As a professional oligonucleotides preparation service provider, we provide high-quality products as well as antisense oligonucleotides preparation services. Based on our successful experience and technology, we are able to provide customized synthesis of gapmer oligonucleotides, such as LNA gapmer oligonucleotides, for different research purposes and applications. And based on our strict quality control system, we can provide first-class solutions and after-sales service for your projects.
A gapmer oligonucleotide typically consists of a central "gap" region of DNA nucleotides flanked by chemically modified nucleotides (often 2'-O-methyl or locked nucleic acids [LNA]) at both ends. This architecture is carefully crafted to balance nuclease resistance, target affinity, and RNase H recruitment.
The design of gapmer oligonucleotide involves first identifying the intervening or targeting RNA or DNA sequence, and then selecting a suitable position on the target sequence as a gap region according to the characteristics and requirements of the target sequence. Next, on both sides of the gap region, complementary sequences are designed which can be base complementarily paired with the remainder of the target sequence. When designing a gapmer oligonucleotide, care also needs to be taken to avoid designing sections with repetitive sequences or self-binding, as well as the need to consider the stability and specificity of the nucleic acid. Where available, the design can be aided by the use of auxiliary tools and software, such as online oligonucleotide design tools or gene editing design tools. These tools can provide base complementarity assessment, sequence characterization, and other design parameters.
BOC Sciences delivers high-performance, fully customized gapmer oligonucleotide synthesis solutions for researchers seeking potent, RNase H-mediated gene silencing tools. Our services go beyond generic synthesis—we operate as an extension of your research team, providing deep scientific insight, technical precision, and end-to-end workflow integration.
BOC Sciences offers a specialized ASO (Antisense Oligonucleotide) Gapmer Library Synthesis Service designed to accelerate high-throughput screening and functional genomics studies. This service enables researchers to efficiently generate diverse gapmer libraries targeting multiple gene sequences or transcript variants, facilitating rapid identification of potent antisense candidates.
Leveraging our advanced synthesis platform and quality assurance systems, BOC Sciences empowers your antisense research with robust, high-quality ASO gapmer libraries designed to expedite discovery and validation phases.
At BOC Sciences, gapmer oligonucleotide design is not based on generic antisense guidelines—we apply a precision-engineering strategy that integrates transcript-specific features, nuclease accessibility, and molecular pharmacology to achieve high knockdown potency and biological fidelity.
(1) Rational Design Based on Target RNA Accessibility
We employ advanced bioinformatics tools—including RNAfold, Sfold, and MFE structural mapping—to predict accessible, single-stranded regions within the target transcript. These regions are essential for efficient hybridization and subsequent RNase H recruitment. Critical criteria include:
This design logic significantly increases the probability of functional knockdown across multiple model systems.
(2) Optimized Gap Architecture for RNase H Activation
Our standard gapmer configuration typically follows the structure: (3–5 modified bases) – (8–10 DNA bases) – (3–5 modified bases).
The central DNA "gap" (gapmer core) is engineered to provide the substrate for RNase H cleavage and the flanking regions are stabilized using 2'-O-methyl, 2'-MOE, or LNA to:
Each gap is designed with careful thermodynamic profiling, including:
(3) Structure–Activity–Stability (SAS) Triad Optimization
We do not treat binding, activity, and stability as isolated properties. Instead, our approach balances:
This SAS triad is iteratively modeled during the design stage, allowing us to predict and mitigate issues such as premature degradation, incomplete knockdown, or non-specific interactions.
At BOC Sciences, we understand that the performance and stability of gapmer oligonucleotides critically depend on precise chemical modifications tailored to the intended research application. Our synthesis platform supports an extensive array of advanced modifications that enhance nuclease resistance, binding affinity, and cellular uptake, enabling researchers to optimize therapeutic potential and experimental reliability. Key modification capabilities include:
| Modification Capabilities | Description | Price |
| Backbone Chemistry | We incorporate full or partial phosphorothioate (PS) backbone modifications to dramatically improve nuclease stability without compromising RNase H activity. Our proprietary protocols ensure uniform PS incorporation, minimizing batch variability and off-target effects. | Inquiry |
| Sugar Moiety Modifications | To reinforce hybridization affinity and metabolic durability, we expertly integrate:
| Inquiry |
| Nucleobase Modifications | When required, BOC Sciences can introduce nucleobase analogues to reduce off-target interactions or incorporate fluorophores for tracking and imaging studies. | Inquiry |
| Terminal Functionalizations and Labels | We offer a broad portfolio of 5' and 3' conjugations, for example:
| Inquiry |
| Targeted Conjugation Services | To enhance cellular delivery and tissue targeting, our team custom conjugates gapmers with peptides, lipids, cholesterol, or polyethylene glycol (PEG). These modifications improve pharmacodynamics by facilitating endosomal escape, reducing renal clearance, or enabling receptor-mediated uptake. | Inquiry |
Each modification is applied using proprietary optimized chemistries and synthesis protocols that preserve oligonucleotide integrity and biological function. Our stringent in-process monitoring guarantees the accuracy and reproducibility of complex modifications, ensuring that your gapmers perform exactly as designed.
