ssDNA (Single-Stranded DNA Synthesis)


ssDNA Synthesis service provides up to 10,000 nt of full sequence-verified fragments quickly and affordably. Our ssDNA Synthesis fragments are derived from clonally purified double-stranded DNA (dsDNA), producing the highest quality results possible.

Recent research in CRISPR/Cas9 technology has shown that the use of long ssDNA donor templates greatly enhances the efficiency of homology-directed repair (HDR) enabling researchers to optimize the process of efficiently generating transgenic animal models and cell lines. As the leader in complex gene sequences, you can trust GENEWIZ from Azenta Life Sciences for sequence-verified ssDNA synthesis for CRISPR gene knock-in, in-vitro transcription, and much more.


What is the purpose of ssDNA?

ssDNA, or single-stranded DNA, is a nucleotide sequence involved in DNA replication and DNA repair.


What is the difference between dsDNA and ssDNA?

dsDNA stands for double-stranded DNA, which is two complimentary DNA strands forming a helical shape bound by hydrogen bonds. ssDNA stands for single-stranded DNA, and has a lower stability compared to dsDNA. Due to its double-stranded nature and strong hydrogen bond linkage, dsDNA is resistant to formaldehyde (unlike ssDNA).


ssDNA Synthesis Applications

Antibody Discovery: Engineer customized cell lines or transgenic mouse models to study in vivo immune responses
Food technology: Modify genomes of agricultural crops to study pathogenic resistance for improved food security
Cancer Biology: Generate CRISPR gene insertions to study oncogene function for targeted therapeutics
Biofuels: Precise genome editing to optimize metabolic pathways for biofuel production

CRISPR Gene Knock-In Workflow

Double-stranded breaks are generated through CRISPR/Cas9 editing, then repaired by the endogenous cellular pathways of non-homologous end joining (NHEJ) and HDR. While the HDR pathway has consistently proven successful in copying genetic information via homologous recombination, insertion of exogenous genetic material is a challenge due to the inherent inefficiencies of HDR. Double-stranded DNA has historically been the template of choice for gene insertions, but recent research has shown the superiority of ssODNs as a donor template for HDR. Offering much higher efficiency to insert long sequences with shorter homology arms, ssDNA has become the preferred donor template for this process. Azenta now offers the longest (up to 10,000 nt) ssDNA fragments on the market, allowing insertion of long sequences with high efficiency and reduced cellular toxicity or off-target integration compared to dsDNA donors.

Figure 1.1. Guide RNA forms a complex with Cas9 directing enzyme to cleave target DNA resulting in a double-stranded break (DSB).

Figure 1.2. Homology directed repair after DSB in the presence of a ssDNA donor template results in precise gene knock-in.

ssDNA Advantages for CRISPR Gene Editing

Lower cellular toxicity compared to dsDNA after cellular delivery
Low off-target integration for more reliable gene knock-ins
High specificity knock-in templates for homology directed repair
High efficiency donors for targeted insertions and gene replacements


Enter to win $1,000 towards GENEWIZ
Multiomics & Synthesis Solutions*

*Terms and conditions apply

Fastest and Longest ssDNA Available

Length Available Yield Turnaround Time
151-500 nt 2, 3, 6, 10, 20, or 40 µg Starting at 10 Business Days
501 - 2,000 nt 3, 6, 10, 20, or 40 µg Starting at 15 Business Days
2,001 - 8,000 nt Starting at 20 Business Days

Please note: 50% off complementary sequence for every order. Custom discount available for customer-supplied dsDNA. 

Email to submit custom inquiries for orders >8,000 nt.

Single-Stranded DNA Features & Benefits

Ph.D.-level consultation and support – Our dedicated Project Management team will tailor the order to your exact specifications and support your project from start to finish.
Advanced capabilities – Standard ssDNA synthesis service ranging from 150 nt to 8000 nt in length, with difficult stretches, like highly repetitive, AT- or GC-rich DNA. For ssDNA over 8000 nt in length, please contact
AAV control applications – Synthesize ITR at each end of transgene. For the application such as AAV NGS library control, AAV qPCR control or AAV DNA ladder control.
Quality control – Stringent quality control process with a 100% sequence accuracy guarantee. Residue rate of dsDNA lower than 0.5%.

Rapid delivery – Industry-leading turnaround time to keep your project running on time.
Yield flexibility – Choose 2, 3, 6, 10, 20, or 40 µg of lyophilized fragments.

Case Study

Webinar | Understanding biological mechanisms to better predict the evolution of antibiotic resistance

The rapid and wide-spread evolution of antibiotic resistance is threatening global health. In this webinar, presented by Dr. Mato Lagator, Wellcome Trust, Royal Society Sir Henry Dale Fellow, University of Manchester, you will learn about different approaches to study evolutionary processes that underpin the emergence of resistance. Special focus is given on how these methods can be utilized to improve drug development and longevity.

Watch Now

ssDNA Deliverables

  • Sequence verified
  • 2, 3, 6, 10, 20, or 40 µg lyophilized DNA
  • Certificate of Analysis (COA) including gel image, sequence trace data with alignment, and sequence files

ssDNA Quality Control

  • Sequence confirmation via Sanger sequencing
  • Size verification by gel electrophoresis
  • S1 nuclease digestion test


*Samples must arrive at the Azenta New Jersey laboratory before 10:00 am EST to qualify for Same Day service. Note that direct-sequencing templates are not available for our Same Day service.

Email | Phone (1-877-436-3949, Ext. 3)