GeneArt Strings DNA Fragments are custom-made, uncloned, double-stranded linear DNA fragments up assembled from synthetic oligonucleotides using the same high-quality process developed for GeneArt Gene Synthesis making them ideal for multi-fragment assembly with our GeneArt Gibson Assembly® cloning Kits.
All Strings DNA fragments can be designed and optimized for protein expression at no extra cost and are also available as Strings DNA Libraries and GeneArt High-Q Strings DNA Fragments.
How to order
Why pay for delivery? With GeneArt Strings DNA Fragments there are no delivery fees.
You may also send a completed Excel submission form to geneartsupport@thermofisher.com
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The advantages of Strings DNA Fragments
Strings DNA Fragments are assembled from synthetic oligonucleotides using the same high-quality process developed for GeneArt Gene Synthesis (Figure 1) and are delivered dried and ready for resuspension, cloning, and screening for identification of the correct clone. They are delivered in a tube format order and are a fast and smart alternative for getting your synthetic gene cloned into your expression plasmid.
The proprietary Invitrogen GeneOptimizer algorithm provides significant gains in downstream protein expression compared to wild-type sequences and there are no additional adaptors to remove.
- Affordable—GeneArt Strings DNA fragments are a cost-effective alternative to doing your own PCR or fully cloned genes
- Flexible—Full gene design and cloning flexibility; clone with any downstream method of choice
- Fast—At least 200 ng of GeneArt Strings DNA Fragments are produced in as little as 3-4 business days
- Optimized—GeneArt GeneOptimizer software realizes significant gains in downstream protein expression
Figure 1. Producing a synthetic gene using GeneArt Strings DNA Fragments and the versatility of Strings. Strings DNA Fragments can cloned directly using virtually any cloning method and also can be used to assemble constructs using technology such as GeneArt Gibson Assembly Cloning Kits.
Production times and sequence ranges
| Sequence Range | Production time (business days)* |
|---|---|
| DNA Fragments 200–600 bp | 3-5 |
| DNA Fragments 601–1,000 bp | 3-4 |
| DNA Fragments 1,001–2,000 bp | 4-5 |
| DNA Fragments 2,001–3,000 bp | 6-8 |
| DNA Libraries: IUPAC ntd | 10-15 |
*Production time is the number of business days required to synthesize GeneArt Strings DNA products in our manufacturing facility. Delivery time is in addition to production time and depends on the destination of the shipment.
Example applications – cloning with Strings DNA Fragments
GeneArt Gibson Assembly Cloning
One, two, and three Strings DNA fragments of 1 kb were assembled using the GeneArt Gibson Assembly HiFi Cloning Kit in pcDNA 3.4 vector using Invitrogen TOP10 competent cells.
Figure 2. GeneArt Gibson Assembly HiFi kits provide high cloning efficiency using single- to multiple-insert designs.
Restriction enzyme cloning example
Eight Strings DNA Fragments up to 3,000 bp were cloned using 5’ AscI and 3’ PacI restriction enzymes. After ligation and transformation, bacteria were plated and incubated overnight at 37°C. Eight (<1 kb) or 16 (>1 kb) colonies were picked, and colony PCR was performed to identify full-length clones; four to eight full-length clones were sequenced to determine the number of sequence-correct clones.
Figure 3. The percentage of clones with correct length as identified by colony PCR (cloning efficiency) and the percent of sequence-correct clones (fidelity) based on the number of full-length clones.
GeneArt Type IIs Assembly example
Eight Strings DNA Fragments of different lengths up to 2,800 bp with suitable sequence ends (AarI recognition sequence and 6 bp stuffer nucleotides) were used for direct assembly with the GeneArt Type IIs Assembly Kit Aar I. The resulting four genes were 5,056 bp, 5,061 bp, 5,267 bp, and 5,448 bp long. After ligation and transformation, bacteria were plated and incubated overnight at 37°C. Sixteen colonies were picked and colony PCR was performed to identify full-length clones. For all four assembled genes, eight colonies were sequenced to determine the number of sequence-correct clones.
Figure 4. The percentage of clones with correct length as identified by colony PCR (cloning efficiency) and the percent of sequence-correct clones (fidelity) based on the number of full-length clones.
GeneArt Seamless Cloning example
Ten Strings DNA Fragments up to 3,000 bp were cloned using the GeneArt Seamless Cloning and Assembly Kit (Cat. No. A13288). After ligation and transformation, bacteria were plated and incubated overnight at 37°C. Eight (<1 kb) or 16 (>1 kb) colonies were picked, and colony PCR was performed to identify full-length clones; four to eight full-length clones were sequenced to determine the number of sequence-correct clones.
Figure 5. The percentage of clones with correct length as identified by colony PCR (cloning efficiency) and the percent of sequence-correct clones (fidelity) based on the number of full-length clones.
