Custom DNA and RNA oligonucleotides incorporating 5mC, 5hmC, 5fC, 5caC, 5hmU, m6dA/m6A, zebularine and specialty base analogs for methylation analysis, DNA repair, protein-binding studies and assay development.
Bio-Synthesis manufactures custom oligonucleotides containing epigenetic base modifications and nucleobase analogs for methylation research, DNA repair studies, transcription regulation analysis, protein-binding assays, sequencing controls and assay development.
Modified bases can be incorporated into DNA oligos, RNA oligos, primers, probes, synthetic controls and reference standards. Our team can help evaluate sequence context, analog placement, synthesis compatibility, purification approach and analytical QC requirements.
Common programs include bisulfite sequencing controls, methylation-sensitive PCR controls, CpG methylation models, DNA repair substrates, protein-DNA binding substrates and NGS or qPCR assay standards.
Use the tabs to compare modified-base categories, biological applications and design considerations without duplicating a separate reference table.
5mC, 5hmC, 5fC, 5caC
8-oxoG, dU, abasic models
inosine, universal bases
m6dA, m6A, zebularine, 7-deaza
Epigenetic and base analog oligos are most useful when the modification is selected around the assay mechanism, biological model and detection platform.
◎ Methylation Analysis
◆ DNA Damage & Repair
✦ Protein Binding
● Sequencing Controls
Common modified bases for methylation and hydroxymethylation assay controls.
Recommended Bases
5mC, 5hmC, 5fC and 5caC for methylation-state modeling.
Typical Uses
Bisulfite sequencing controls, MSP/qPCR controls and CpG methylation standards.
Design Focus
Define CpG position, strand orientation, amplicon region and control concentration.
Modified base substrates for lesion, repair and polymerase studies.
8-oxoG, dU, abasic-site models and lesion analogs.
Base-excision repair, glycosylase assays, lesion bypass and damage-response studies.
Place lesions at defined positions and select duplex, hairpin or probe formats
Defined modified-base oligos for protein-DNA and protein-RNA interaction studies.
5mC, 5hmC, halogenated bases, fluorescent bases and affinity-tagged analogs.
EMSA, pull-down, transcription-factor binding, methyl-binding protein assays.
Preserve binding motif, spacing, duplex context and detection handle placement.
Synthetic reference standards for sequencing, PCR and assay validation.
ssDNA, dsDNA, primers, probes, amplicon controls and spike-in standards.
NGS controls, qPCR controls, methylation panels and assay calibration.
Match target region, modification state, concentration, purification and QC package.
Modified bases can be designed into multiple oligonucleotide formats depending on your assay and downstream readout.
Position-specific modified-base DNA oligos for methylation, repair and binding studies.
RNA analog-containing oligos for epitranscriptomic and RNA-protein studies when compatible.
Modified-base primers, probes and assay oligos for PCR, qPCR and hybridization workflows.
Synthetic standards, spike-ins and reference oligos for sequencing and assay validation.
A successful modified-base oligo project connects the biological question with sequence design, analog placement, synthesis compatibility, purification and analytical QC.
Select methylated, oxidized, lesion, wobble or specialty base analogs.
Define base position, strand, duplex context, assay region and format.
Incorporate modified bases using compatible solid-phase oligo chemistry.
Use desalting, HPLC, PAGE or project-specific purification.
Confirm purity and identity using analytical methods appropriate for the construct.
Provide final oligo, documentation, concentration and packaging format.
Bio-Synthesis supports analytical characterization strategies for modified-base oligonucleotides using methods that evaluate purity, identity, sequence-specific requirements and final release attributes.
Modified bases can affect chromatography, ionization, stability and assay performance. QC should be selected around the sequence, modification type and final use.
Purity assessment and method-specific chromatographic profile.
Mass identity confirmation where compatible with sequence and modification.
Size and purity review for selected oligo lengths and formats.
CoA, concentration, yield and project-specific release information.
Sequence Context
Some analogs require special placement and synthesis review.
Duplex Controls
Complementary strand, annealing and duplex format available when needed.
Assay Readiness
Optional packaging, plates, concentration normalization and reference standards.
Modified-base oligos require controlled synthesis, careful purification and analytical release methods matched to the modification and application.
Bio-Synthesis supports custom synthesis, conjugation, purification, analytical characterization and documentation for delivery-enabled oligonucleotide programs.
Connect modified-base design with related Bio-Synthesis capabilities for DNA, RNA, probes, controls and analytical support.
Custom DNA synthesis with modified bases, purification and QC options.
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DNA base analog catalog and custom base-level chemistry support.
RNA base analogs for epitranscriptomics, probes and RNA structure studies.
Custom probes, primers and assay oligos for quantitative PCR workflows.
Degenerate bases, mixed-base oligos and synthetic controls for sequencing workflows.
Aptamer synthesis, modification and binding-substrate design support.
Modified DNA oligos with base, sugar, backbone, spacer and labeling options.
Release testing, purity, identity and analytical QC support for modified oligos.
Evaluate base analog, position, oligo length, duplex context and purification strategy.
HPLC/UPLC, LC-MS, PAGE, CoA, concentration and custom documentation support.
Use this section to support scientific credibility while keeping the page focused on modified-base design, synthesis and analytical verification.
Suggested page note:Literature references are provided for scientific background. Final modified-base oligonucleotide design should be evaluated within the sequence, modification position, synthesis scale, purification method, analytical QC and application model.
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