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DNA & RNA Oligonucleotide Purification Services

High-quality oligonucleotide purification services for DNA and RNA, including PAGE, RP-HPLC, IE-HPLC, dual HPLC, RNase-free, and sterile in vivo-grade workflows. Transparent pricing by scale to support routine primers, complex long oligos and in vivo research oligonucleotides.

Request a quote Overview DNA Purification Pricing RNA Purification Pricing
PDNA & RNA Oligos PAGE & HPLC Purification RNase-Free Workflows In Vivo-Grade Sterile Options
Overview Purification Methods DNA Pricing RNA Pricing Related Services Contact

Oligonucleotide Purification Overview

Oligonucleotide synthesis produces a mixture of full-length product and truncated “failure” sequences. Each coupling cycle is less than 100% efficient, so as the oligo length increases, the percentage of full-length material decreases. Oligonucleotide purification removes these impurities and delivers a more defined product, improving performance, reducing background, and increasing reproducibility. Our oligonucleotide purification services are designed for researchers who need reliable, high-purity DNA and RNA oligos for critical experiments.

We provide a complete purification portfolio for both DNA and RNA oligos, from workhorse PCR primers to long, heavily modified and in vivo-grade oligonucleotides. Our services cover PAGE, multiple HPLC modes, dual-purification for highest purity, RNase-free handling and sterile filtration for in vivo research applications.

Routine Research

Efficient oligonucleotide purification for PCR, qPCR, sequencing and genotyping primers, with options scaled to cost and turnaround requirements.

Cloning & Long Oligos

Higher stringency PAGE and HPLC oligonucleotide purification for long oligos, gene-assembly fragments, CRISPR repair templates and probes where truncated products are unacceptable.

In Vivo & RNA Work

RNase-free and in vivo-grade oligonucleotide purification workflows with sterile filtration and additional polishing for oligonucleotides destined for cell-based or animal studies.

All oligos are for research use only and are not intended for diagnostic or therapeutic use.

Oligonucleotide Purification Methods We Offer

In vivo Purification Badge: Sterile + Na⁺ indicates oligos that include 0.22 μm sterile filtration and Na⁺ counterion exchange (final sodium salt form), produced in a low-endotoxin, nuclease-controlled workflow for in vivo and ex vivo research.
DNA Oligo Purification
  • PAGE – Size-based separation on polyacrylamide gels. Typical purity ~95–99%. Ideal for long oligos, cloning, gene assembly and CRISPR donors.
  • RP-HPLC – Reverse-phase chromatography separating by hydrophobicity. Workhorse purification for short to medium DNA oligos and many unmodified primers.
  • IE-HPLC – Ion-exchange HPLC separating by charge/length. Excellent for longer or high-GC oligos and sequences with secondary structure.
  • Dual HPLC (RP + IE) – Two-step purification providing very high purity for challenging sequences and sensitive assays.
  • Dual PAGE/HPLC – PAGE followed by HPLC for maximal removal of truncated and chemically modified species.
  • RNase-Free HPLC – HPLC purification performed under RNase-controlled conditions, ideal for DNA templates used in transcription or RNA workflows.
  • In Vivo GF Sterile + Na⁺ – Gel-filtration–based polishing with extensive buffer exchange, 0.22 μm sterile filtration, and Na⁺ counterion exchange (final sodium salt form) in a low-endotoxin, nuclease-controlled workflow. Recommended for in vivo and ex vivo research oligos.
  • In Vivo HPLC Sterile + Na⁺ – High-stringency HPLC combined with 0.22 μm sterile filtration and Na⁺ counterion exchange, using a low-endotoxin, nuclease-controlled process for in vivo-grade DNA oligos (research use only, not GMP).
RNA Oligo Purification
  • RNase-Free PAGE – High-resolution gel purification under strictly RNase-free conditions. Recommended for long RNAs, gRNAs, antisense oligos and critical functional assays.
  • RNase-Free HPLC – Reverse-phase HPLC purification with full RNase-free handling. Ideal for short to medium RNA oligos, siRNA and many modified RNAs.
  • RNase-Free IE-HPLC – Ion-exchange HPLC performed under RNase-free conditions. Provides excellent length-based separation for longer or high-GC RNA sequences.
  • RNase-Free Dual HPLC (RP + IE) – Two-step RP- and IE-HPLC purification in an RNase-free workflow, delivering very high purity for demanding RNA applications.
  • RNase-Free In Vivo GF Sterile + Na⁺ – RNase-free gel filtration with extensive buffer exchange, 0.22 μm sterile filtration, and Na⁺ counterion exchange for RNA intended for cell delivery or animal work.
  • In Vivo RNase-Free HPLC Sterile + Na⁺ – High-stringency RNase-free HPLC combined with 0.22 μm sterile filtration and Na⁺ counterion exchange in a low-endotoxin workflow for in vivo research-grade RNA oligos.
  • In Vivo RNase-Free Dual HPLC Sterile + Na⁺ – Combined RP and IE HPLC under RNase-free, in vivo-grade conditions with 0.22 μm sterile filtration and Na⁺ counterion exchange, providing our highest-purity sterile RNA for in vivo and ex vivo delivery studies.