GeneArt Seamless Assembly example with multiple Strings Fragments
Strings DNA Fragments are offered in lengths up to 3,000 bp. However, GeneArt Seamless assembly technology can be used to directly assemble two Strings DNA Fragments up to 1 kb without pre-cloning of the subfragments. If you want to assemble more Strings DNA Fragments or longer Strings DNA Fragments using seamless assembly technology, we generally recommend pre-cloning of the subfragments to limit the screening effort needed to find the correct clone after assembly. Alternatively, you can use GeneArt Type IIs assembly technology.
Twelve Strings DNA fragments of different lengths up to 1 kb with suitable sequence ends (15 bp homology to the vector or to the next fragment) were used for direct assembly with the GeneArt Seamless Cloning and Assembly Kit (Cat. No. A13288). The resulting six genes were 1,375 bp, 1,466 bp, 1,536 bp, 1,590 bp, 1,647 bp, and 1,853 bp long. After ligation and transformation, bacteria were plated and incubated overnight at 37°C. Sixteen colonies were picked, and colony PCR was performed to identify full-length clones. For all six assembled genes, six colonies were sequenced to determine the number of sequence-correct clones.
Figure 6. The percentage of clones with correct length as identified by colony PCR (cloning efficiency) and the percent of sequence-correct clones (fidelity) based on the number of full-length clones.
Gateway cloning example with GeneArt Strings DNA Fragments
Five Strings DNA Fragments up to 1,000 bp with attB sites were cloned into pDONR 221. After ligation and transformation, bacteria were plated and incubated overnight at 37°C. Eight colonies were picked, and colony PCR was performed to identify full-length clones; four to seven full-length clones were sequenced to determine the number of sequence-correct clones.
Figure 7. The percentage of clones with correct length as identified by colony PCR (cloning efficiency) and the percent of sequence-correct clones (fidelity) based on the number of full-length clones.
GeneArt Gibson Assembly Cloning
One, two, and three Strings DNA fragments of 1 kb were assembled using the GeneArt Gibson Assembly HiFi Cloning Kit in pcDNA 3.4 vector using Invitrogen TOP10 competent cells.
Figure 2. GeneArt Gibson Assembly HiFi kits provide high cloning efficiency using single- to multiple-insert designs.
Restriction enzyme cloning example
Eight Strings DNA Fragments up to 3,000 bp were cloned using 5’ AscI and 3’ PacI restriction enzymes. After ligation and transformation, bacteria were plated and incubated overnight at 37°C. Eight (<1 kb) or 16 (>1 kb) colonies were picked, and colony PCR was performed to identify full-length clones; four to eight full-length clones were sequenced to determine the number of sequence-correct clones.
Figure 3. The percentage of clones with correct length as identified by colony PCR (cloning efficiency) and the percent of sequence-correct clones (fidelity) based on the number of full-length clones.
GeneArt Type IIs Assembly example
Eight Strings DNA Fragments of different lengths up to 2,800 bp with suitable sequence ends (AarI recognition sequence and 6 bp stuffer nucleotides) were used for direct assembly with the GeneArt Type IIs Assembly Kit Aar I. The resulting four genes were 5,056 bp, 5,061 bp, 5,267 bp, and 5,448 bp long. After ligation and transformation, bacteria were plated and incubated overnight at 37°C. Sixteen colonies were picked and colony PCR was performed to identify full-length clones. For all four assembled genes, eight colonies were sequenced to determine the number of sequence-correct clones.
Figure 4. The percentage of clones with correct length as identified by colony PCR (cloning efficiency) and the percent of sequence-correct clones (fidelity) based on the number of full-length clones.
GeneArt Seamless Cloning example
Ten Strings DNA Fragments up to 3,000 bp were cloned using the GeneArt Seamless Cloning and Assembly Kit (Cat. No. A13288). After ligation and transformation, bacteria were plated and incubated overnight at 37°C. Eight (<1 kb) or 16 (>1 kb) colonies were picked, and colony PCR was performed to identify full-length clones; four to eight full-length clones were sequenced to determine the number of sequence-correct clones.
Figure 5. The percentage of clones with correct length as identified by colony PCR (cloning efficiency) and the percent of sequence-correct clones (fidelity) based on the number of full-length clones.
GeneArt Seamless Assembly example with multiple Strings Fragments
Strings DNA Fragments are offered in lengths up to 3,000 bp. However, GeneArt Seamless assembly technology can be used to directly assemble two Strings DNA Fragments up to 1 kb without pre-cloning of the subfragments. If you want to assemble more Strings DNA Fragments or longer Strings DNA Fragments using seamless assembly technology, we generally recommend pre-cloning of the subfragments to limit the screening effort needed to find the correct clone after assembly. Alternatively, you can use GeneArt Type IIs assembly technology.
