RNA Therapeutic & Research Solutions | Eclipsebio https://eclipsebio.com Accelerate RNA discovery to clinic Sun, 22 Feb 2026 15:48:23 +0000 en-US hourly 1 https://wordpress.org/?v=6.9.4 https://eclipsebio.com/wp-content/uploads/2023/07/cropped-favicon-150x150.jpg RNA Therapeutic & Research Solutions | Eclipsebio https://eclipsebio.com 32 32 RNA Therapeutic Solutions https://eclipsebio.com/solutions/rna-therapeutic-solutions/ Fri, 24 May 2024 18:24:16 +0000 https://eclipsebio.com/newdev/?post_type=solutions&p=10297

End-to-End RNA Therapeutic Support

Eclipsebio delivers end-to-end RNA therapeutic solutions that help developers design, evaluate, and advance RNA medicines with confidence. By integrating AI-driven design, rapid RNA prototyping, and deep sequencing analytics, we shorten development timelines, reduce risk, and support successful translation from discovery to scale.

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RNA development tailored to your needs

Eclipsebio supports RNA therapeutic programs at any stage. Teams can engage across the full closed loop of design, make, and test to rapidly iterate and optimize candidates using integrated AI, RNA prototyping, and sequencing-based analytics. For teams with existing capabilities, we plug in where needed, whether that is design-only optimization, testing-only characterization, or connecting you with validated manufacturing partners for scale-up. This flexible approach enables faster decisions, reduced risk, and confident progress toward the clinic.

Talk to an RNA expert

Develop with confidence

Eclipsebio supports RNA drug development across the full lifecycle, working with teams from early-stage startups to global biopharma. Our integrated design, prototyping, and analytics capabilities enable confident decisions and reduced risk at every stage of development

Optimize RNAs for what matters

Traditional RNA design approaches often optimize for a single objective, such as yield or expression, creating downstream tradeoffs in stability and performance. eNAVIGATE applies multi-objective optimization using machine learning models trained on over 29,000 data points to balance manufacturability, expression, and stability for your specific target product profile.

Compare design tradeoffs across multiple performance dimensions. Four sequence designs for the same protein are shown, each tailored for a specific goal such as increased manufacturability or increased protein production.

Prototype fast. Scale with confidence.

We have optimized our in-house capabilities to support rapid RNA prototyping, including challenging constructs such as linear mRNAs greater than 5 kb. This enables fast, iterative design cycles until the optimal candidate is identified. Once a lead is selected, our network of validated manufacturing partners supports efficient and reliable scale-up.

Example fragment analyzer trace from an in-house RNA construct, demonstrating high yield and integrity suitable for iterative design and validation.

Unparalleled resolution for RNA quality

Our sequencing-first approach to RNA characterization and quality control provides actionable insights into RNA therapeutic biology that are not accessible with traditional assays. From identifying the precise sources of dsRNA impurities to mapping the effects of LNP formulation on RNA stability, our platform delivers the resolution needed to support confident development decisions.

This plot shows dsRNA levels across an RNA sequence, highlighting regions that contribute to dsRNA formation. Line thickness and color indicate each base’s relative contribution to dsRNA generation.

What our
partners say

"Eclipsebio’s analysis of RNA folding has provided valuable insights necessary to understand the impact of RNA sequence and chemical modifications on secondary structures…to help improve the design of our RNAs and rationalize our internal findings."

"At Acuitas we are interested in how modifications to LNP formulations can impact efficacy and stability. Eclipsebio’s eSHAPE assay has potentially revealed direct correlations between LNP composition and RNA secondary structure, further adding to our understanding of the mechanism of action for RNA-LNP systems."

Advance your RNA program with confidence

Our integrated design, prototyping, and sequencing-based analytics help teams make better decisions at every stage of RNA therapeutic development. Contact us to learn how Eclipsebio can support your program, whether you need targeted expertise or a full lab-in-the-loop solution.

Contact us
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Small Oligonucleotide Solutions https://eclipsebio.com/solutions/small-oligonucleotide-solutions/ Tue, 28 May 2024 08:25:18 +0000 https://eclipsebio.com/newdev/?post_type=solutions&p=10326

Accelerate Small Oligonucleotide Development

By integrating our cutting-edge technologies with our one-of-a-kind bioinformatics workflows, we have developed a unique platform for identifying effective targets for small oligonucleotides while screening for off-target effects. Learn more about our approach to small oligonucleotide design and validation below.

