a><strong>kindler@knauer.net</strong><span><strong><svg><use></use></svg></strong></span></a></li></ul></blockquote><p><i><strong>Stay tuned for more insights in the “Oligos Made Easy” series.</strong></i></p>

Oligos Made Easy - Part 4: HILIC

News from LabRulezLCMS Library - Week 10, 2026

<h3><strong>Two Dimensions, One Solution: Advancing Oligonucleotide Analysis with 2D-LC</strong></h3><h4><strong>Why Consider 2D-LC for Oligonucleotide Analysis?</strong></h4><p>In oligonucleotide analytics, achieving reliable and precise results is not optional—it is fundamental. These biomolecules are inherently complex, often containing truncated sequences, structural variants, and a wide range of impurities. Such complexity frequently exceeds the separation capabilities of conventional one-dimensional liquid chromatography (1D-LC). As a result, critical components may coelute or remain unresolved, limiting analytical confidence.</p><p><strong>Two-dimensional liquid chromatography (2D-LC) </strong>offers a powerful alternative by significantly enhancing separation performance. By combining two complementary separation mechanisms, 2D-LC improves resolution, sensitivity, and overall analytical reliability. This enables a much deeper understanding of oligonucleotide samples and their compositional intricacies.</p><blockquote><h4><strong>Previous parts from the Oligos Made Easy</strong> <strong>series</strong></h4><ul><li><strong>Part 1: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6808"><strong>Overview</strong></a></li><li><strong>Part 2: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6846"><strong>AEX</strong></a></li><li><strong>Part 3: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6880"><strong>IP-RP</strong></a></li><li><strong>Part 4: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6912"><strong>HILIC</strong></a></li><li><strong>Part 5: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6944"><strong>SEC</strong></a></li><li><strong>Part 6: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6982"><strong>Column Navigator</strong></a></li><li><strong>Part 7: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/7012"><strong>Large Scale AEX</strong></a></li><li><strong>Part 8: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/7045"><strong>Sepapure oliGO</strong></a></li></ul></blockquote><h4><strong>Moving Beyond the Limits of 1D-LC</strong></h4><p>For many years, 1D-LC has served as a standard tool for biopharmaceutical characterization. However, its inherent limitations become apparent when dealing with highly complex mixtures. The selectivity of a single chromatographic dimension is restricted, and the lack of orthogonality in retention mechanisms often results in insufficient separation. As sample complexity increases, the resolving power of 1D-LC becomes inadequate.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_1_2_D_LC_Principle_Graphic_by_KNAUER_43e04d32a2.jpg" alt="KNAUER: Figure 1 - 2D-LC Principle (Graphic by KNAUER)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_1_2_D_LC_Principle_Graphic_by_KNAUER_43e04d32a2.jpg 245w," sizes="100vw" width="1291" height="391"></p><p>Two-dimensional LC addresses these limitations by coupling two chromatographic separations, which can be either similar or fundamentally different. Each dimension targets different physicochemical properties of analytes, enabling the resolution of compounds that would otherwise overlap. In essence, 2D-LC introduces an additional level of separation capacity, allowing analysts to disentangle coeluting species that remain unresolved in a single dimension.</p><p>An important practical consideration is that the overall analysis time is governed by the second dimension. Because fractions from the first dimension must be processed sequentially, the second dimension must operate rapidly and efficiently. High-speed separations in the second dimension are therefore essential to maintain system performance and data quality.</p><h4><strong>Architecture of a 2D-LC System</strong></h4><p>At its core, a 2D-LC system relies on precise coordination between its components. The <strong>setup typically consists</strong> of <strong>two chromatographic columns</strong>, <strong>two pumping systems</strong>, and a <strong>switching valve</strong> that enables fraction transfer between dimensions. The sample is introduced through an autosampler and first separated on the primary column. Fractions of interest are then transferred into a loop via a switching valve and subsequently introduced into the second column for further separation.