Twelve Strings DNA fragments of different lengths up to 1 kb with suitable sequence ends (15 bp homology to the vector or to the next fragment) were used for direct assembly with the GeneArt Seamless Cloning and Assembly Kit (Cat. No. A13288). The resulting six genes were 1,375 bp, 1,466 bp, 1,536 bp, 1,590 bp, 1,647 bp, and 1,853 bp long. After ligation and transformation, bacteria were plated and incubated overnight at 37°C. Sixteen colonies were picked, and colony PCR was performed to identify full-length clones. For all six assembled genes, six colonies were sequenced to determine the number of sequence-correct clones.
Figure 6. The percentage of clones with correct length as identified by colony PCR (cloning efficiency) and the percent of sequence-correct clones (fidelity) based on the number of full-length clones.
Gateway cloning example with GeneArt Strings DNA Fragments
Five Strings DNA Fragments up to 1,000 bp with attB sites were cloned into pDONR 221. After ligation and transformation, bacteria were plated and incubated overnight at 37°C. Eight colonies were picked, and colony PCR was performed to identify full-length clones; four to seven full-length clones were sequenced to determine the number of sequence-correct clones.
Figure 7. The percentage of clones with correct length as identified by colony PCR (cloning efficiency) and the percent of sequence-correct clones (fidelity) based on the number of full-length clones.
Sequence design and screening recommendations
Strings DNA products can be cloned using any available cloning method, just make sure to design the ends of your sequence according to the respective requirements.
You can simply paste the sequence into the online order form of the GeneArt Strings Assistant and proceed to the cart to order. Alternatively, you can use the convenient GeneArt Classic portal sequence editing and optimization functions. Depending on your desired cloning system, you may need to modify the 5′ and 3′ ends of your sequence to enable proper insertion into your desired vector.
For example, for cloning Strings DNA products by restriction enzymes/ligation, we generally recommend adding additional stuffer nucleotides to both ends of your sequence to ensure efficient enzyme binding. If blunt cloning methods are used (e.g., Invitrogen TOPO technology), we recommend that you add 5–10 nucleotides of random stuffer DNA on both ends of the fragment, preserving functional DNA elements needed for downstream applications (by their very nature, linear DNA fragments are not entirely free of small terminal truncations).
Table 1. Examples for cloning methods and recommended sequence design.
| Restriction enzyme cloning | Add desired 5′ and 3′ restriction enzyme sequences, plus stuffer nucleotides |
| GeneArt Type IIs Assembly | Add desired 5′ and 3′ restriction enzyme sequences, plus stuffer nucleotides |
| Invitrogen GeneArt Seamless Cloning and Assembly | Add 15 bp sequence overlap (or more, depending on the kit) to vector or adjacent insert |
| Invitrogen Gateway Cloning | Add attB sites to enable proper recombination into Invitrogen pDONR vector |
| Invitrogen Zero Blunt TOPO PCR Cloning | Strings Fragments are blunt ended, so 5–10 stuffer nucleotides are recommended to compensate for small terminal truncations |
| TA and Invitrogen TOPO TA Cloning | Strings Fragments are blunt-ended and need to be adenylated using a Taq polymerase in the presence of dATP to add end-terminal A-overhangs |
Strings DNA Fragments are PCR amplicons of assembled oligonucleotides, ready for screening to identify the correct clone. Strings DNA Fragments are bulk sequence-controlled as part of the QC process to help ensure that your desired sequence is present in the fragment pool. To identify a correct clone >90% of the time, we recommend to use the screening guidelines in Table 2.
Table 2. Recommended screening of Strings DNA Fragments.
| Strings DNA Fragments up to 1 kb | Sequence 2 to 4 full-length clones |
| Strings DNA Fragments 1–2 kb | Sequence 3 to 5 full-length clones |
| Strings DNA Fragments 2–3 kb | Sequence 4 to 8 full-length clones |
Screening recommendations and application examples
Figure 8. Cloned Strings Fragments. Two Strings DNA Fragments (each 2640 bp) were cloned into GeneArt standard cloning vector pMA, and six colonies were analyzed by colony PCR followed by agarose gel electrophoresis. (Amplicons are longer since primer design for colony PCR adds ~ 100 bp 5’ & 3’ each)
High-Q Strings DNA Fragments
GeneArt High-Q Strings DNA Fragments are similar to our Strings DNA Fragments but are synthesized with exceptionally high accuracy standards meaning that downstream screening efforts are significantly reduced.
Reduced screening efforts
GeneArt High-Q Strings DNA Fragments reduce the required screening effort by at least 60% compared to competitor products and help enable direct assembly of 5 kb constructs with reasonable screening effort. Based on the error rates determined for the different products, we calculated the number of clones that need to be sequenced in order to identify a correct clone with a probability of 98% (Figure 9).
