Methylated Oligonucleotides for Mutagenesis & Methylation

Purpose-built base lesions and methylated nucleobases for site-specific mutagenesis, DNA damage & repair studies, and epigenetic mechanism mapping. End-to-end design, synthesis, purification, and QC—from RUO to GMP-like supply.

Overview

Bio-Synthesis provides a curated portfolio of methylated oligonucleotides and oligonucleotide methylation chemistries—spanning mutagenesis and methylation base modifications—spanning methylated purines/pyrimidines, oxidative lesions, and deamination/depurination models—to enable precise placement of biologically relevant adducts within DNA. These site-specific lesions power studies in polymerase fidelity, BER/NER/MMR pathway mapping, epigenetic readouts, and structure–function analysis.

  • Application-driven design: lesion placement within CpG, promoters, hairpins; strand and spacing tuned to your assay.
  • Assay-ready formats: single oligos, validated duplexes, and plated libraries with barcodes & LIMS-ready labels.
  • Comprehensive QC: HPLC/UPLC, LC-MS, OD260, optional endotoxin; sequence + modification map on CoA.
45+ Years ISO 9001 / 13485 RUO → GMP-like Bench → Kilo

About Our Service — Custom Methylated Oligonucleotide Synthesis

1
Design & Consultation

Lesion choice, strand/position & sequence context; duplex/plate layout aligned to your readout.

Output: annotated sequence
map
2
Synthesis & Purification

Custom amidites/CPGs, specialty coupling; HPLC/UPLC or PAGE, desalting & lyophilization.

Output: purified oligo(s)
3
Analytics & Verification

LC-MS confirmation, duplex assembly & Tm; optional endotoxin and nuclease challenge.

Output: CoA + data pack
4
Scale & Documentation

µmol → multi-gram with RUO → GMP-like documentation aligned to your QMS.

Output: batch record &
documentation

Products — Methylated Oligonucleotides for Mutagenesis

Product / Modification Description Function Application Code
N6-Me-dA N6-methyl-deoxyadenosine (6mA) Epigenetic mark mimic Reader protein binding; restriction sensitivity [N6Me-dA]
N6-Ac-N6-Me-dA N6-acetyl-N6-methyl adenine analog H-bond disruption; reader challenge Epigenetic screens; structural assays [N6AcN6Me-dA]
1-Me-dA 1-methyl-deoxyadenosine Replication blocking lesion Polymerase bypass; repair preference [1Me-dA]
1-Me-dG 1-methyl-deoxyguanosine Base pairing perturbation Fidelity assays; alkylation repair models [1Me-dG]
O6-Me-dG O6-methyl-deoxyguanosine Mispairs with T; mutagenic MGMT activity; MMR assays [O6Me-dG]
O4-Me-dT O4-methyl-deoxythymidine Mispairs with G; mutagenic Alkylation damage models [O4Me-dT]
O2-Me-dT O2-methyl-deoxythymidine Minor groove methyl; polymerase bias Bypass & fidelity mapping [O2Me-dT]
N3-Me-dC N3-methyl-deoxycytidine Positively charged lesion; replication block BER/NER interplay; cytotoxic lesion studies [N3Me-dC]
Technical Notes
  • Controls: Include unmethylated and alternative-position methyl controls (e.g., O2-Me-dT vs O4-Me-dT) to deconvolute groove-specific effects.
  • MGMT assays: For O6-Me-dG, consider paired time-course with MGMT present/absent to quantify repair kinetics.

Product / Modification Description Function Application Code
8-oxo-dG 8-oxo-7,8-dihydro-dG Mispairs with A BER (OGG1/MUTYH) mapping [8oxo-dG]
8-oxo-dA 8-oxo-7,8-dihydro-dA Miscoding lesion Oxidative stress & BER assays [8oxo-dA]
Thymidine Glycol 5,6-dihydroxy-5,6-dihydro-dT Replication block NTHL1/NEIL pathway studies [ThyGly]
5-OH-dC 5-hydroxy-deoxycytidine Demethylation intermediate TET/BER turnover [5OH-dC]
5-OH-dU 5-hydroxy-deoxyuridine Transition bias BER substrate specificity [5OH-dU]
5-hm-dU 5-hydroxymethyl-deoxyuridine Hydroxymethyl U Epigenetic turnover; BER mapping [5hme-dU]
5-hm-dC 5-hydroxymethyl-deoxycytidine Oxidized 5mC analog Epigenetic dynamics; TET pathway [5hme-dC]
Technical Notes
  • Light/oxygen sensitivity: 8-oxo lesions and glycol forms are labile; aliquot and store at −20 °C; avoid prolonged light exposure.
  • Bypass setup: Place lesions 3–6 nt from primer terminus to detect arrest and misincorporation during primer extension.