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Find accessible regions to target

To be effective, the oligonucleotide needs to be able to bind to its target. This binding can be limited by RNA structure, competing miRNA activity, and regulatory protein binding. Discover how our solutions provide a multiomic characterization of target genes.

Identify open RNA structures

With our eSHAPE technology we obtain validated data on the RNA secondary structure of a target gene, outperforming predictive algorithms that use the sequence alone. This structure information can be used to select target regions that are accessible and free of protein regulation.

Predicted structures do not include the contribution of cellular factors that can limit therapeutic binding. In contrast, eSHAPE provides direct evaluation of structure in the cellular environment.

Locate competing miRNA activity

With our miR-eCLIP+ technology, we directly measure where and how miRNAs bind across the transcriptome. This information can be used to identify competing miRNAs for siRNA treatments or to select miRNAs to target for anti-miRs.

Direct detection of miRNA binding in the 3’ UTR of E2F3. Each row is a different miRNA and peaks are where that specific miRNA binds.

Validate
therapeutic effects

Many therapeutics have failed once they enter clinical trials due to limited on-target effects or problematic off-target effects. With our solutions, we provide a holistic identification of on-target and off-target activity.

Identify off-target siRNA binding

Our miR-eCLIP+ technology directly measures both miRNA and siRNA binding, making it a powerful tool for examining where and how off-target activity is occurring. Off-target binding can occur through both seed-based binding and compensatory binding, and our technology distinguishes between these for siRNA optimization.

Validated siRNA off-target binding in the coding sequence of the gene COPRs. The siRNA was designed to target the gene APP.

Transcription and translation off-targets

Off-target effects are not limited to just the transcriptome, the translatome can be affected as well. With our eRibo Pro technology we measure both RNA expression (RNA-Seq) and translation (ribosome profiling), providing a more complete view of how a therapeutic affects cellular activity.

Identification of genes with differential RNA expression following treatment with an siRNA targeting APP. All off-target genes bind with compensatory binding, including the 5’ seed and part of the 3’ region of the siRNA.

What our
partners say

"Eclipsebio was the only company that could perform the robust siRNA off-target binding analysis we needed. Their experimental results provided important additional insights into our own internal findings. We look forward to continuing to work with Eclipsebio in the future."

"The miR-eCLIP technology is a robust and reproducible assay…Eclipsebio provides excellent data analysis support and outstanding technical service."

Slack Lab

Contact us today to learn how our team can help you

Our small oligonucleotide solutions enable the selection of optimal targets, coupled with the direct measurement of off-target binding. Contact us today to learn how our team can help you achieve your small oligonucleotide goals.

Contact us
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Small Molecule Solutions https://eclipsebio.com/solutions/small-molecules-solutions/ Tue, 28 May 2024 10:35:04 +0000 https://eclipsebio.com/newdev/?post_type=solutions&p=10333

Small Molecule Target Biology & Validation

Through the integration of our sequencing-first assays and advanced bioinformatics workflows, we enable precise identification of disease-relevant and druggable RNA targets for small molecule discovery. Our platform reveals accessible regulatory regions, target engagement, and downstream biological effects that guide confident hit and lead selection. From early target discovery through off-target and mechanism-of-action validation, we provide the multidimensional data needed to de-risk small molecule development and accelerate progress toward the clinic.

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Small Molecules

Effective small molecule therapeutics depend on selecting the right target and understanding how modulation impacts biology. Using sequencing-first technologies, we enable precise identification of disease-relevant RNA targets, validate mechanism of action, and detect transcriptome-wide off-target effects early. Our integrated approach provides a deeper view of target biology and therapeutic activity, helping teams make confident decisions and reduce downstream development risk.

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Target Identification

Mechanism-of-Action Validation

Off-Target Profiling

Contact us

Find accessible regions to target

To be effective, therapeutics need to target unique and druggable regions of disease-causing genes. Learn how our solutions provide a comprehensive review of target biology allowing for optimal therapeutic design.

Identify open RNA structures

With our eSHAPE technology we can obtain validated information on the RNA secondary structure of a target gene. This structure information can be used to select drug candidates that target druggable pockets that are free of competition from proteins and miRNAs. It can also be used to directly measure where small molecules bind to a target RNA.