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_2_2_D_LC_System_Configuration_Example_Graphic_by_KNAUER_f5747adf3a.jpg" alt="KNAUER: Figure 2 -  2D LC System Configuration Example (Graphic by KNAUER)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_2_2_D_LC_System_Configuration_Example_Graphic_by_KNAUER_f5747adf3a.jpg 245w," sizes="100vw" width="859" height="517"></p><p>The <strong>valve plays a crucial role</strong> in this process, acting as the interface between both chromatographic dimensions. Its function is to alternately <strong>collect fractions from the first dimension and inject them into the second dimension</strong> under high-pressure conditions. Various valve configurations can be employed, including ten-port or eight-port valves with dual-loop arrangements, or synchronized six-port valves. Regardless of configuration, the underlying principle remains the same: <strong>while one loop is being filled, the other is being flushed into the second dimension</strong>.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_3_Schematic_figure_of_ten_port_left_and_eight_port_valve_right_2_position_setup_for_2_D_LC_Graphic_by_KNAUER_9209661ea8.jpg" alt="KNAUER: Figure 3 - Schematic figure of ten-port (left) and eight-port valve (right) 2-position setup for 2D-LC (Graphic by KNAUER)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_3_Schematic_figure_of_ten_port_left_and_eight_port_valve_right_2_position_setup_for_2_D_LC_Graphic_by_KNAUER_9209661ea8.jpg 245w," sizes="100vw" width="1287" height="406"></p><p>This alternating process requires <strong>precise timing</strong>. The second-dimension separation must be completed before the next fraction is ready for transfer. Consequently, synchronization between flow rates, loop volumes, and switching intervals is essential for maintaining chromatographic integrity.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_4_Schematic_figure_KNAUER_eight_port_2_position_valve_for_2_D_LC_Graphic_by_KNAUER_f9a5f06f5f.jpg" alt="KNAUER: Figure 4 - Schematic figure KNAUER eight-port 2 position valve for 2D-LC (Graphic by KNAUER)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_4_Schematic_figure_KNAUER_eight_port_2_position_valve_for_2_D_LC_Graphic_by_KNAUER_f9a5f06f5f.jpg 245w," sizes="100vw" width="756" height="391"></p><h4><strong>Applying 2D-LC to Oligonucleotide Analysis</strong></h4><p>In oligonucleotide workflows, 2D-LC combines two complementary separation strategies to address sample complexity. The <strong>first dimension</strong> is typically used for <strong>bulk separation</strong> based on properties such as <strong>size, charge, or polarity</strong>. Techniques such as <strong>size-exclusion chromatography</strong> (SEC), <strong>anion-exchange chromatography</strong> (AEX), <strong>ion-pair reversed-phase chromatography </strong>(IP-RP), <strong>hydrophilic interaction chromatography</strong> (HILIC), or <strong>mixed-mode chromatography</strong> (MMC) are commonly applied. This step reduces sample complexity and can also serve as an online desalting stage, removing salts and buffer components that could interfere with downstream detection, particularly when mass spectrometry is used.</p><p>Following this initial separation, selected fractions are transferred to the second dimension. This transfer can be performed either selectively or comprehensively, depending on the analytical goal. The second dimension is typically optimized for high-resolution separation, allowing detailed characterization of closely related species such as truncated oligonucleotides, sequence variants, or chemically modified impurities. When coupled with mass spectrometry, this setup enables accurate identification and sequencing.</p><p>A <strong>key advantage of 2D-LC</strong> lies in the <strong>flexibility of combining different stationary phases and mobile phase</strong> conditions.&nbsp;</p><p>Numerous separation combinations are possible, including:</p><ul><li>SEC×AEX</li><li>HILIC×IP-RP</li><li>IEC×IP-RP</li><li>IP-RP×IP-RP</li><li>AEX×HIC</li><li>MMC×SEC,</li><li>and even chiral×RP systems.&nbsp;</li></ul><p>This adaptability allows tailored workflows for specific analytical challenges.</p><h4><strong>Heart-Cutting vs. Comprehensive 2D-LC</strong></h4><p>When implementing 2D-LC, two primary transfer strategies are commonly used: <strong>heart-cutting</strong> and <strong>comprehensive transfer</strong>. Each approach offers distinct advantages depending on the analytical objective.</p><p><strong>Heart-cutting 2D-LC</strong> focuses on selected regions of interest from the first dimension. Only specific peaks or time windows are transferred to the second dimension for further analysis. This approach allows extended separation time and higher resolution in the second dimension, making it particularly suitable for targeted investigations of known critical compounds. However, because only selected fractions are analyzed, unexpected impurities outside the selected region may remain undetected.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_5_2_D_LC_Single_Heart_Cut_Principle_Graphic_by_KNAUER_b1b400784b.jpg" alt="KNAUER: Figure 5 - 2D-LC Single Heart-Cut Principle (Graphic by KNAUER)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_5_2_D_LC_Single_Heart_Cut_Principle_Graphic_by_KNAUER_b1b400784b.jpg 245w," sizes="100vw" width="1276" height="319"></p><p>In contrast, <strong>comprehensive 2D-LC</strong> transfers the entire eluate from the first dimension into the second dimension in a continuous manner. This approach provides a complete and detailed representation of the sample, making it ideal for research and development, impurity profiling, and regulatory applications. While more demanding in terms of speed and system performance, comprehensive 2D-LC ensures full sample coverage.