Since this number exponentially increases with the total size of the DNA fragment, differences in error rate become particularly substantial as fragments get longer.
High-Q Strings DNA Fragments reduce the required screening effort by at least 60% compared to competitor products, and enable direct assembly of 5 kb constructs with reasonable screening effort (Figure 10).
Figure 9. The number of clones that need to be sequenced in order to identify a correct clone with a probability of 98%. At 1,000 bp insert length we determined 2 clones with the GeneArt High-Q Strings DNA Fragments vs. 5 clones with both suppliers’ products—resulting in a 60% reduction in screening efforts.
Figure 10. Number of clones required to choose the correct one using 3 different error rates. The impact of a lower error rate is shown as the insert length increases.
Production times and product offerings
| Sequence range | Production time (business days)* |
|---|---|
| DNA Fragments 200–1,200 bp | 6-9 |
*Production time is the number of business days required to synthesize GeneArt High-Q Strings DNA Fragment products in our manufacturing facility. Delivery time is in addition to production time and depends on the destination of the shipment.
GeneArt Strings DNA Fragments are custom-made, uncloned, double-stranded linear DNA fragments, available in lengths from 200 base pairs (bp) to 3,000, assembled from synthetic oligonucleotides using the same process developed for GeneArt high-quality gene synthesis. Strings Fragments can be used to quickly clone your gene of interest. At least 200 ng of Strings DNA Fragments are produced within 3-5 (up to 1,000 bp) or 8 (from 1,000 to 3,000 bp) business days. GeneArt Strings DNA Fragments can be designed, sequence optimized, and ordered online and are a cost-effective and smart alternative to clone your expression plasmid.
While we used to offer Strings DNA Fragments between 100 – 150 bp, this is unfortunately no longer possible.
Strings Fragments are amplicons (PCR amplificates) of assembled oligonucleotides; an intermediate product of the gene synthesis production process. This process results in a pool of fragments, and cloning and screening need to be carried out to identify the correct clone. To ensure that correct fragments are present in the pool, Strings Fragments are bulk sequence-controlled before shipment.
Strings DNA Fragments are shipped dried, ready for resuspension and cloning. Before using, we recommend that you spin down the tube contents, add some water to the bottom of the tube to get the desired concentration, and let it incubate for at least 1 hour at room temperature (alternatively incubate at 4°C overnight). Subsequently, resuspend carefully and use immediately. For longer storage, resuspended Strings DNA Fragments should be dispensed into aliquots and frozen at –20°C. Please avoid freeze-thaw cycles.
No. Strings DNA Fragments from 200 to 1,000 bp are produced in 5 business days and Strings DNA Fragments from 1,000 to 3,000 bp are produced in 8 business days. Depending on the nature of the sequence, production time can vary.
Yes. Since you need to perform the cloning to obtain your final gene, Strings DNA Fragments prices are always below those for gene synthesis.
Yes. We recommend using the GeneArt web order portal for ordering, where you can use the free gene editing and optimization functions to adjust the sequence to meet your needs. After editing and optimization, please check again that the final sequences of the fragment(s) are exactly as needed for further processing in your lab (e.g., potential homologous overlaps of the fragments or restriction sites and buffer bases needed for cloning).
No, subcloning and assembly services are not available for Strings DNA Fragments, as they are designed to offer you the fastest and most affordable way to get access to your genes. If you do not want to clone your gene yourself, we recommend that you order full gene synthesis service.
Yes, it is possible to directly assemble 2 Strings Fragments without pre-cloning. Thermo Fisher Scientific offers several technologies for seamless assembly, e.g., GeneArt Type IIs Assembly or GeneArt Seamless Cloning and Assembly. Please refer to the application examples section on this page for more information. Depending on the sequence length and the number of subfragments you want to assemble, the screening effort to find a correct clone can be high. We therefore generally recommend pre-cloning the subfragments to limit the screening effort required to find a correct clone after assembly.
No. Strings DNA Fragments are limited to 200 to 3,000 bp. If your sequence is longer, you need to order it as gene synthesis or assemble your gene from two or more Strings DNA Fragments. In addition, the Strings DNA Fragments manufacturing process is streamlined to very quickly and cost-effectively provide you with your gene product. If your sequence is complex, you may receive a message that it cannot be produced as a Strings DNA Fragment due to high complexity. In that case, we recommend modifying your sequence to match the production criteria (given below) or ordering your gene as gene synthesis. In many cases, optimizing your sequence using the portal function enables manufacturing with the Strings Fragments process. If it is still not able to be produced, you can manually edit the sequence to enable production.
Important production criteria are:
- GC content between 20% to 80% (in peaks, not overall content)
- No long secondary structures or sequence repetitions
- No A/T stretches >25 bp nor G/C stretches >20 bp
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