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Custom Modified Oligos Synthesis Service

Custom Modified Oligonucleotides are synthetic nucleic acids that incorporate non-natural chemical groups, fluorescent dyes, quenchers, linkers, or backbone stabilizing modifications. These specialized molecules are vital tools in cutting-edge research, serving as advanced molecular probes, therapeutic agents (e.g., antisense), aptamers, and components of sophisticated nanotechnology and biosensors. The successful synthesis of these complex molecules requires specialized chemistry and rigorous purification protocols.

CD Biosynsis offers a comprehensive Custom Modified Oligos Synthesis Service , providing access to one of the industry's broadest catalogs of modifications, including over 100 fluorescent labels, quenchers, non-standard bases, conjugation linkers (e.g., thiols, amines), and stabilizing chemistries (e.g., LNA, PTO). Leveraging advanced solid-phase synthesis and mandatory HPLC purification, we guarantee the highest coupling efficiency and purity for your complex modified oligos, accelerating your diagnostic, therapeutic, and bioconjugation projects.

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Highlights Applications Products & Solutions Workflow FAQ

Highlights

Our expertise in complex chemical synthesis ensures reliable delivery of challenging modified oligos:

  • Broad Modification Catalog: Access to over 500 catalog and non-catalog modifications, including functional groups (NH _2, SH), complex fluorophores (ATTO, Alexa Fluor), and exotic bases.
  • Dual/Multiple Labeling: Expertise in synthesizing oligos with multiple labels (e.g., two different dyes, or a dye/quencher pair) at precise internal or terminal positions, verified by dual Mass Spectrometry.
  • Stabilizing Chemistries: Routine synthesis of oligos incorporating LNA (Locked Nucleic Acid), 2'-O-Methyl, and Phosphorothioate (PTO) linkages for enhanced nuclease resistance and binding affinity.
  • Guaranteed High Purity: Mandatory HPLC or PAGE purification for all modified oligos to ensure the functional integrity and high activity of the final product.

Applications

Modified oligos are driving innovation in diagnostics, therapeutics, and materials science:

Therapeutic Oligonucleotides

           

Synthesis of siRNA, ASO (Antisense Oligos), and miRNA inhibitors with backbone modifications (PTO, 2'-O-Me) for stability and delivery.

Aptamers & Bioconjugation

Production of high-affinity aptamers and oligos with reactive functional groups (Thiol, Azide) for conjugation to proteins, nanoparticles, or surfaces.

Biosensors & Nanotechnology

Synthesis of fluorescently labeled oligos and specialized structural oligos (e.g., sticky-end, hairpins) for DNA origami and molecular switches.

FRET & Single-Molecule Imaging

Precision synthesis of oligos with specific FRET pairs for distance measurement and high-brightness dyes for single-molecule microscopy (SMF).

Products & Solutions

Our expertise covers the most complex and advanced oligonucleotide modifications available.

Fluorescent & Quencher Labeling

Terminal or internal labeling with FAM, Cy3/Cy5, Alexa Fluor dyes, and BHQ quenchers, with confirmed high coupling efficiency.

Backbone & Sugar Modifications (ASO Grade)

Incorporation of PTO (Phosphorothioate), LNA, 2'-O-Methyl RNA, and Morpholino groups for therapeutic applications.

Reactive Functional Groups

Attachment of Amino (NH _2), Thiol (SH), Biotin, Phosphate, and Click Chemistry (Azide/Alkyne) linkers for covalent conjugation.

Non-Standard & Labeling Bases

Synthesis incorporating Inosine, Locked Nucleic Acid (LNA), Deaza bases, and various T and A internal labels.

Ultra-High Purity (PAGE & Dual HPLC)

Provision of ultra-pure oligos required for structure determination, X-ray crystallography, and NMR applications.

Workflow

Our specialized workflow is tailored to accommodate the unique challenges of complex chemical modifications:

  • Design Review and Chemical Planning: Thorough technical review of the desired modification, ensuring chemical compatibility. Complex linkers and multiple modifications require specific synthesis cycles and deprotection protocols.
  • Specialized Synthesis Cycles: Oligo synthesis is executed using precise coupling times and conditions specific to the non-standard phosphoramidites (e.g., LNA, PTO). Multiple internal modifications are added sequentially.
  • Rigorous Purification: All modified oligos require HPLC or PAGE purification to isolate the desired full-length, fully modified product from side products, which often have co-eluting characteristics.
  • Advanced Quality Control: QC includes Mass Spectrometry (to verify the exact molecular weight of the modification) and analytical HPLC (to confirm purity). For fluorescent oligos, the labeling efficiency is also confirmed.
  • Final Delivery & Consultation: Products are shipped with detailed documentation (COA, MS/HPLC traces) and specialized instructions for handling and storage, given the unique chemical properties.

We provide unparalleled support for your chemically complex projects:

  • Guaranteed Functionality: High purity ensures that the functional group (e.g., Thiol, Dye) is attached to the full-length oligo, maximizing downstream reaction success.
  • Complex Chemistry Success: Our R&D team regularly synthesizes novel or highly challenging modification combinations that are rejected by automated online synthesis systems.
  • Therapeutic Grade Preparation: Expertise in producing ASO-grade oligos with PTO backbones and other stabilizing modifications suitable for preclinical development.
  • Confidentiality Assured: Strict protection of all proprietary chemical structures and sequences submitted for custom modification projects.

FAQ (Frequently Asked Questions)

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Why do modified oligos require HPLC over standard purification?

Chemical modifications, particularly bulky dyes and functional groups, significantly alter the oligo's chemical properties. HPLC is essential to separate the fully modified, full-length product from both unmodified and truncated sequences that still carry the modification, which can co-migrate with the desired product in standard methods.

What is the lead time for a custom modified oligo?

The timeline varies significantly based on the modification type (e.g., standard FAM is faster than PTO backbone). Simple modifications typically require 5-7 business days, while highly complex or non-catalog modifications may require 2-4 weeks due to specialized synthesis and extended QC.

Can I combine multiple different modifications on one oligo?

Yes. We routinely synthesize oligos with complex combinations, such as an amino group on the 5' end, a BHQ quencher internally, and PTO linkages throughout the backbone. This requires specialized, multi-step synthesis and is handled via custom quote.

Do you offer conjugation of oligos to proteins or nanoparticles?

Yes, as an extended service. We can synthesize the oligo with the necessary reactive group (Thiol, Azide), and then perform the covalent bioconjugation reaction to a client-provided target (Antibody, BSA, Gold Nanoparticle).

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