Predicted structures do not include the contribution of cellular factors that can limit accessibility. eSHAPE provides direct evaluation of structure in the cellular environment.

Locate unique druggable regions

With different diseases, a given gene can use different UTRs (regulatory regions outside the coding sequence). Our End-Seq technology directly identifies where UTRs are located, supporting the identification of druggable regions specific to the disease.

A 5’ UTR is more active in cancerous samples and not in healthy samples, making it a potential target for selective regulation in cancer.

Find protein effectors

RNA-binding proteins have been implicated in ASO activity and are frequent targets for small molecules and aptamers. With our RBP-eCLIP technology, we identify where a given protein binds across the transcriptome revealing information on potential proteins to block or mimic with small molecule drugs and to confirm protein activity for ASO efficacy.

Browser track showing the binding of a protein involved in splicing in the intron of RTEL1.

Validate
therapeutic effects

Many therapeutics have failed once they enter clinical trials due to limited on-target effects or problematic off-target effects. With our solutions we provide a holistic identification of on-target and off-target activity.

Transcription and translation effects

With eRibo Pro we directly measure changes in RNA expression (RNA-Seq) and translation (ribosome profiling), allowing for a comprehensive view of how a therapeutic affects cellular activity.

Identification of a stall in translation following treatment with the drug PF-846.

What our
partners say

"End-Seq assays are an invaluable part of our target assessment process at Ribometrix. The data are robust and often reveal novel 5’ and 3’ ends that aren’t reflected in public databases. Having this knowledge significantly influences strategic decisions around target selection in our RNA-targeting drug development process."

"Eclipsebio was instrumental in helping us characterize a small molecule-RNA interaction discovered by our platform. The Eclipsebio team worked closely with us to adapt their eSHAPE workflow to suit our needs, promptly delivered a complete data package, and generously followed-up."

De-risk small molecule discovery early

We deliver comprehensive insight into target biology, mechanism of action, and off-target liabilities, enabling smarter target selection and more efficient small molecule development.

Contact us
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Basic Research Solutions https://eclipsebio.com/solutions/basic-research-solutions/ Tue, 28 May 2024 10:56:36 +0000 https://eclipsebio.com/newdev/?post_type=solutions&p=10338

RNA Biology Research Services

Deep insights into RNA biology require multiomic, data-rich approaches. To support academic researchers investigating key aspects of RNA biology we have developed a portfolio of cutting-edge capabilities that reveal RNA structure, translation, and more. Discover how below.

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Explore RNA across multiple dimensions

With our platform of orthogonal technologies, academic researchers can obtain a deeper understanding of RNA biology. We offer solutions to examine regulation, translation, and RNA structure all with in-depth and easy to understand analytical reports.

Determine RNA secondary structure

With our eSHAPE technology we can obtain validated measurements of the RNA secondary structure of a gene in different contexts, including directly after in vitro transcription or within the context of the cell.

Predicted structures do not include the contribution of cellular factors, such as proteins, that can limit accessibility. eSHAPE provides direct evaluation of structure in the cellular environment.

Explore transcription and translation

Within the same assay, eRibo Pro provides information on RNA expression (RNA-Seq) and translation (ribosome profiling). With this information, researchers can gain mechanistic insights into how an experimental change affects a system across multiple dimensions.

Torin 1 suppresses translation of specific genes (right) without affecting RNA levels (left).

Examine miRNA regulation

miRNAs are key regulators of RNA stability and translation. With our miR-eCLIP+ assay, we directly determine where and how miRNAs bind across the transcriptome. This provides unparalleled insights into miRNA biology and regulation across cell lines and tissues.

Direct detection of miRNA binding in the 3' UTR of E2F3. Each row is a different miRNA and peaks are where the miRNA binds.

Locate regulation by proteins

All RNAs in the cell are bound by proteins that regulate their stability, translation, and localization. With RBP-eCLIP, researchers can determine exactly where a given RNA-binding protein acts including what gene features it binds to and what sequence motifs it recognizes.

Browser tracks showing the binding of a splicing protein in the intron of RTEL1.

