Thermo Fisher Nucleic Acid Synthesis Reagents for Oligo Manufacturing

You’re building DNA/RNA oligos that need to work the first time—this Collection brings Thermo Fisher’s core reagents together in one place so you can choose quickly and order confidently. As a distributor, Iright supplies a broad range of genuine Thermo Fisher phosphoramidites, CPG supports, labels, cycle reagents, and QC resources with responsive documentation support.

What This Nucleic Acid Synthesis Collection Covers

This page maps every step of the oligo workflow—from monomers and supports to modification, purification, and QC—so you can match reagents to application without guesswork. You’ll find overview guidance, best-fit use cases, and a shortlist of verified Thermo Fisher part numbers, with Iright on hand to quote, bundle, and provide certificates where needed.

Core Oligo Synthesis Reagents: DNA/RNA Phosphoramidites, CPG, Cycle Kits

Choosing the right building blocks and supports determines yield, purity, and downstream performance. Use the notes below to align DNA/RNA phosphoramidites, CPG supports, and cycle reagents with your platform and target purity before you scale.

• DNA/RNA phosphoramidites. Thermo Fisher offers standard DNA and RNA amidites alongside 2′-modified and specialty chemistries for different instruments and use levels, from RUO to process development. Families include DNA, RNA, dye-labeled, structural, linkers/spacers, and succinates.

• CPG supports (controlled-pore glass). Select pore size, loading, and linkage (universal vs nucleoside-specific) to balance synthesis scale and purity. Ready-to-use CPG columns are available for common scales.

• Cycle chemistry. Ensure activator, oxidizer/sulfurizing, capping A/B, and deprotection conditions are compatible with your modifications and dyes. (Instrument-specific bottle formats exist for Expedite and MerMade systems.)

Modified Oligos: Fluorophores, Quenchers (BHQ/MGB), and Functional Groups

Assay sensitivity and specificity often hinge on the label/quencher pair or functional handle. This section helps you align labeling choices with optical setup, hybridization behavior, and storage constraints.

Typical options include fluorophores (6-FAM, HEX, TET, Cy-series), quenchers (BHQ/MGB), and functional groups (biotin, amine, thiol, azide, phosphate). Match emission/absorption to your qPCR instrument or imager and consider label position (5′, internal, 3′) to maintain Tm and avoid spectral bleed. (6-FAM dye phosphoramidite for 5′ labeling is a staple in probe design.)

Oligo Purification and QC: Desalt, OPC, HPLC/PAGE, and Certificates

Purity requirements vary by application, so calibrate purification and documentation to the assay’s risk tolerance. As purity rises, so do time and cost—choose the lowest level that reliably meets performance targets.

• Desalt/OPC for routine primers and screening.

• HPLC (RP/IEC) or PAGE for qPCR/diagnostic-style probes and short, highly modified sequences.

• QC & docs. Retain UV data, chromatograms, and certificate of analysis (CoA) for audits and method transfer; Thermo Fisher provides batch-specific CoAs for core items like nucleoside amidites.

Applications Map: PCR/qPCR Probes, Cloning, NGS Adapters, and Beyond

With the chemistry landscape in place, map reagents to common methods to avoid re-optimization later. The pointers below emphasize compatibility and purity rather than exhaustive recipes.

• PCR/qPCR & digital PCR. Use dye/quencher pairs with minimal spectral overlap and consider HPLC-purified probes for consistent baselines. 6-FAM/BHQ-1 is a common starting point; MGB can tighten melting behavior for shorter probes.

• Cloning & gene expression. Standard DNA amidites and universal CPG supports are typically sufficient; confirm deprotection conditions for sensitive internal motifs.

• NGS adapters/indexing. Favor higher purity and verified phosphorylation as required; document lot-level QC to simplify troubleshooting and validation.

• Custom modalities (ASO/siRNA, structural studies). Leverage specialty/structural amidites and 2′-modified chemistries; align sulfurization and deprotection to preserve modifications.

Popular Families: Phosphoramidites, CPG Supports, Probes, and Deprotection

To speed browsing, here are high-interest Thermo Fisher families you’ll often combine in one order. Use them as anchor categories for internal navigation and filtering.

• DNA Phosphoramidites (standard bases; bottle formats for Expedite/MerMade platforms). 

• RNA & 2′-Modified Phosphoramidites (for RUO through process development).

• Dye-Labeled Phosphoramidites (e.g., 6-FAM for 5′ attachment).

• Structural/Linker/Spacer Amidites (optimize length/geometry of probes and conjugates).

• CPG Supports/Columns (universal vs nucleoside-specific; common 500 Å pore size).

Quick Buyer’s Guide: Match Modifications, Supports, and Purity to Use Case

Use this cheat-sheet to align decisions across application, purity, and documentation. Confirm details in your SOP and instrument manual before committing to scale.

At-a-glance guide

• qPCR probes (TaqMan-style): 6-FAM (or HEX/TET) + BHQ/MGB; HPLC-purified; retain CoA and chromatograms.

• Routine PCR primers: standard DNA amidites; desalt/OPC; universal CPG; instrument-compatible bottles (Expedite/MerMade).

• NGS adapters/indexes: higher purity (HPLC/PAGE as needed); ensure terminal phosphorylation if required; document lot and method version.

• Functionalized capture oligos: biotin/amine/thiol/azide handles; match linker length to binding geometry; store protected from light when labeled.

Featured SKUs (Verified Thermo Fisher Part Numbers)

Below are representative items frequently used in oligo workflows. Part numbers and product names are taken from Thermo Fisher sources; verify final availability/region before checkout.

Nucleic Acid Synthesis FAQs: Selection, Compatibility, and Storage

This quick FAQ removes common blockers before you order. If your case is edge-conditioned (e.g., unusual internal labels or novel linkers), contact Iright for a method review.

Q1. Which purification level should I choose for qPCR probes?
For most 5′-dye/3′-quencher probes, HPLC purification is recommended to stabilize baselines and Ct values; PAGE may be selected for very short or highly modified probes that benefit from size resolution. Keep batch-level QC for traceability. 

Q2. How do I pick fluorophore/quencher pairs?
Start with your instrument’s optics and multiplex plan. 6-FAM/BHQ-1 is a common baseline; expand with HEX/TET or Cy channels while avoiding spectral crosstalk. Consider MGB for shorter probes with tighter melting behavior.

Q3. Will these reagents work with my synthesizer?
Thermo Fisher ships specific bottle formats and compatibility notes for Expedite and MerMade platforms; always match bottle thread/volume and verify cycle reagents against your SOP.

Q4. What documents ship with my order?
CoAs and product specifications are available for key amidites and supports. Retain lot numbers and chromatograms for audits and method transfer.

Q5. Any storage cautions for dye-labeled amidites and CPG?
Protect light-sensitive dyes; store desiccated and at recommended temperatures. Bring reagents to room temperature before opening to minimize condensation; reseal promptly after use.