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Large-Scale DNA Synthesis

Scalable single-stranded and double-stranded DNA production with advanced DNA chemistry options, purification, release QC, documentation, and process-development support from feasibility through scale-up.

Large-Scale DNA Synthesis Overview

ISO 9001:2015 / ISO13485:2016 45+ Years of Expertise U.S.A. Facilities-Texas GLP/GMP-Aligned ssDNA up to 200 Bases dsDNA up to 200 bp Modified DNA Bases Modified Linkages Modified Sugars Purification & release QC Scale-Up Support

Bio-Synthesis provides large-scale DNA synthesis through an integrated manufacturing platform that combines process development, synthesis, purification, analytical testing, and scale-up under a controlled quality framework.

Our capabilities support both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) production, from milligram to gram-scale quantities, including complex and modified DNA constructs for research, diagnostic, and commercial applications.

Through extensive collaboration with customers, our workflows have been optimized to ensure scalability, reproducibility, and consistent quality across projects ranging from early-stage development to large-scale manufacturing.

Large-scale DNA synthesis workflow from design and feasibility to scale-up and delivery

From Process Development to Large-Scale Production

Each project follows a structured workflow designed to transition efficiently from concept to production:

  • Design & Feasibility: sequence evaluation, modification strategy, and scale planning
  • Synthesis: optimized phosphoramidite chemistry for yield and fidelity
  • Purification: HPLC, PAGE, and application-specific purification strategies
  • Quality Control: LC-MS, HPLC, impurity profiling, and release testing
  • Documentation: Certificates of Analysis (CoA), batch records, and traceability
  • Scale-Up & Delivery: transition from pilot to production-scale manufacturing
Platform advantage: This end-to-end approach enables Bio-Synthesis to deliver high-purity DNA with consistent performance, full traceability, and scalable manufacturing aligned with research and regulatory requirements.

Large-Scale DNA Synthesis Platform

DNA oligonucleotides can be engineered at three structural levels: the nucleobase, the deoxyribose sugar, and the internucleotide backbone linkage. This architecture-based approach allows DNA to be optimized for hybridization, stability, nuclease resistance, labeling, conjugation, and biological function.

Large-scale DNA synthesis platform showing DNA base, deoxyribose sugar, and phosphate backbone modification sites
DNA can be engineered at the base, sugar, and backbone level while being supplied as ssDNA or dsDNA at scale.

Base-Level Engineering

Modified DNA bases and nucleobase analogs can tune recognition, labeling, hybridization, and functional behavior.

Sugar-Level Engineering

Modified sugar systems can improve duplex behavior, structural rigidity, and nuclease resistance.

Backbone-Level Engineering

Modified linkages can alter stability, charge, degradation profile, and biological performance.

Standard Large-Scale DNA Pricing Scope

Bio-Synthesis supports large-scale DNA production through optimized synthesis, purification, and scale-up workflows. Our platform enables both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) manufacturing, including modified DNA constructs for research, diagnostic, and commercial applications.

The pricing below applies to standard unmodified DNA oligonucleotides up to 100 bases. For longer sequences (up to 200 bases/base pairs), duplex DNA, or modified DNA, please contact us or request a custom quote.

Large-Scale Single-Stranded DNA (ssDNA)

Price for sequences up to 100 bases. For DNA oligos >100 bases, contact us.

Scale Purification Price (USD)
25 mg HPLC $2,150
100 mg HPLC $2,300
250 mg HPLC $2,650
500 mg HPLC $3,100
1 gram HPLC $4,200
5 grams HPLC $10,000
10 grams HPLC $18,500
100 grams HPLC $175,000
>200 grams HPLC Inquire

Large-Scale Duplex DNA (dsDNA)

Price for sequences up to 100 bases. For duplex DNA >100 bases, contact us.

Scale Purification Price (USD)
25 mg HPLC $3,870
100 mg HPLC $4,180
250 mg HPLC $4,770
500 mg HPLC $5,580
1 gram HPLC $7,560
5 grams HPLC Inquire
10 grams HPLC Inquire
100 grams HPLC Inquire
Need custom DNA?
Bio-Synthesis supports ssDNA and dsDNA up to 200 bases/base pairs, including modified DNA constructs.

DNA Modifications Available at Scale

Bio-Synthesis can incorporate DNA-focused modifications into large-scale oligonucleotide projects, including position-specific modifications across nucleobases, sugars, backbone linkages, termini, and internal sites.

Modified DNA Bases

DNA base modifications and nucleobase analogs for altered recognition, labeling, epigenetic studies, and hybridization tuning.

