The development of antisense oligonucleotide (ASO) therapies demands high-throughput, precision-driven platforms capable of generating chemically diverse and biologically potent libraries. At BOC Sciences, we specialize in the preclinical synthesis of ASO Gapmer libraries designed to support rapid screening, lead optimization, and mechanistic studies in antisense drug discovery. Our synthesis capabilities are strategically designed to meet the stringent demands of pharmaceutical, academic, and biotech partners engaged in RNA-targeted therapeutic research.
An ASO gapmer library is a curated collection of antisense oligonucleotides designed to selectively bind RNA transcripts and trigger degradation through endogenous RNase H1. Each gapmer typically consists of a central DNA "gap" flanked by chemically modified nucleotides—such as 2'-O-methyl (2'-OMe), 2'-O-methoxyethyl (2'-MOE), or locked nucleic acids (LNAs)—to enhance nuclease resistance and binding affinity.
This hybrid design allows for:
Gapmer libraries are most commonly deployed in high-throughput screening assays to identify lead sequences capable of downregulating disease-related transcripts, including non-coding RNAs, which are not amenable to traditional small molecule targeting.
At BOC Sciences, we recognize that the success of antisense oligonucleotide (ASO) gapmer screening projects hinges on a meticulously engineered synthesis process that integrates thoughtful design, advanced chemical techniques, and adaptable production capabilities. Our ASO Gapmer Library Synthesis services therefore encompass three fundamental and interdependent dimensions—Library Design and Types, Synthesis Chemistry and Methodologies, and Scale and Format Flexibility. This comprehensive approach ensures that each synthesized library is not only scientifically robust but also precisely tailored to meet the complex and evolving needs of antisense research. By combining cutting-edge design algorithms, industry-leading synthesis protocols, and scalable production formats, BOC Sciences delivers an end-to-end solution that empowers researchers to accelerate target validation, functional genomics, and therapeutic discovery with unmatched accuracy, reproducibility, and operational efficiency.
BOC Sciences offers sophisticated and customizable gapmer library design solutions that align precisely with diverse research objectives and target complexities. Our design strategies ensure maximal efficacy, specificity, and adaptability for preclinical antisense applications.
| Gapmer Library Types | Description | Price |
| Tiling Libraries | These libraries systematically cover contiguous regions of the target RNA, such as entire exons, introns, or untranslated regions. By creating overlapping gapmers across the sequence, tiling libraries enable comprehensive functional mapping of transcript regions, facilitating identification of the most accessible and effective knockdown sites. This approach is essential for targets with complex secondary structures or isoform diversity. | Inquiry |
| Mutation and Mismatch Libraries | To refine specificity and investigate sequence-dependent activity, we design libraries that incorporate deliberate single or multiple nucleotide mismatches. These variant libraries help delineate off-target effects and elucidate structure-activity relationships, providing critical data for lead optimization and toxicity reduction. | Inquiry |
| Functional and Regulatory Element Libraries | Targeting non-coding RNA, splice junctions, microRNA binding sites, or other regulatory elements requires precise gapmer configurations. We tailor these libraries with specialized gap and wing designs to enhance RNase H recruitment and minimize interference with normal transcript processing, enabling mechanistic studies of gene regulation. | Inquiry |
| Custom Libraries for Complex Targets | For targets with known polymorphisms, alternative splicing, or RNA editing sites, we offer bespoke library designs that incorporate sequence variants and modification patterns. This customization ensures robust targeting across heterogeneous transcript populations, critical in disease-relevant contexts. | Inquiry |
Across all library types, BOC Sciences applies rigorous in silico tools to optimize nucleotide composition, avoid self-dimerization and secondary structure pitfalls, and predict RNA accessibility, thereby maximizing functional performance and minimizing nonspecific interactions. Our design service is a collaborative process, aligning closely with client goals to deliver gapmer libraries that enable precise, high-confidence screening outcomes.
At BOC Sciences, our synthesis chemistry and methodologies for gapmer libraries are engineered to meet the highest standards of precision, reproducibility, and functional performance. We employ advanced solid-phase phosphoramidite chemistry optimized specifically for the unique structural requirements of ASO gapmers, ensuring each oligonucleotide achieves superior stability, specificity, and biological activity.