Map 5' and 3' UTRs

With different diseases, a given gene can use different UTRs (untranslated regulatory regions outside the coding sequence). Our End-Seq technology directly identifies where UTRs start and end, providing a fuller understanding of how genes are regulated in a given condition.

A unique 5’ UTR is active in cancerous samples and not in healthy samples, making it a potential target for selective regulation in cancer.

Detect RNA modifications

Complexes of RNA-binding proteins write and remove methylation on RNA transcripts, and this methylation has been implicated in a number of critical biological processes. With m6A-eCLIP, we provide per-base resolution of where methylated adenosines are located across the transcriptome.

Browser tracks showing the location of methylated adenosines on C2orf88.

What our
partners say

"My lab had a fantastic experience working with Eclipsebio. They made the experiment we sought to do approachable, and the staff was available to help and discuss the project every step of the way."

Attardi Lab

“The Eclipsebio team is awesome. They work closely with their customers to ensure the success of their experiments…the Eclipse team designed an experimental pipeline that led to the identification of hundreds of binding RNAs.”

Beliakova-Bethell Lab

Contact us today to learn how our team can help you

Our unique portfolio of proprietary technologies provides unparalleled insights into RNA biology. Contact us today to learn how our team can help you achieve your basic research goals.

Contact us
The post Basic Research Solutions first appeared on Eclipsebio.]]>
eVERSE https://eclipsebio.com/solutions/everse/ Sat, 22 Feb 2025 22:34:35 +0000 https://eclipsebio.com/?post_type=solutions&p=12910

RNA Training Data for AI Drug Discovery

Do you need high-quality data for AI-powered drug discovery? Leveraging our years of experience in profiling key aspects of RNA biology, eVERSE provides the data needed for target discovery and drug design.

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Multidimensional data for AI success

Developing next-generation therapeutics with AI/ML demands data that’s reproducible and captures every key aspect of RNA biology. With eVERSE, our partners gain access to a comprehensive suite of RNA profiling technologies—from revealing secondary structures that influence siRNA potency to quantifying translation rates critical for RNA vaccine efficacy. Discover below how eVERSE delivers the essential data for AI-driven success.

High-quality reference data for all aspects of RNA biology

With eVERSE, we transform raw biological data into high-quality, AI-ready datasets for RNA-based medicines, small oligonucleotides, and small molecule therapeutics. Our sequencing assays and bioinformatics workflows capture RNA biology’s complexities, enabling precise AI model training.

RNA secondary structure revealed

eSHAPE directly measures RNA secondary structure in buffer conditions and in cells, providing the data needed to train AI models to:

  • Improve RNA therapeutic stability by improving structure predictions
  • Design effective siRNAs by targeting accessible regions
  • Develop small molecule therapies that target druggable pockets

eSHAPE-supported structure of a gene in the context of cellular factors such as RNA-binding proteins.

Discover the UTR landscape

UTRs are uniquely expressed in disease states and regulate the stability and translation of genes. By including data on UTR usage into AI models, drug developers can improve:

  • Cell-specific regulation of RNA-based therapies
  • The selection of small molecules against disease-specific targets
  • The design of small oligonucleotides to specific isoforms

A 5’ UTR is more active in cancerous samples and not in healthy samples, making it a potential target for selective regulation in cancer.

Map miRNA binding

miRNAs regulate the stability of RNA molecules and are implicated in a number of diseases. Incorporation of miRNA data into AI models allows drug developers to:

  • Fine-tune RNA activity into specific cell types
  • Design ASOs to limit miRNA binding
  • Avoid competition for siRNA therapies

Direct detection of miRNA binding in the 3' UTR of E2F3. Each row is a different miRNA. Peaks are where that specific miRNA binds.

Need other data?

If your AI/ML models need specific data from one of our assays, our team can generate reproducible measurements with any of our technologies. Contact us to learn more and get the training data needed for AI success.

Request data

What our
partners say

"Eclipsebio has been an invaluable partner to Deep Genomics. They've helped us generate massive miRNA-related datasets for training AI models, and have designed and conducted bespoke assays to illuminate the mechanism underlying some of our lead therapeutic compounds."

"End-Seq assays are an invaluable part of our target assessment process at Ribometrix. The data are robust and often reveal novel 5’ and 3’ ends that aren’t reflected in public databases. Having this knowledge significantly influences strategic decisions around target selection in our RNA-targeting drug development process."

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