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Figure_6_Full_Comprehensive_2_D_LC_Principle_Graphic_by_KNAUER_e13da63ef1.jpg" alt="KNAUER: Figure 6 - Full Comprehensive  2D-LC Principle (Graphic by KNAUER)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Figure_6_Full_Comprehensive_2_D_LC_Principle_Graphic_by_KNAUER_e13da63ef1.jpg 245w," sizes="100vw" width="1327" height="292"></p><p>In practice, <strong>hybrid approaches may also be employed</strong>, combining targeted heart-cutting with broader comprehensive analysis to balance resolution and coverage.</p><h4><strong>Practical Considerations for Method Development</strong></h4><p>Successful implementation of 2D-LC for oligonucleotide analysis requires careful method design.&nbsp;</p><h5><strong>1. Column selection</strong>&nbsp;</h5><p>It is a critical starting point, as the combination of stationary phases must provide sufficient orthogonality while maintaining compatibility between mobile phases. Typically, the first dimension is optimized for general separation of oligonucleotide size or class, while the second dimension focuses on sequence-specific resolution and compatibility with mass spectrometry.</p><h5><strong>2. Mobile phase selection&nbsp;</strong></h5><p>Differences in pH and organic modifiers can significantly influence separation behavior, but incompatibility between dimensions can compromise performance. Therefore, mobile phases must be designed as a coordinated system. The use of volatile buffers, such as ammonium acetate, is often preferred for MS-based detection.</p><h5><strong>3. Instrumentation&nbsp;</strong></h5><p>The switching valve must operate reliably under high pressure, with precise timing to ensure accurate fraction transfer. Loop volumes must be carefully selected to avoid overfilling, as excessive loading can lead to sample loss and distortion due to flow profile effects. As a general guideline, loops should not be filled beyond approximately 70% of their capacity.</p><h5><strong>4. Method development&nbsp;</strong></h5><p>Typically begins with optimization of the second dimension, as it dictates overall system timing. Fast separations using short columns and steep gradients are often required to maintain sufficient sampling frequency. Once the second dimension is established, the first dimension can be adjusted to achieve optimal resolution and compatibility.</p><h4><strong>Final Remarks</strong></h4><p>Two-dimensional liquid chromatography represents a powerful advancement in oligonucleotide analysis, enabling the resolution of complex mixtures that exceed the capabilities of conventional 1D approaches. By combining orthogonal separation mechanisms, 2D-LC reveals structural details and impurity profiles that would otherwise remain hidden.</p><p>However, achieving optimal performance requires careful balancing of multiple factors, including column chemistry, mobile phase compatibility, system timing, and data acquisition. When properly implemented, 2D-LC provides a robust and highly informative platform for modern oligonucleotide characterization.</p><blockquote><ul><li>If you're planning to set up or optimize your oligonucleotide workflow, feel free to contact us at <a href="sales@knauer.net"><strong>sales@knauer.net</strong></a>. Stay tuned for more exciting insights into the Oligonucleotide world in our “<strong>Oligos Made Easy</strong>” series.</li></ul></blockquote>

Oligos Made Easy - Part 9: 2D-LC

<h4><strong>Let’s begin with a simple question: what do we actually mean by high throughput?</strong></h4><p><strong>In the laboratory, high throughput usually refers to the ability to analyze tens, hundreds, or even thousands of samples per day, either across a laboratory workflow or on a single analytical system. Achieving this requires more than just a fast method. It depends on reliable instrumentation, automation, sufficient sample capacity, and smart system design that minimizes idle time between runs.</strong></p><p>In this article, we look at the key requirements for high-throughput HPLC analysis and how they are addressed in the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/2371"><strong>HTQC system</strong></a>.</p><h4><strong>Speed</strong></h4><p>High-throughput HPLC workflows typically rely on short methods. This includes both the chromatographic runtime and the cycle time of the injection module.</p><p>With the HTQC system, fast gradient applications up to 1200 bar can be implemented using two integrated UHPLC high-pressure gradient pumps.