High-purity circular DNA and RNA oligonucleotides engineered for rolling circle amplification, padlock probes, molecular inversion probes, in situ assays, biosensors, NGS workflows and synthetic circular RNA research.
Circular oligonucleotides are single-stranded DNA or RNA molecules whose 5′ and 3′ ends are covalently joined to form a closed ring. By eliminating free termini, circular oligos can improve resistance to exonuclease degradation and support highly specific probe-based and amplification-based workflows.
Bio-Synthesis supports custom circular oligonucleotide synthesis from design review through precursor synthesis, circularization, purification, analytical QC and delivery. Projects may include simple circular DNA/RNA, dumbbell oligonucleotides, padlock probes, molecular inversion probes, RCA templates, labeled circular probes and custom modified constructs.
Circularization changes the oligo from a linear strand into a covalently closed architecture. That structural change is useful when assays need stronger nuclease resistance, ligation-dependent specificity, continuous polymerase extension or spatially localized signal amplification.
Closed circular structures remove free ends, increasing resistance to exonuclease digestion and improving functional lifetime in nuclease-rich environments.
Circular templates can support rolling circle amplification, enabling long concatemeric products and sensitive detection formats.
Padlock probes and MIPs use target-dependent ligation, helping distinguish closely related targets, SNPs and low-abundance sequences.
Designs can include DNA, RNA, dumbbell structures, fluorophores, quenchers, spacers, affinity tags and click-compatible handles.
This section should stay on the page because it explains the science and benefits behind the service. The redesign presents the same information as a technology selector instead of long text blocks.
circle • dumbbell • padlock
enzymatic • click closure
stability • specificity • RCA
scale • purification • QC
Enzymatic ligation can create a native phosphodiester junction. It is commonly selected for padlock probes, MIPs and RCA workflows where polymerase compatibility is important.
Click circularization can provide robust chemical closure when enzyme-free methods or bioorthogonal handles are preferred.
Closed-loop topology can reduce susceptibility to exonucleases compared with linear oligos.
Circular templates support continuous extension by strand-displacing polymerases in RCA.
Target-dependent ligation strategies help improve specificity in detection and genotyping assays.
Instead of another wall of cards, this section prioritizes the highest-value use cases and groups the rest as supporting applications.
Circular templates and ligation-dependent probes are especially useful when the assay needs strong signal generation, high specificity, and spatially localized detection.
Molecular Inversion ProbesTarget capture, gap-fill, circularization and sequencing-compatible enrichment workflows.
Synthetic circRNA ResearchCircular RNA controls and templates where sequence, length and modification feasibility allow.
Biosensors & DNA NanotechnologyStable looped constructs for programmable assemblies, sensors and molecular devices.
Aptamer StabilizationClosed structures that may improve nuclease resistance and functional persistence.
The design section is now an interactive configuration lab. Customers can move through topology, closure chemistry, modifications and release requirements without scanning a page full of repeated cards.
Simple circular DNA/RNA works well for circular templates and stability studies. Padlock probes and molecular inversion probes are better when target-dependent ligation, gap-fill or sequencing workflows are required.
RCA templates, synthetic controls and closed-loop stability studies.
Stem-loop constructs for nuclease-resistant probes and research architectures.
Target-dependent ligation, SNP discrimination, in situ assays and target enrichment.
Enzymatic circularization is preferred when a native phosphodiester junction and polymerase compatibility are important. Click circularization is useful for enzyme-free closure, specialty handles or bioorthogonal designs.
Splint-assisted ligation, ligase-compatible termini and native junction design.
CuAAC or SPAAC approaches using azide, alkyne, DBCO or related handles.
Sequence structure, length, junction placement and modification burden should be reviewed before quoting.
Fluorophores, quenchers, affinity tags, spacers and reactive handles can be added, but each modification should be checked for circularization and purification compatibility.
FAM, Cy3, Cy5, TAMRA, HEX, ROX, quenchers and custom dye feasibility.
Biotin, digoxigenin, C3 spacers, HEG, PEG and project-specific linkers.
Amine, thiol, azide, alkyne, DBCO and other click-compatible modifications.
Complex circular constructs need release criteria that match the application. A padlock probe, RCA template and circular RNA control may require different QC evidence.
HPLC, PAGE or project-specific cleanup depending on length, structure and modifications.
Mass confirmation where compatible, circular/linear tracking and optional exonuclease challenge.
RCA or assay-specific validation can be added when performance evidence is needed.
A simpler visual workflow keeps the live-site process but reduces card fatigue across the page.
Sequence, topology, target region, modifications, scale and assay constraints.
Linear DNA/RNA synthesis with required termini, labels, spacers or handles.
Enzymatic ligation or click closure with method-matched cleanup.
Purity, identity, circularity checks, optional RCA validation and documentation.
Quote tip: For padlock probes and MIPs, include the target sequence, ligase/polymerase plan and readout method so arm design and junction placement can be reviewed.
Circular oligos require confirmation that the product is not just synthesized, but successfully circularized, purified and fit for the intended assay.
QC packages may include analytical HPLC, PAGE purification, LC-MS or MALDI-TOF identity confirmation, exonuclease resistance testing, OD260 quantitation, documentation and optional RCA performance checks.
Analytical HPLC, UPLC, PAGE or method-matched release testing for circularized products.
LC-MS or MALDI-TOF where size and chemistry permit, with documentation for release.
Exonuclease resistance testing can help distinguish circular material from linear precursor.
Optional RCA or assay-specific validation may be added when the application requires performance evidence.
Track precursor, ligation product and purification outcome to reduce ambiguity.
Padlock, MIP and RCA projects may require different release criteria.
CoA, concentration, purity, identity, format and custom documentation options.
The live-site case study is now presented as proof first, with the detailed sequence and analytical image available without overwhelming the page.
Project goal: synthesize a high-purity circular 91-mer single-stranded DNA oligonucleotide for gene expression and structural studies.
Gel mobility and ESI-MS data support the successful conversion from linear 91-mer ssDNA to circular ssDNA.
Gel image and ESI mass spectra from the 91-base circular ssDNA case study. Click to enlarge; close from the overlay.
Target 28128.1; observed 28126.9
Target 28110.1; observed 28111.1
>95% by denaturing PAGE
Circular ssDNA, 91 bases
This section turns the case study into a practical production recommendation, so visitors understand what Bio-Synthesis would typically evaluate, manufacture, purify, and release for a similar circular oligonucleotide project.
Design ligation-ready 91-mer ssDNA precursor with compatible termini.
Use enzymatic ligation when a native phosphodiester junction is preferred.
Use denaturing PAGE or HPLC to separate circular product from linear precursor and side products.
Confirm product by gel comparison, exonuclease resistance, and ESI-MS identity.
Deliver lyophilized circular ssDNA with purity, MW confirmation, and documentation.
Shows the mobility difference between linear and circular products and helps confirm successful circularization.
Confirms the expected molecular weight after ligation and supports identity release.
Removes unligated linear precursor, truncated oligos, and side products before delivery.
Use these internal links to connect circular oligo customers with synthesis, modification, scale-up and QC services that naturally support circular projects.
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Get help selecting topology, ligation method, labels and feasibility path.
Add purification, identity, circularity and functional validation options.
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