Product / Modification Description Function Application Code
dU Deoxyuridine (U in DNA) Deamination mimic of dC UNG excision; mutational scanning [dU]
dI Deoxyinosine (hypoxanthine) Degenerate pairing (A/C/G/T) Randomization; mismatch controls [dI]
dX, 2′-deoxyXanthosine Deamination product of dG Mismatch pairing; repair substrate BER/MMR studies; fidelity [dX]
8-Amino-dA 8-amino-deoxyadenosine H-bond/stacking perturber Fidelity and structural probes [8Am-dA]
8-Amino-dG 8-amino-deoxyguanosine Conformational perturbation Structural and binding studies [8Am-dG]
Technical Notes
  • UNG workflows: Pair dU-containing templates with UNG treatment vs untreated controls to quantify excision and downstream polymerase effects.
  • Mixed libraries: dI enables degenerate positions (N) for scanning mutagenesis; combine with targeted lesions to probe context effects.

Technology & Design Considerations

Designing oligonucleotides with mutagenesis and methylation lesions requires balancing **biological relevance**, **stability**, and **assay compatibility**. Bio-Synthesis integrates advanced solid-phase synthesis, specialty amidites, and duplex assembly workflows to ensure your constructs model damage and epigenetic marks with precision.

Key Design Strategies
  • Lesion Placement: Embed lesions 3–6 nt from primer sites for bypass assays; seat within CpG islands or promoters for epigenetic readouts.
  • Context Control: Provide unmodified controls and sequence variants to isolate lesion-specific effects.
  • Duplex Assembly: Strand balancing and annealing protocols validated to protect labile lesions.
  • Scale Flexibility: From µmol pilot lots to multi-gram development batches, all supported by RUO → GMP-like documentation.
Technology Highlights
Custom Lesion Amidites Specialty Coupling Protocols HPLC/UPLC & LC-MS QC Annealed Duplex Delivery ISO 9001 / 13485

Need help choosing the right lesion or methylated base?

Tell us your readout (fidelity, repair, blocking, reader binding) and we’ll recommend placement, purification, and QC—then scale from mg to multi-gram.

FAQ

Which lesions best model alkylation vs oxidation?

Alkylation: O6-Me-dG, O4-Me-dT, O2-Me-dT, 1-Me-dA, 1-Me-dG, N3-Me-dC. Oxidation: 8-oxo-dG/dA, thymidine glycol, 5-OH-dC/dU, 5-hm-dC/dU.

Can you deliver duplexes or plates ready for screening?

AAAAYes—annealed duplexes, pooled libraries, or 96/384-well plates with barcodes. We can mirror your LIMS IDs and provide sequence maps

What QC is included?

HPLC/UPLC and LC-MS are standard. Optional PAGE, endotoxin testing, and custom LC-MS methods are available for labile lesions.

Do you support RUO to GMP-like documentation?

Yes—ISO 9001/13485 operations with RUO→GMP-like documentation, batch records, and traceability to support regulated workflows.

What are methylated oligonucleotides used for in mutagenesis?

Methylated oligonucleotides enable controlled base modifications (e.g., O6‑Me‑dG, O4‑Me‑dT, N3‑Me‑dC) to probe polymerase fidelity, mismatch repair, and lesion bypass.

Do you offer custom methylated oligonucleotide synthesis?

Yes. We provide custom oligonucleotide methylation and synthesis with HPLC/UPLC and LC‑MS QC, RUO→GMP‑like documentation, and annealed duplex delivery on request.

How do I choose between “methylated oligonucleotides” vs “oligonucleotide methylation” in design?

Use methylated oligonucleotides when specifying a finished reagent; use oligonucleotide methylation to discuss the process. We can help translate your assay needs into the right construct.

Speak to a Scientist

Please avoid confidential details; we can arrange an NDA if needed.

Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 40+ years of delivering high quality, fast and scalable synthetic biology solutions.