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Fig_1_2_HPG_pumps_of_HTQC_system_left_P_8_1_L_max_pressure_1240_bar_right_P_6_1_L_max_pressure_1000_bar_4d4873ff2f.jpg" alt="KNAUER: Fig. 1–2  HPG pumps of HTQC system, left: P 8.1L (max. pressure 1240 bar), right: P 6.1L (max. pressure 1000 bar)" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Fig_1_2_HPG_pumps_of_HTQC_system_left_P_8_1_L_max_pressure_1240_bar_right_P_6_1_L_max_pressure_1000_bar_4d4873ff2f.jpg 245w," sizes="100vw" width="1266" height="386"></p><p>We will not discuss the full details of transferring classical HPLC methods to fast, high-resolution UHPLC methods here, but UHPLC implementation can dramatically reduce total analysis time.</p><p>Let’s use a hypothetical example. Imagine Giorgia, a randomly chosen name, working in pharmaceutical quality control in 1998. She must have travelled back in time, because she would have been too young to work in a lab then, but the example still works. With a classical HPLC method, each sample takes approximately 75 minutes, including equilibration, analysis, and backflushing of a 250 × 4.6 mm ID column. This type of method has been common in QC laboratories around the world. During an eight-hour working day, Giorgia can analyze around six samples.</p><p>Now let’s transfer the same method to UHPLC. The improvement is substantial. Analysis time, equilibration time, and backflushing time are all reduced to under six minutes per sample. Giorgia can now process around 90 samples in one working day.</p><p>You may wonder why the HTQC system requires two UHPLC gradient pumps. We will come back to that shortly.</p><p>The next way to increase speed is to reduce injector cycle time. Injection procedures and washing steps can sometimes take a significant amount of time. This is where the LH 8.1 liquid handler becomes important.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Fig_3_KNAUER_LH_8_1_Liquid_Handler_77ab506ca6.webp" alt="KNAUER: Fig. 3  KNAUER LH 8.1 Liquid Handler" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Fig_3_KNAUER_LH_8_1_Liquid_Handler_77ab506ca6.webp 129w," sizes="100vw" width="800" height="971"></p><p>The LH 8.1 supports overlapped injections. This means that the next injection can already be prepared while the current analysis is still running. Necessary cleaning steps of the injection system are still maintained, but idle time is reduced.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Fig_4_Schematic_buildup_of_injections_with_and_without_overlapped_injections_af089ba652.webp" alt="KNAUER: Fig. 4 Schematic buildup of injections with and without overlapped injections" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Fig_4_Schematic_buildup_of_injections_with_and_without_overlapped_injections_af089ba652.webp 245w," sizes="100vw" width="1920" height="452"></p><p>Let’s return to Giorgia. By using overlapped injections in her QC method, she saves about one minute per sample. This increases her capacity to approximately 105 samples per day.</p><h4><strong>Sample Throughput</strong></h4><p>A high-throughput system must also be able to handle and store a sufficient number of samples. Here, the LH 8.1 provides another major advantage. In the long-rail version, it can be equipped with up to three robotic coolers.</p><p>With three coolers, each containing three drawers, the system can hold nine 10 × 13 sample trays. That means a total capacity of 1170 vials. The samples are also temperature controlled.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Fig_5_6_Robotic_Cooler_with_two_10x6_trays_LH_8_1_887_version_with_two_Robotic_Coolers_855b10c2a3.jpg" alt="KNAUER: Fig. 5–6 Robotic Cooler with two 10x6 trays, LH 8.1 (887 version) with two Robotic Coolers" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Fig_5_6_Robotic_Cooler_with_two_10x6_trays_LH_8_1_887_version_with_two_Robotic_Coolers_855b10c2a3.jpg 245w," sizes="100vw" width="1262" height="503"></p><p>Combined with the low eluent consumption typical of UHPLC, this large sample capacity makes it possible to extend operation from an eight-hour workday to 24-hour operation.</p><p>For Giorgia and her QC lab, this changes everything again. The same UHPLC method, including overlapped injections, can now run continuously around the clock. This allows approximately 320 samples to be processed per day.</p><p>Is that enough? Maybe not. As the blog title suggests: we just can’t get enough.</p><h4><strong>Automation</strong></h4><p>In addition to a standard 6-port, 2-position injection valve, the HTQC system includes an additional valve. This special column-switching and backflushing valve enables two columns to be operated alternately within a single UHPLC system.</p><p>While one column is used for analysis, the second column can be backflushed and equilibrated in the reverse flow direction at the same time. This is particularly useful for reducing matrix effects, which are often encountered in QC laboratories when complex sample matrices are analyzed. It also helps reduce overall method runtime.