The synthesis of gapmer oligonucleotides at BOC Sciences follows a meticulously controlled, multi-stage workflow designed to ensure precision, reproducibility, and high purity. Each stage is optimized to address the unique chemical complexities and modification patterns of gapmers, delivering products that meet stringent research standards.
This structured workflow ensures that every gapmer oligonucleotide from BOC Sciences meets stringent quality standards, enabling reliable and reproducible outcomes in your preclinical research.
Our synthesis platform incorporates state-of-the-art chemical modifications—including phosphorothioate backbones and high-affinity flanking nucleotides such as LNA and 2'-MOE—resulting in gapmers with exceptional nuclease resistance and improved target binding. This precision engineering ensures sustained activity in biological systems, crucial for robust gene silencing.
We provide flexible design options tailored to your project requirements, including variable oligonucleotide length, modification patterns, and conjugation with functional groups (e.g., fluorescent dyes, biotin, peptides). This adaptability supports diverse applications from functional genomics to molecular diagnostics.
Every gapmer oligonucleotide undergoes multi-level quality assurance processes—HPLC or PAGE purification, mass spectrometry verification, UV quantification, and optional endotoxin testing. Our strict standards guarantee high purity (>90%) and reproducibility, empowering reliable experimental results.
We combine automated synthesis technology with optimized workflows to deliver rapid project completion without compromising quality. Production scales range from small discovery batches to multi-gram quantities, supporting both research and early-stage development phases efficiently.
Our experienced scientific team offers dedicated support in sequence design, modification selection, and troubleshooting. This consultative approach helps optimize oligonucleotide performance and minimizes off-target effects, saving valuable research time and resources.
Gapmer oligonucleotides serve as a powerful tool for targeted gene silencing, enabling precise modulation of gene expression in diverse biomedical research areas. Their unique structural features and chemical stability facilitate effective RNase H-mediated cleavage of complementary RNA, making them indispensable in advanced molecular biology and therapeutic development research.
Gapmers are extensively employed in functional genomics to dissect gene roles by selectively knocking down mRNA transcripts. This targeted silencing allows researchers to delineate gene function, signaling pathways, and molecular networks in both in vitro and in vivo model systems. By transiently or stably reducing expression levels of disease-relevant genes, gapmers enable elucidation of gene contributions to cellular phenotypes, growth, differentiation, and apoptosis.
In the preclinical drug development pipeline, gapmers serve as critical molecular tools for target validation. Their ability to efficiently silence candidate genes helps assess the therapeutic potential of specific molecular targets before committing to costly small molecule or biologic development. This precise gene modulation reduces the risk of off-target effects commonly observed with other modalities, increasing confidence in target-drug associations.
Non-coding RNAs, including long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), have emerged as crucial regulators in gene expression and disease. Gapmer oligonucleotides offer a robust strategy to selectively degrade these often nuclear-localized transcripts that are refractory to traditional RNA interference approaches. This has profound implications in cancer biology, neurodegeneration, and epigenetic regulation research.
Gapmers are increasingly applied in antiviral strategies targeting viral RNA genomes or transcripts essential for replication. By directing RNase H cleavage to these viral sequences, gapmers can effectively suppress viral load and disrupt infection cycles. Their enhanced stability and specificity make them suitable for in vitro and ex vivo evaluation of novel antiviral compounds and mechanisms.
The blood-brain barrier and complex neural environment present challenges for RNA therapeutics. Gapmers with tailored chemical modifications show improved pharmacokinetics and stability in neural tissues, making them attractive candidates for modulating pathogenic gene expression in neurodegenerative diseases such as Huntington’s disease, amyotrophic lateral sclerosis (ALS), and Alzheimer’s disease. Preclinical models benefit from gapmer-mediated gene knockdown to study disease progression and therapeutic intervention.
By selectively knocking down transcripts involved in chromatin remodeling and transcription factor expression, gapmers allow detailed exploration of epigenetic regulation mechanisms. This contributes to understanding how gene expression is modulated dynamically in development, differentiation, and pathological states.
Yes, we provide a wide range of custom modifications including fluorescent dyes, biotin, cholesterol, peptides, and other conjugates to facilitate downstream applications such as imaging, pull-down assays, or cellular uptake.
Absolutely. We specialize in synthesizing highly complex oligonucleotides with multiple chemical modifications tailored to improve stability, specificity, and efficacy.
Typical gapmers range from 14 to 20 nucleotides, featuring a central DNA gap (usually 8–10 bases) flanked by chemically modified nucleotides. To maximize RNase H activity and binding affinity, BOC Sciences provides expert design consultation using target mRNA accessibility data and thermodynamic analysis to tailor the gapmer for effective gene silencing.
Yes. Our team offers advanced bioinformatics support to minimize off-target effects by evaluating sequence specificity, secondary structure, and transcriptome-wide homology. This reduces experimental risk and improves knockdown efficacy.
Synthesized gapmers are typically delivered lyophilized for optimal stability. Upon receipt, we recommend storage at -20°C under dry conditions. Reconstituted solutions should be aliquoted and stored at -80°C to avoid freeze-thaw degradation.
Yes. BOC Sciences supports custom conjugation strategies including peptide, lipid, or polymer attachments to enhance cellular uptake or tissue targeting, designed to fit your experimental needs.
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