  • 5-methyl-dC and other epigenetic base variants
  • Deoxyuridine, inosine, and base analogs
  • Halogenated and functionalized bases
  • Fluorescent or affinity-labeled bases

Modified Sugars

DNA-compatible sugar modifications and analog systems to tune structure, duplex stability, and enzymatic resistance.

  • 2-prime modified sugar analogs where compatible
  • Locked or constrained sugar systems
  • Arabino and other sugar-modified DNA analogs
  • Custom sugar-modified nucleotide incorporation

Backbone Linkages

Internucleotide linkage modifications can improve stability, nuclease resistance, and biological performance.

  • Phosphorothioate linkages
  • Mixed-backbone DNA designs
  • Phosphoramidate-type linkages where feasible
  • Other custom linkage chemistries on request

Terminal Modifications

5-prime and 3-prime terminal modifications for labeling, immobilization, conjugation, blocking, and downstream attachment.

  • 5-prime or 3-prime amine modifications
  • Thiol, azide, alkyne, DBCO, biotin
  • Phosphate, spacer, and blocking groups
  • Fluorophores and quenchers

Internal Labels & Spacers

Internal modifications can be placed within the sequence for probe design, structural spacing, or functional presentation.

  • Internal fluorophores and quenchers
  • Internal biotin or affinity tags
  • Spacer arms and abasic sites
  • Reactive internal handles

Conjugation-Ready DNA

DNA can be prepared with functional groups for coupling to peptides, proteins, antibodies, polymers, nanoparticles, surfaces, or small molecules.

  • Amine, thiol, azide, alkyne, DBCO, NHS-compatible designs
  • Biotin, digoxigenin, and affinity tags
  • Linker-controlled spacing
  • Custom conjugation support available
Design principle: modified DNA can be engineered across base, sugar, and backbone chemistry while also supporting terminal labels, internal modifications, and conjugation-ready functional handles.

Large-Scale Manufacturing Capabilities

Bio-Synthesis supports scalable DNA manufacturing from feasibility and pilot batches through larger production requirements. Large-scale DNA projects can be developed around sequence length, chemistry, target quantity, purification needs, and final application.

Flexible Scale

Production can be planned from development-scale quantities to larger research, diagnostic, or therapeutic-development lots.

  • Milligram to gram-scale planning
  • Custom batch-size evaluation
  • Recurring production support

Complex DNA Builds

Support for long, modified, duplex, and conjugation-ready DNA constructs where standard catalog workflows are not sufficient.

  • ssDNA up to 200 bases
  • dsDNA up to 200 base pairs
  • Modified base, sugar, backbone, label, or linker options

Scale-Up Workflow

Projects can be optimized before scale-up to reduce synthesis, purification, and recovery risks.

  • Coupling strategy review
  • Deprotection and cleavage planning
  • Purification route selection
Manufacturing focus: large-scale DNA production should be treated as a controlled workflow — not simply a larger version of small-scale oligo synthesis.

Purification, Quality Control, and Documentation

Large-scale DNA quality depends on both synthesis and downstream purification. Bio-Synthesis can pair large-scale DNA synthesis with purification, analytical testing, release QC, and documentation packages appropriate for research, diagnostic, GLP-aligned, or GMP-supportive workflows.

Purification Options

Purification is selected based on sequence length, modification type, impurity profile, scale, and required final purity.

  • RP-HPLC or IP-RP-HPLC
  • IEX / charge-based purification
  • PAGE for size-critical separation
  • Dual purification for demanding projects
  • Diafiltration or buffer exchange when needed

Release QC Testing

QC panels can verify identity, purity, impurities, residuals, general attributes, and safety-related parameters.

  • Identity by LC-MS, ESI-MS, or MALDI-TOF
  • Purity by HPLC, CE, or IEX
  • Impurity profiling for shortmers and variants
  • Residual solvents by GC
  • Elemental impurities by ICP-MS

Documentation Package

Documentation can be scaled from basic analytical reports to audit-ready release packages.

  • Certificate of Analysis (CoA)
  • HPLC chromatograms and MS reports
  • Batch and purification summaries
  • Method transfer or validation reports
  • Custom release documentation on request
QC Category Representative Methods Purpose
Identity LC-MS, MALDI-TOF, enzymatic digest mapping Confirm molecular mass and support sequence verification when required.
Purity / Impurities RP-HPLC, IP-RP-HPLC, CE, IEX Quantify full-length product, shortmers, n-1/n-2 species, and process-related impurities.
Residuals GC, ICP-MS, conductivity, UV/OD260 Assess residual solvents, elemental impurities, salts, and concentration.
General / Safety Karl Fischer water, pH, appearance, endotoxin, bioburden Support release specifications for higher-control workflows.
QC positioning: for large-scale DNA, release testing and documentation help customers move from “received oligo” to “qualified material” for downstream use.

