Antisense oligonucleotides (ASOs) represent one of the most powerful and rapidly evolving classes of therapeutic agents in modern molecular medicine. As short, synthetic nucleic acid sequences, typically 12 to 25 nucleotides in length, ASOs leverage the fundamental principle of sequence complementarity to selectively modulate gene expression. By binding to specific target RNA molecules (pre-mRNA, mRNA, or ncRNA), ASOs can elicit distinct biological outcomes, transforming the treatment landscape for both common and rare genetic disorders.
CD BioGlyco specializes in the precision manufacturing of custom ASOs, providing researchers and therapeutic developers with the high-quality, modified oligonucleotides essential for accelerating discovery, preclinical validation, and clinical development. The core mechanism of action often involves RNase H-mediated degradation of the target mRNA (using DNA-based Gapmers) or steric hindrance to modulate RNA splicing, thereby correcting aberrant protein production or function.
Achieving therapeutic efficacy with ASOs requires overcoming critical pharmacological hurdles, primarily systemic degradation by nucleases and efficient delivery to target tissues. We utilize state-of-the-art chemical synthesis platforms to incorporate advanced modifications that enhance stability, affinity, and bioavailability. These modifications define the generation and functional properties of the oligonucleotide therapeutic:
The fundamental modification replaces a non-bridging oxygen atom with sulfur in the phosphodiester linkage. This modification significantly increases resistance to endo- and exonucleases, prolonging the ASO's half-life in vivo and enabling systemic administration.
Second-generation modifications are introduced at the 2'-position of the ribose sugar. These enhancements boost RNA binding affinity (Tm), further stabilize the oligo against nuclease attack, and are key components in high-performing Gapmer designs.
Third-generation bicyclic nucleic acids (BNAs) that "lock" the ribose ring, providing the highest possible binding affinity to the target RNA. Their use permits shorter oligo lengths, enhancing specificity and reducing off-target effects.
A chimeric structure featuring central deoxyribonucleotides (the "gap") flanked by nuclease-resistant wings (e.g., 2'-MOE or LNA). The gap section activates RNase H upon binding to the target RNA, leading to efficient mRNA degradation.
Strategic conjugation of ligands, such as N-acetylgalactosamine (GalNAc), to the ASO enables highly specific, receptor-mediated uptake into target cells, dramatically improving potency and therapeutic index, especially for hepatic targets.
We provide a flexible, modular service scope designed to meet the evolving needs of your therapeutic program, ensuring a smooth transition across developmental phases:
High-throughput, cost-effective synthesis for early-stage target validation, in vitro screening, and preliminary animal studies.
Elevated quality standards with enhanced traceability, stricter purity requirements (typically >90-95% by HPLC), and mandatory endotoxin/bioburden testing, suitable for GLP toxicology studies.
Specialized services for attaching delivery ligands (e.g., GalNAc, peptides, lipids) to enhance tissue targeting.
Synthesis of large panels of ASOs incorporating a wide variety of modifications (LNA, BNA, various 2' substitutions) for lead candidate screening and optimization.
Initial target sequence analysis, computational design of Gapmer or steric-blocking motifs, selection of appropriate chemical modifications (e.g., PS, MOE, LNA), and optimization for high-yield synthesis and stability.
Automated, high-fidelity synthesis utilizing phosphoramidite chemistry on controlled pore glass (CPG) solid supports. This step builds the oligonucleotide base-by-base, incorporating chosen backbone (PS) and sugar (MOE, LNA) modifications.
Chemical treatment to separate the synthesized ASO strand from the CPG support (cleavage) and to remove protecting groups from the nucleobases and linkages (deprotection). Temperature and reagent control are critical for minimizing side-product formation.
Multi-stage purification processes tailored to the required quality grade. Includes desalting (SePOP) for RUO grades, or comprehensive anion exchange/reverse phase high-performance liquid chromatography (HPLC) for high-purity pre-clinical grade materials to remove truncated sequences and synthesis by-products.
Comprehensive analytical testing, including mass spectrometry (MS) for sequence identity confirmation, HPLC/capillary electrophoresis (CE) for purity determination, UV spectrophotometry for quantitation, and endotoxin/bioburden testing for in vivo grades.
Drying, formulation in specified buffer solution, customized packaging (tubes, plates), and generation of detailed certificates of analysis (CoA) and full batch traceability documentation necessary for regulatory submission.