Key Chemical Features:
Synthesis Methodologies:
By integrating these advanced chemical modifications and meticulous synthesis methodologies, BOC Sciences guarantees gapmer libraries with exceptional uniformity, reproducibility, and functional efficacy, empowering researchers to achieve reliable and robust gene-silencing results in their ASO studies.
BOC Sciences recognizes that preclinical research demands versatile synthesis scales and adaptable library formats to meet diverse experimental workflows and throughput requirements. Our Gapmer Library service offers unparalleled flexibility in both production scale and delivery format, ensuring seamless integration into your screening and validation pipelines.
This comprehensive scale and format flexibility positions BOC Sciences as a trusted partner capable of adapting to evolving research demands and accelerating the pace of antisense oligonucleotide discovery.
To ensure precision and reliability in every ASO gapmer library we deliver, BOC Sciences follows a meticulously structured synthesis workflow. This process guarantees that each library meets rigorous quality and customization standards tailored to your research needs.
The process begins with a detailed discussion to understand the client's target genes, desired gapmer chemistry, library scale, and experimental goals. This step ensures alignment on technical specifications, timelines, and any special requests.
Based on the target RNA sequences provided, our bioinformatics team generates candidate gapmer sequences covering relevant transcript regions. Advanced algorithms evaluate RNA secondary structures, GC content, potential off-target sites, and hybridization thermodynamics to refine sequence selection for maximal efficacy.
Selected gapmers undergo solid-phase phosphoramidite synthesis, integrating client-specified chemical modifications such as phosphorothioate backbones and locked nucleic acids. Strict process controls optimize coupling efficiency to reduce truncations and impurities.
Post-synthesis, oligonucleotides are purified via HPLC or PAGE to achieve high purity. Each sequence is verified by LC-MS or MALDI-TOF mass spectrometry to confirm accurate molecular weight and sequence integrity, ensuring the reliability of the library.
Purified gapmers are dispensed into plates (96- or 384-well) or tubes according to client requirements. Concentrations are normalized to facilitate downstream screening consistency. Barcode labeling and detailed plate maps are generated to support sample tracking and integration with automated platforms.
Comprehensive QC assessments verify oligonucleotide concentration, purity, and identity post-formatting. Detailed analytical reports and certificates of analysis accompany each shipment, providing transparency and confidence for clients.
Libraries are packaged in RNase-free, moisture-proof, and temperature-controlled conditions to maintain oligonucleotide stability during transit. Logistics are optimized for timely delivery worldwide.
Following shipment, dedicated technical support is available to assist with library integration, troubleshoot issues, and provide guidance for experimental design, maximizing the utility of the ASO gapmer library.
This structured, rigorous workflow ensures that every ASO gapmer library delivered by BOC Sciences meets stringent quality standards, enabling researchers to accelerate gene-silencing studies with confidence.
With extensive experience in synthesizing chemically modified ASOs, BOC Sciences ensures precise incorporation of diverse modifications such as locked nucleic acids (LNA), 2'-O-methoxyethyl (2'-MOE), and phosphorothioate backbones. This expertise guarantees libraries with superior stability, enhanced binding affinity, and robust RNase H activation.
We collaborate closely with clients to design gapmer libraries optimized for target specificity and functional performance. Our flexible synthesis workflows accommodate varying gap lengths, chemical modifications, and sequence complexity, enabling bespoke solutions that align with your research objectives.
Our state-of-the-art automated synthesis platforms support large-scale parallel production, enabling delivery of hundreds to thousands of gapmers with high reproducibility. Rigorous quality control through LC-MS, HPLC, and UV ensures every oligonucleotide meets stringent purity and identity standards.
BOC Sciences delivers complex gapmer libraries within industry-leading timelines without compromising quality. Whether you require screening-scale quantities or larger amounts for validation, we offer scalable synthesis to fit your project scope.
We provide detailed analytical reports, sequence annotations, and customized plate formatting to facilitate seamless integration into your screening workflows. This transparent documentation enhances traceability and data reliability throughout your preclinical studies.
Choosing BOC Sciences for your ASO gapmer library synthesis means partnering with a leader who combines cutting-edge technology, deep scientific insight, and customer-centric service to empower your antisense research initiatives.
ASO gapmer libraries are invaluable tools across multiple domains of preclinical research and drug discovery, providing a versatile platform for targeted gene silencing with high specificity and efficacy. Their applications span from fundamental biological research to therapeutic candidate identification, enabling breakthroughs in understanding gene function and disease mechanisms.