Quality Systems & Compliance Support

Process Development

Custom DNA projects can benefit from early feasibility review, pilot synthesis, purification optimization, and analytical-method planning before committing to larger-scale manufacturing.

  • Sequence and modification feasibility review
  • Protecting group and coupling strategy evaluation
  • Pilot synthesis with real-time analytical feedback
  • Purification route optimization
  • Scale-up risk assessment

Quality & Compliance Support

Quality support can be aligned with the intended use of the DNA material, from RUO to diagnostic or therapeutic-development programs.

  • ISO 9001 / ISO 13485 quality-system alignment
  • GLP-oriented documentation where appropriate
  • GMP-supportive release panels and QA oversight
  • ICH Q2(R2)-style method validation support
  • USP/EP-aligned safety and release testing options
Compliance note: the right quality package depends on the intended application, regulatory stage, final formulation, and customer-specific release requirements.

Process Transfer & cGMP Scale-Up Support

Following successful development and pilot-scale production, Bio-Synthesis supports the transition of DNA oligonucleotide projects into larger-scale and regulated manufacturing workflows.

DNA manufacturing pathway from R&D to pilot, GMP, and commercial scale

Our team works closely with customers to ensure that synthesis, purification, and analytical methods are reproducible and transferable from research-scale to production-scale environments. Our goal is to be your long-term manufacturing partner—delivering high-purity DNA oligonucleotides at every stage of your program, with the quality, reliability, and documentation your success depends on.

  • Process transfer: transition of synthesis and purification workflows to larger-scale production
  • Scale-up optimization: adjustment of reaction conditions, purification, and yield recovery
  • Analytical method transfer: ensuring consistency in QC testing and release criteria
  • Documentation support: batch records, method descriptions, and traceability
  • cGMP readiness: support for projects requiring higher levels of quality control and regulatory alignment
Scale-up pathway: projects can progress from feasibility and pilot synthesis to large-scale production, with process control and documentation supporting downstream regulatory or commercial requirements.

Applications of Large-Scale DNA Synthesis

Gene Editing Templates

Large-scale ssDNA or dsDNA formats for donor templates, repair templates, and CRISPR-related workflows.

Diagnostic Probes

High-purity DNA probes with optional labels, quenchers, spacers, and affinity tags for assay development.

Synthetic Biology

Custom DNA sequences for assembly workflows, functional testing, and engineered biology applications.

Hybridization Assays

ssDNA and dsDNA for binding studies, annealing experiments, capture assays, and sequence-specific detection.

Therapeutic Development

Modified DNA oligonucleotides for antisense, stability, nuclease resistance, targeting, and delivery research.

Conjugation & Surface Attachment

DNA with reactive handles for attachment to peptides, proteins, antibodies, polymers, nanoparticles, and surfaces.

FAQ

What length can Bio-Synthesis provide for large-scale DNA?
Bio-Synthesis can provide large-scale ssDNA up to 200 bases and dsDNA up to 200 base pairs. Standard price table scope should be limited to unmodified ssDNA up to 100 bases.
Does the standard price table include dsDNA?
No. The standard price table should apply to unmodified single-stranded DNA up to 100 bases. dsDNA formats are quoted separately.
Can modified DNA be made at large scale?
Yes. Modified DNA can include modified bases, modified sugars, modified backbone linkages, terminal modifications, internal labels, spacers, and conjugation handles.
What QC documentation is available?
Documentation can include CoA, chromatograms, mass spectrometry reports, purity data, batch summaries, method-transfer reports, or custom release documentation depending on project scope.
Can process development support scale-up?
Yes. Projects can include feasibility review, pilot synthesis, purification optimization, analytical method planning, and scale-up support before larger production.
Are RNA bases included on this page?
No. This page is written to focus on DNA synthesis and DNA-compatible modifications only. RNA synthesis is listed only as a related service.

Contact & Quote Request

For the fastest review, send the DNA sequence, requested format, length, quantity, desired modifications, purification requirement, QC/documentation requirements, and intended application.

Fast quote checklist

  • Format: ssDNA, dsDNA duplex, or complementary strand pair
  • Sequence length and quantity required
  • Modification class: base, sugar, backbone, label, spacer, or linker
  • Modification position: 5-prime, 3-prime, internal, or sequence-specific
  • Purification, QC, CoA, release testing, and final delivery requirements

Fastest path

Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 45+ years of delivering high quality, fast and scalable synthetic biology solutions.