Journal: Nucleic Acids Research
DOI: 10.1093/nar/gkaf392
IF: 13.1
Published: 2025
Results: In this study, the authors introduce ASOptimizer, a deep learning-based web server designed to optimize the chemical modifications of ASOs for enhanced therapeutic efficacy. Recognizing that manual ASO design is resource-intensive and complex due to the vast combinatorial space of sequences and modifications, they developed a user-friendly platform that allows researchers to input a nucleotide sequence and receive a ranked list of promising modification patterns, such as MOE or LNA, based on predicted inhibition rates. The system leverages a graph neural network trained on over 100,000 experimental data points to model ASO efficacy, employing a learning-to-rank approach for accuracy. Validation against external patent data and previous studies demonstrated strong correlations, with Pearson coefficients up to 0.85, confirming the model's reliability. Accessible via an intuitive web interface, ASOptimizer eliminates the need for deep learning expertise, aiming to accelerate ASO development and broaden adoption in gene therapy, with future plans to incorporate toxicity prediction and additional modifications.
Therapeutic Research in Genetic Diseases
ASOs are used to treat rare genetic disorders by modulating RNA processing. This includes exon skipping (e.g., eteplirsen for Duchenne muscular dystrophy) to restore the reading frame, and splice switching (e.g., nusinersen for spinal muscular atrophy) to promote inclusion of a critical exon, thereby producing functional proteins.
Inhibition of Gene Expression in Various Diseases
Traditional "gapmer" ASOs bind to target mRNA via Watson-Crick base pairing and recruit RNase to degrade the RNA. This direct suppression of gene expression is applied in treating hereditary transthyretin amyloidosis (e.g., inotersen) and is being investigated for metabolic diseases, cancers, and viral infections.
Neurological and Neuromuscular Disorders
ASOs can be delivered intrathecally to directly target the central nervous system. This enables treatment of previously untreatable neurodegenerative diseases, such as amyotrophic lateral sclerosis (tofersen) and Huntington's disease, by reducing the production of toxic proteins or mutant RNAs.
Research and Target Validation Tools
In preclinical research, ASOs serve as powerful, rapid tools for functional genomics. They allow for the specific, reversible knockdown of gene expression in vitro and in vivo to validate novel drug targets and study gene function without permanent genetic modification.
High-Fidelity Synthesis Platforms
This foundation utilizes automated solid-phase synthesizers with optimized protocols to achieve consistently high coupling efficiency and extremely low impurity levels. This precision is critical for successfully incorporating complex chemical modifications at scale, ensuring reproducible synthesis that meets stringent quality and regulatory guidelines for therapeutic development.
Specialist Complex Chemistry
We possess deep, specialized expertise in synthesizing challenging ASO constructs. This includes the precise incorporation of multiple constrained nucleotides (e.g., LNA, BNA/cEt) and the complex assembly of advanced architectures like Gapmers, which are essential for enhancing target binding affinity, metabolic stability, and overall drug efficacy.
Comprehensive Analytical Support
Every batch is supported by a mandatory, rigorous analytical package. This includes high-resolution mass spectrometry for definitive identity confirmation and a full suite of purity analyses using capillary electrophoresis and various HPLC methods (e.g., IEX, RP) paired with multiple detectors (UV, CAD) to comprehensively characterize purity, integrity, and impurity profiles.
Exceptional Lead Candidate Throughput
Our platform leverages state-of-the-art automation, optimized parallel synthesis, and streamlined purification to rapidly generate large, diverse libraries of screening candidates. This high-throughput capability dramatically accelerates the initial hit-to-lead and lead optimization phases, compressing the overall drug discovery timeline.
As we transitioned from RUO to preclinical studies, the need for stringent QC became critical. CD BioGlyco's documentation and consistent 98%+ purity significantly streamlined our submission package. The process continuity saved us months.
— Director R., Regulatory Affairs, Pharmaceutical Development
We rely heavily on complex, long-chain ASO conjugates. CD BioGlyco is the only CDMO that consistently hits our required specifications for both oligo sequence integrity and conjugation efficiency. Excellent technical support.
— Manager D., Oligonucleotide Synthesis Development
We utilized their GalNAc ASO conjugation service for our novel liver target. The potency data we achieved with their conjugated material was world-class. Highly professional and scientifically rigorous.
— VP Therapeutics, Preclinical Operations
To help you fully achieve your therapeutic development goals, we offer a suite of complementary oligonucleotide services optimized for drug delivery and RNA modulation:
Targeted Delivery Conjugation Services
Utilizing the GalNAc ligand for highly efficient, ASGPR-mediated delivery, specializing in the development of silencing RNA therapeutics against liver targets.
Our core offering is for maximizing the potency and therapeutic index of your antisense oligonucleotide directed against hepatic mRNA targets.
Enabling targeted delivery of miRNA mimics or inhibitors to the liver for functional studies and therapeutic development.
CD BioGlyco is committed to providing the highest quality ASO synthesis service to accelerate your journey from bench to bedside. Leverage our two decades of scientific expertise and cutting-edge manufacturing capabilities to ensure the success of your oligonucleotide therapeutic program. Contact us!
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