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DNA & RNA Oligonucleotide Purification Services

PAGERP-HPLCIE-HPLCDual HPLCRNase-FreeIn Vivo-Grade Sterile Options
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Overview Method Guide Methods DNA Pricing RNA Pricing Related Services FAQ Contact
Overview

Purification strategies matched to sequence complexity and downstream use

Oligonucleotide synthesis produces a mixture of full-length product and truncated failure sequences. As oligo length increases, the percentage of full-length material decreases. Purification removes impurities and delivers a more defined product, improving performance, reducing background and increasing reproducibility.

Bio-Synthesis supports DNA and RNA purification workflows for routine PCR primers, qPCR probes, cloning, gene assembly, CRISPR repair templates, antisense oligos, siRNA, gRNA and in vivo research oligonucleotides. Available purification options include PAGE, RP-HPLC, IE-HPLC, dual HPLC, RNase-free workflows and sterile in vivo-grade processing for research applications requiring higher purity and analytical consistency.

PCR

Routine Research

Cost-effective purification options for PCR, qPCR, sequencing and genotyping workflows.

LONG

Cloning & Long Oligos

Higher-stringency PAGE and HPLC purification for long oligos, gene assembly and CRISPR donors.

RNA

RNA & In Vivo Work

RNase-free and in vivo-grade options with sterile filtration and sodium counterion exchange.

Research use only: All oligos are for research use only and are not intended for diagnostic or therapeutic use.
Application Guidance

Choose the right purification method

Use this simplified guide to select a practical purification level based on oligo type and downstream application.

Application Recommended Purification Why it fits
Routine PCR / sequencing primers Desalt or RP-HPLC Balances cost, turnaround and purity for standard amplification.
qPCR probes / dye-labeled oligos RP-HPLC or IE-HPLC Improves separation of dye, quencher and truncated products.
Long DNA / cloning / gene assembly PAGE, IE-HPLC or Dual HPLC Reduces truncated sequences that interfere with assembly or cloning.
CRISPR HDR donors / ssDNA PAGE or Dual HPLC Supports higher full-length purity for editing workflows.
siRNA, antisense, sgRNA or modified RNA RNase-Free HPLC or Dual HPLC Protects RNA integrity while improving purity.
In vivo / ex vivo studies In Vivo Grade Sterile + Na⁺ Includes sterile filtration, sodium salt form and low-endotoxin workflow.
Purification Methods

DNA and RNA purification workflows

In vivo badge: Sterile + Na⁺ indicates 0.22 μm sterile filtration and Na⁺ counterion exchange in a low-endotoxin, nuclease-controlled workflow.

DNA Oligo Purification

  • PAGE – Size-based separation. Typical purity ~95–99%. Ideal for long oligos, cloning, gene assembly and CRISPR donors.
  • RP-HPLC – Reverse-phase chromatography. Workhorse purification for short to medium DNA oligos and many primers.
  • IE-HPLC – Charge/length separation. Useful for longer, high-GC or structured sequences.
  • Dual HPLC – Two-step RP + IE purification for challenging sequences and sensitive assays.
  • Dual PAGE/HPLC – Maximal removal of truncated and chemically modified species.
  • RNase-Free HPLC – For DNA templates used in transcription or RNA workflows.
  • In Vivo GF Sterile + Na⁺ – Buffer exchange and polishing for in vivo or ex vivo research oligos.
  • In Vivo HPLC Sterile + Na⁺ – High-stringency HPLC for in vivo-grade DNA oligos, research use only.

RNA Oligo Purification

  • RNase-Free PAGE – High-resolution gel purification for long RNAs, gRNAs, antisense oligos and critical functional assays.
  • RNase-Free HPLC – Reverse-phase HPLC with RNase-free handling for siRNA and modified RNA.
  • RNase-Free IE-HPLC – Length/charge separation for longer or high-GC RNA sequences.
  • RNase-Free Dual HPLC – RP + IE HPLC for demanding RNA applications.
  • RNase-Free In Vivo GF Sterile + Na⁺ – Buffer exchange and sterile filtration for RNA intended for cell delivery or animal work.
  • In Vivo RNase-Free HPLC Sterile + Na⁺ – Low-endotoxin RNase-free HPLC workflow.
  • In Vivo RNase-Free Dual HPLC Sterile + Na⁺ – Highest-purity sterile RNA option for in vivo and ex vivo 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
100 nmole $75.00 $50.00 $50.00 $105.00 n/a $95.00 $95.00
250 nmole $105.00 $85.00 $85.00 $155.00 $165.00 $125.00 $125.00
1 µmole $165.00 $95.00 $95.00 $235.00 $285.00 $185.00 $185.00
2 µmole $250.00 $170.00 $170.00 $385.00 $495.00 $265.00 Inquire
5 µmole $650.00 $305.00 $305.00 $625.00 $1,150.00 $405.00 Inquire
10 µmole $1,300.00 $475.00 $475.00 $960.00 $1,750.00 $655.00 Inquire
15 µmole $1,750.00 $695.00 $695.00 $1,260.00 Inquire $895.00 Inquire

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 $1,125.0
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

Technical notes for oligonucleotide purification planning

These practical notes summarize when higher-purity workflows are recommended, what in vivo-grade processing adds, and how purity selection affects final yield.

When to Use Higher Purity

  • Oligos longer than 40–50 bases or sequences with complex secondary structure.
  • Cloning, mutagenesis, long-range PCR and gene assembly workflows.
  • Fluorescently labeled probes, quenched probes and dual-labeled qPCR assays.
  • CRISPR guides, HDR templates, antisense oligos and siRNA applications.

In Vivo-Grade Considerations

  • Additional attention to residual salts, organic solvents and small-molecule impurities.
  • Sterile 0.22 μm filtration of the final oligonucleotide product.
  • Low-endotoxin workflow for cell culture, ex vivo and animal study use.
  • Recommended for oligos used directly in vivo or in functional delivery assays.

Yield vs Purity

  • Higher purity typically reduces final yield because truncated species are removed.
  • Sequence composition, GC content, homopolymers and hairpins can also affect yield.
  • Dual HPLC, PAGE/HPLC and in vivo-grade workflows generally provide lower yield but cleaner product.
  • Select the lowest purification level that still meets assay requirements to balance cost, yield and performance.

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.
More FAQ'sAll FAQ's
Contact & Quote Request

Need help selecting an oligo purification strategy?

For the fastest review, share your oligo type, sequence length, modifications, desired scale, purification target and intended application. Our team can recommend the most suitable purification method and provide a detailed quote.
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Email: Info@Biosyn.com
Phone: 800-227-0627 (US/CAN)
Phone: +001-972-420-8505 (INT)

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Greetings, Researchers,

Please be advised that any information, guidelines, write-ups, and oral/video/graphic content on our website are intended solely as general guidelines.
It is the researcher's sole responsibility to conduct thorough research on the design of products intended for their experiments before submitting
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