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Fig_7_Exemplary_flow_scheme_of_special_column_switching_valve_d837a71117.webp" alt="KNAUER: Fig. 7 Exemplary flow scheme of special column switching valve" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Fig_7_Exemplary_flow_scheme_of_special_column_switching_valve_d837a71117.webp 127w," sizes="100vw" width="735" height="905"></p><h4><strong>Parallel Processing</strong></h4><p>Remember the earlier question: why does the system use two UHPLC gradient pumps?</p><p>The reason is now clear. The second gradient pump is required to backflush one column while the other column is connected to the analytical flow path through the special switching valve.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Fig_8_Schematic_illustration_of_column_cleaning_equilibration_and_analysis_with_special_backflush_valve_eae2e6f705.webp" alt="KNAUER: Fig. 8 Schematic illustration of column cleaning, equilibration and analysis with special backflush valve" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Fig_8_Schematic_illustration_of_column_cleaning_equilibration_and_analysis_with_special_backflush_valve_eae2e6f705.webp 245w," sizes="100vw" width="1920" height="281"></p><p>Giorgia immediately ordered a second UHPLC pump and the special valve for her QC lab. She now has a complete HTQC system and is very pleased with the result.</p><p>Why? Let’s calculate it one final time. With all automation features in place, Giorgia can clean one column while the other column analyzes a sample. This enables her to process an impressive 600 samples per day.</p><p>Compared with the classical HPLC method she used in 1998, the daily sample throughput has increased from six samples to 600 samples. That is a 100-fold increase.</p><h4><strong>Summary</strong></h4><p>We started with a question, so let’s end with one too: what steps increased the throughput?</p><p>First, the method was scaled down from classical HPLC to a fast UHPLC approach. Then, a second pump and a special column-switching and backflushing valve were added to the UHPLC setup. Together with the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1454"><strong>LH 8.1 liquid handler</strong></a> and its exceptional sample capacity, the HTQC system becomes a flexible and powerful configuration for high-throughput analysis.</p><p>The system can also be coupled to nearly any detector used in HPLC. Because of its ability to operate at very high speed, it is especially well suited for mass spectrometric methods.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Fig_9_Complete_flow_scheme_of_HTQC_system_with_highlighted_system_components_edef36cb42.webp" alt="KNAUER: Fig. 9 Complete flow scheme of HTQC system with highlighted system components" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Fig_9_Complete_flow_scheme_of_HTQC_system_with_highlighted_system_components_edef36cb42.webp 161w," sizes="100vw" width="800" height="775"></p><blockquote><p>For further information on this topic, please contact our authors: <strong>kramer@knauer.net</strong>, <strong>m.myrach@knauer.net</strong></p></blockquote>

Introducing Our System Solution for High Throughput Quality Control – HTQC

<h3><strong>How to Easily Adapt Your Existing HPLC Methods</strong></h3><p>Developing and optimizing an HPLC method is essential for achieving reliable separations, accurate quantification, and reproducible analytical results. As chromatography technology advances, one of the most common optimization strategies is transferring established methods to modern columns with smaller dimensions.</p><p>Although the benefits are clear, many analysts hesitate when it comes to modifying a validated method.</p><blockquote><p>Questions quickly arise: <i><strong>How should the flow rate be adjusted? What injection volume is appropriate? Does the gradient need to be recalculated? Will the retention times change?</strong></i></p></blockquote><p>Even with the necessary equations available, performing all these calculations manually can be time-consuming and prone to errors. Instead of simplifying the workflow, method transfer often becomes an unnecessary obstacle.</p><p>Fortunately, there is an easier solution.</p><h4><strong>Simplify Your HPLC Method Transfer</strong></h4><p>Moving an existing method to a different column does not have to be complicated.</p><p>The <strong>KNAUER HPLC Method Converter</strong> is designed to automate the calculations required for method transfer. Simply enter the parameters of your current method, including the original column dimensions, and specify the dimensions of the new column—length, internal diameter, and particle size. The software instantly calculates the recommended flow rate and injection volume for the new conditions.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_HPLC_Method_Converter_7f7c19f7a3.webp" alt="KNAUER: HPLC Method Converter" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_HPLC_Method_Converter_7f7c19f7a3.webp 210w," sizes="100vw" width="1022" height="759"></p><p>The next step is equally straightforward. Copy the original <strong>gradient profile</strong> into the converter, and the <strong>software automatically generates the corresponding gradient program for the new column</strong>.