DNA Oligonucleotide Purification Pricing (per oligo, USD)

Product Scale PAGE RP-HPLC IE-HPLC Dual HPLC Dual PAGE/HPLC RNase-Free HPLC In vivo GF In vivo HPLC
100 nmole $75.00 $50.00 $50.00 $105.00 n/a $95.00 $95.00 $180.00
250 nmole $105.00 $85.00 $85.00 $155.00 $165.00 $125.00 $125.00 $210.00
1 µmole $165.00 $95.00 $95.00 $235.00 $285.00 $185.00 $185.00 $280.00
2 µmole $250.00 $170.00 $170.00 $385.00 $495.00 $265.00 $265.00 $495.00
5 µmole $650.00 $305.00 $305.00 $625.00 $1,150.00 $405.00 $405.00 $495.00
10 µmole $1,300.00 $475.00 $475.00 $960.00 $1,750.00 $655.00 $655.00 $795.00
15 µmole $1,750.00 $695.00 $695.00 $1,260.00 Inquire $895.00 $895.00 $1,095.00

Pricing is per oligo for purification only and does not include synthesis cost. All In vivo DNA options (In vivo GF and In vivo HPLC) include 0.22 μm sterile filtration and Na⁺ counterion exchange (final sodium salt form) in a low-endotoxin, nuclease-controlled workflow.

RNA Oligonucleotide Purification Pricing (per oligo, all prices in USD)

Product RNase-free PAGE RNase-free HPLC RNase-free IE-HPLC RNase-free Dual HPLC RNase-free In vivo GF In vivo RNase-free HPLC In vivo RNase-free Dual HPLC
100 nmol $125 $130 $130 $169.0 $228 n/a n/a
250 nmol $125 $130 $130 $169.0 $228 $417.00 $521.25
1.0 μmol $210 $205 $205 $266.5 $288 $550.00 $687.50
2.0 μmol $310 $325 $325 $422.5 $288 $730.00 $912.50
5.0 μmol $105 $418 $418 $543.4 $288 $925.00 $1,125.00
10 μmol $1,900 $632 $632 $821.6 $366 $1,055.00 $1,318.75
15 μmol Inquire $832 $832 $1,081.6 $500 $1,415.00 $1,768.75

All RNA purification services are performed in RNase-controlled environments. All In vivo RNA options (RNase-free In vivo GF, In vivo RNase-free HPLC, and In vivo RNase-free Dual HPLC) include 0.22 μm sterile filtration and Na⁺ counterion exchange for in vivo and ex vivo research applications (not GMP).

Technical Notes

When to Use Higher Purity
  • Oligos > 40–50 bases or with complex secondary structure.
  • Cloning, mutagenesis, long-range PCR and gene assembly.
  • Fluorescently labeled probes, quenched probes and dual-labeled qPCR assays.
  • CRISPR guides, HDR templates and antisense/siRNA oligos.
In Vivo-Grade Considerations
  • Additional attention to residual salts, organic solvents and small-molecule impurities.
  • Sterile 0.22 μm filtration of final product.
  • Low-endotoxin workflow for cell culture and animal studies.
  • Recommended for oligos used directly in vivo or ex vivo functional assays.
Yield vs Purity
  • Higher purity typically reduces final yield due to removal of truncated species.
  • Sequence composition (GC content, homopolymers, hairpins) also affects yield.
  • We recommend selecting the lowest purification level that still meets your assay requirements to balance cost and yield.

FAQ

What purification should I choose for my application?

The ideal oligonucleotide purification level depends on oligo length, modifications, complexity and assay sensitivity:

Short PCR / sequencing primers (≤35 nt)
• Desalt or RP-HPLC is usually sufficient.

qPCR probes / dye- or quencher-modified oligos
• RP-HPLC or IE-HPLC recommended; dual HPLC for high-sensitivity assays.

Long DNA (≥50–60 nt), gene assembly oligos
• PAGE or HPLC; dual HPLC for ≥80–100 nt.

CRISPR guides (gRNA), antisense, siRNA
• RNase-free HPLC or RNase-free dual HPLC.

HDR donors / ssDNA (80–200 nt)
• PAGE or dual HPLC for highest full-length purity.

In vivo / ex vivo delivery
• Select any method labeled Sterile + Na⁺.
• In vivo dual HPLC = highest-purity sterile option.

Still unsure? Contact us—we can recommend the minimum purification required for your assay.

What is the difference between RP-HPLC and cartridge purification?

Cartridge purification (“desalt”) only removes salts and small organic impurities. It does not remove truncated failure sequences.

RP-HPLC is true chromatography that separates by hydrophobicity, removing truncated sequences and providing much higher purity than cartridge cleanup.

Use cartridge only for simple primers; RP-HPLC is recommended for probes, long oligos, cloning, qPCR and CRISPR work.

What is the difference between RNase-free and in vivo-grade purification?

RNase-free focuses on protecting RNA from degradation during purification.
In vivo-grade adds:

• 0.22 μm sterile filtration
• Na⁺ counterion exchange (final sodium salt form)
• Low-endotoxin workflow

Choose in vivo-grade for cell delivery, ex vivo and in vivo research.

How much oligo will I receive after purification?

Higher purification removes truncated species and lowers final yield. Long sequences and modified oligos yield less.

Dual HPLC, PAGE/HPLC and all in vivo-grade workflows naturally give the lowest yields.

Does higher purification affect turnaround time?

Yes. PAGE, dual HPLC and in vivo-grade options may extend lead times.

Standard HPLC adds minimal time; dual workflows add more.

What QC is included with purified oligos, and what is optional?

Included: A260 measurement and calculated yield.
Optional Release QC: HPLC traces, mass spectrometry, and additional purity/identity tests.

How should I store and handle purified oligos?

Store lyophilized oligos at –20 °C. Aliquot reconstituted oligos to avoid freeze–thaw cycles. Use nuclease-free buffers for RNA.

Can I combine synthesis and purification into a single order?

Yes. Most customers order synthesis + purification together. Final quotes include synthesis, purification and any QC.

Looking for more detailed information on oligonucleotide purification?
Visit our comprehensive Tech Resource Library:

oligonucleotide purification tech resources

Request an Oligo Purification Quote

Share your oligo sequence type, length, modifications, desired purification level and scale. Our team will recommend the most suitable purification method and provide a detailed quote.

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