ASO gapmer libraries enable comprehensive interrogation of gene function by selectively downregulating target transcripts across diverse regions. By systematically screening multiple gapmer sequences, researchers can identify the most efficacious antisense candidates with robust RNase H-mediated cleavage activity. This approach is particularly valuable for validating novel gene targets implicated in disease pathways, deciphering gene regulatory networks, and characterizing transcript variants. High-throughput libraries allow rapid functional annotation of both coding and non-coding RNAs, advancing our understanding of transcriptome complexity.
For therapeutic development, gapmer libraries provide a powerful tool to screen a broad array of antisense sequences, optimizing for potency, specificity, and minimal off-target effects. Chemical modifications integrated into the gapmers enhance stability, cellular uptake, and target affinity—parameters critical for in vivo efficacy. Systematic exploration of sequence variants within a library facilitates structure–activity relationship (SAR) analyses, informing subsequent medicinal chemistry efforts. This capability accelerates the identification of lead ASOs for a range of indications including oncology, neurodegenerative diseases, metabolic disorders, and rare genetic conditions.
ASO gapmers can be designed to target splice junctions or regulatory elements controlling alternative splicing events. Libraries tiled across splice sites enable researchers to elucidate mechanisms of exon inclusion or skipping, with implications for correcting aberrant splicing patterns linked to disease. These applications extend to studies of RNA maturation, processing, and stability, deepening insights into post-transcriptional gene regulation.
By selectively knocking down transcripts associated with disease states, ASO gapmer libraries assist in validating potential RNA biomarkers. This functional validation strengthens the biological relevance of candidate biomarkers and supports their development as diagnostic or prognostic tools. The ability to rapidly screen numerous sequences enables refinement of biomarker panels with enhanced specificity and sensitivity.
Targeted suppression of multiple genes within a pathway using gapmer libraries allows detailed dissection of signaling cascades and interaction networks. This multiplex approach is critical for unraveling complex biological systems and identifying key regulatory nodes amenable to therapeutic intervention. Libraries designed against gene families or isoforms facilitate the understanding of functional redundancies and compensatory mechanisms.
ASO libraries can be employed to evaluate off-target effects by screening for unintended interactions across the transcriptome. Systematic testing of chemically modified gapmers enables the optimization of sequence specificity and minimization of immune activation or toxicity, enhancing the safety profile of antisense candidates prior to in vivo studies.
Long non-coding RNAs (lncRNAs), microRNAs, and other regulatory RNAs are increasingly recognized as critical disease modulators. ASO gapmer libraries provide a robust platform for selective knockdown of these non-coding transcripts, facilitating functional studies that elucidate their roles in gene expression control, epigenetics, and cellular differentiation.
In sum, BOC Sciences' ASO Gapmer Library Synthesis service supports diverse applications where precision, chemical sophistication, and high-throughput capability are essential. By delivering libraries tailored to the specific scientific or therapeutic question, we empower researchers to accelerate discovery and deepen mechanistic insights with confidence.
Modifications such as phosphorothioate backbones, locked nucleic acids (LNAs), and 2'-O-methyl or 2'-MOE wings improve stability, reduce degradation, and enhance binding affinity to the RNA target. These modifications increase the half-life of gapmers in biological systems and improve RNase H recruitment, critical for effective gene knockdown.
Yes. BOC Sciences provides flexible synthesis scales from nanomole quantities for screening up to milligram quantities for downstream validation, formatted in 96- or 384-well plates or custom layouts to suit your workflow and assay requirements.
We offer consultation services including sequence alignment, off-target prediction, and thermodynamic analysis to guide selection of gapmer sequences and modifications. This collaboration ensures your library is optimized for target engagement and minimal off-target activity.
Design algorithms incorporate homology screening against transcriptome databases to exclude sequences with significant complementarity to non-target RNAs. Chemical modifications and gap length adjustments also contribute to specificity. We recommend iterative design and empirical validation.
Libraries are supplied in RNase-free 96- or 384-well plates, with options for normalized concentrations, barcoding, and custom plate maps to seamlessly integrate with automated liquid handling and screening systems.
Properly lyophilized gapmers are stable for extended periods (typically 1–2 years) when stored at -20°C, protected from moisture and light. We provide detailed storage guidelines to preserve oligonucleotide integrity.
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