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_HPLC_Method_Converter_2_8ba46e78bc.webp" alt="KNAUER: HPLC Method Converter - Gradients" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_HPLC_Method_Converter_2_8ba46e78bc.webp 195w," sizes="100vw" width="1440" height="1150"></p><p>For even greater confidence, the converter also allows you to <strong>enter chromatographic peak information</strong>. Based on these data, it <strong>predicts the expected retention times</strong> under the new conditions. While experimental verification on the HPLC system is still recommended, these predictions provide an excellent starting point for method optimization.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_HPLC_Method_Converter_3_34f16bb3bf.webp" alt="KNAUER: HPLC Method Converter - Chromatograms" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_HPLC_Method_Converter_3_34f16bb3bf.webp 196w," sizes="100vw" width="1024" height="814"></p><p>The converter was developed with <strong>one primary objective:</strong> making <strong>HPLC method adaptation faster, easier, and more reliable </strong>while reducing the effort required from the user. Its intuitive interface, modern design, and automatic calculations help save valuable laboratory time—and it is available free of charge.</p><h4><strong>Modernize Your Methods and Improve Laboratory Efficiency</strong></h4><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_HPLC_Method_Converter_4_31e7188db4.webp" alt="KNAUER: Modernize Your Methods and Improve Laboratory Efficiency" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_HPLC_Method_Converter_4_31e7188db4.webp 245w," sizes="100vw" width="720" height="449"></p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_HPLC_Method_Converter_5_815a7bf889.webp" alt="KNAUER: HPLC Method Converter - Results" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_HPLC_Method_Converter_5_815a7bf889.webp 194w," sizes="100vw" width="1440" height="1157"></p><p>One of the major advantages of the <strong>KNAUER HPLC Method Converter</strong> is its compliance with <strong>USP General Chapter &lt;621&gt;</strong>.</p><p>For <strong>pharmaceutical laboratories</strong>, chromatographic methods must comply with pharmacopeial requirements that ensure product quality and patient safety. Historically, many USP methods were developed using larger HPLC columns that no longer reflect the capabilities of modern chromatography systems.</p><p>Current USP, <strong>European Pharmacopoeia (Ph. Eur.)</strong>, and <strong>Japanese Pharmacopoeia (JP)</strong> guidelines now permit specific adjustments to column dimensions and particle size for both isocratic and gradient methods. These changes are allowed provided that defined relationships between chromatographic parameters are maintained.</p><p>The KNAUER Method Converter automatically checks whether the selected column dimensions remain within the permitted USP limits. If the proposed changes comply with the guidelines, the software confirms that the method can be transferred while remaining pharmacopeia compliant. This removes uncertainty from the method conversion process and helps laboratories modernize their analytical workflows with confidence.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_HPLC_Method_Converter_6_c9d1e28c54.webp" alt="Unsplash: Illustrative picture" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_HPLC_Method_Converter_6_c9d1e28c54.webp 245w," sizes="100vw" width="720" height="449"></p><h4><strong>Increase Productivity While Reducing Solvent Consumption</strong></h4><p>Updating HPLC methods is not only about shortening analysis times—it also supports more sustainable laboratory practices.</p><p>Using shorter columns together with optimized flow rates significantly reduces solvent consumption, lowering operating costs and decreasing the amount of hazardous chemical waste generated during routine analyses. Faster separations also improve instrument throughput, enabling more samples to be processed within the same amount of time.</p><p>Modernizing chromatographic methods therefore delivers a dual benefit: greater laboratory productivity and a smaller environmental footprint. With only a few simple adjustments, laboratories can improve efficiency while supporting more sustainable analytical workflows.</p>

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Based in Berlin, KNAUER is a medium-sized, owner-managed company that has been serving the sciences since 1962. We develop and manufacture scientific instruments of superior quality for liquid chromatography, including: Analytical HPLC/UHPLC, Preparative HPLC, Fast protein liquid chromatography (FPLC), Multi-column chromatography/Simulated moving bed (SMB) chromatography. High pressure dosing, in-line detection systems, and osmometry are additional business areas.

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