gene-strings-dna-fragments

Synthetic genes ready to clone—affordable for every lab

GeneArt® Strings™ DNA Fragments can now be ordered from 100 to 3,000 base pairs with improved sequence fidelity.

GeneArt® Strings™ DNA Fragments are custom-made, uncloned, double-stranded linear DNA fragments from 100 base pairs (bp) to 3,000 bp in length, assembled from synthetic oligonucleotides using the same process developed for GeneArt® high-quality gene synthesis. Strings™ Fragments are delivered dried, ready for resuspension and screening to enable the identification of the correct clone. Strings™ Fragments are a fast and smart alternative to get your synthetic gene and clone your expression plasmid.

At least 200 ng of Strings™ DNA Fragments are produced within 5 (for up to 1,000 bp) or 8 (for 1,000 to 3,000 bp) business days. Strings™ Fragments can be designed, optimized for protein expression, and ordered within our online order portal.

Order online

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  • Affordable—Strings™ DNA Fragments are a cost-effective alternative to gene synthesis
  • Flexible—full gene design and cloning flexibility; enter your sequence and directly edit, optimize, and order through our online portal
  • Fast—Strings™ DNA Fragments—100 to 3,000 bp—are produced within 5 or 8 business days, ready for cloning and sequencing in your lab.*

*Depending on the nature of the sequence, production time can vary. Delivery times are in addition to the specified production times and depend on location.


Quick links


How to order

Option 1:

Order online

Order online via our web portal

  • Conveniently enter, edit, and optimize your sequences in our electronic web order portal.
  • Directly order your Strings™ DNA Fragments online.
 

Option 2:

Request via email

Order via Excel® spreadsheet (mark-up fees applies)

Your sequences will be synthesized as entered. If your sequences are complex and cannot be produced as Strings™ DNA Fragments, you will be notified to modify your sequences.

Deliverables and storage

Strings™ DNA Fragments are suspended in 10 mM Tris pH 8.5 buffer and delivered dried (>200 ng), ready for resuspension and cloning. We recommend that you centrifuge tubes prior to opening, add the appropriate amount of water to the bottom of the tube, and incubate at least 1 hour at room temperature (alternatively incubate at 4°C overnight). After incubation, carefully resuspend Strings™ DNA Fragments and use immediately. If not used immediately, resuspended Strings™ DNA Fragments should be aliquoted and frozen at –20°C. Please avoid freeze-thaw cycles.

Complete usage instructions can be found in the Strings Product Bulletin. Figure 1 shows an image of seven Strings™ DNA Fragments of 2,600–2,800 bp, resuspended and separated using agarose gel electrophoresis.

Figure 1. Strings™ DNA Fragments after gel electrophoresis (1% agarose gel, DNA marker is 1 kb DNA Ladder)


Biosecurity check

The GeneArt® production team performs a biosecurity screen on each sequence entered. In the event your order does not pass this analysis, you will be contacted to determine the best way to proceed.

Sequence design

Strings™ DNA Fragments 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 web portal and proceed to the cart to order. Alternatively, you can use the convenient GeneArt® 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 Fragments 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., 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 lists some points to consider for frequently used cloning methods.

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

GeneArt® Seamless Cloning and Assembly

Add 15 bp sequence overlap (or more, depending on the kit) to vector or adjacent insert

Gateway® Cloning

Add attB sites to enable proper recombination into pDONR™ vector

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 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

Table 1. Examples for cloning methods and recommended sequence design.


Screening recommendations and application examples

Strings™ Fragments are PCR amplicons of assembled oligonucleotides, ready for screening to identify the correct clone. Strings™ 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.

Strings™ Fragments up to 1 kb

Sequence 2 to 4 full-length clones

Strings™ Fragments 1–2 kb

Sequence 3 to 5 full-length clones

Strings™ Fragments 2–3 kb

Sequence 4 to 8 full-length clones

Table 2. Recommended screening of Strings™ DNA Fragments.

 

An example for a screening analysis of cloned Strings™ DNA Fragments is given in Figure 2.

Figure 2. 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. (amplificates are longer since primer design for colony PCR adds ~ 100 bp 5’ & 3’ each)


Application examples

Restriction enzyme cloning example

8 Strings™ 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. 8 (<1 kb) or 16 (>1 kb) colonies were picked, and colony PCR was performed to identify full-length clones; 4 to 8 full-length clones were sequenced to determine the number of sequence-correct clones.



The figure shows 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 with multiple Strings™ DNA Fragments

Eight Strings™ DNA Fragments of different lengths up to 2,800 bp with suitable sequence ends (Aar I recognition sequence and 6 bp stuffer nucleotides) were used for direct assembly with the GeneArt® Type IIs Assembly Kit Aar I (Cat. No. A15916). The resulting 4 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. 16 colonies were picked and colony PCR was performed to identify full-length clones. For all 4 assembled genes, 8 colonies were sequenced to determine the number of sequence-correct clones.

 


The figure shows 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

10 Strings™ 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; 4 to 8 full-length clones were sequenced to determine the number of sequence-correct clones.

The figure shows 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™ Fragments or longer Strings™ 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 6 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 6 assembled genes, 6 colonies were sequenced to determine the number of sequence-correct clones.


The figure shows 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

Five Strings™ 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; 4 to 7 full-length clones were sequenced to determine the number of sequence-correct clones.

The figure shows 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.


Frequently asked questions (FAQs)

What are Strings™ DNA Fragments?

GeneArt® Strings™ DNA Fragments are custom-made, uncloned, double-stranded linear DNA fragments, available in lengths from 100 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 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.

How are Strings™ DNA Fragments quality-controlled?

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.

How are Strings™ DNA Fragments delivered?

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.

Is the production time of all length categories of Strings™ DNA Fragments the same?
No. Strings™ DNA Fragments from 100 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.

Are Strings™ DNA Fragments always cheaper than gene synthesis?

Yes. Since you need to perform the cloning to obtain your final gene, Strings™ DNA Fragments prices are always below those for gene synthesis.

Are there any gene editing and gene optimization functions available when ordering Strings™ DNA Fragments?

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).

Do you offer services for subcloning or assembly of Strings™ DNA Fragments to larger genes?

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.

Do you offer the usage of degenerated oligonucleotides to build gene libraries with Strings™ DNA Fragments?

No. Strings™ Fragments production is only offered with A/C/G/T bases. No mixed degenerate bases and no “modified" bases (e.g., inosine, uridine) can be used for production. If you need a service for randomizing specific residues of the DNA, e.g., for directed molecular evolution, we offer our Directed Evolution services. Please see GeneArt® Controlled Randomization Service and GeneArt® Combinatorial Libraries Featuring TRIM Technology

Can I use Strings™ DNA Fragments to assemble larger genes?

Yes, it is possible to directly assemble 2 Strings™ Fragments without pre-cloning. Life Technologies 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.

Are all sequences producible as Strings™ DNA Fragments?

No. Strings™ DNA Fragments are limited to 100 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

What do I need to consider when cloning Strings™ DNA Fragments?

Please refer to the section near the top of the page: "Screening Recommendations & Application Examples".


Different ways to obtain your gene

  Classical PCR & cloning Synthetic DNA fragments Gene synthesis
How we can help you

PCR cloning & reagents

GeneArt® Gene Synthesis Kit

GeneArt® Strings™ DNA Fragments GeneArt® Gene Synthesis and Subcloning Service
Advantage
  • Full cost control
  • Every step in your hand
  • Fast & affordable
  • Design flexibility
  • Gene optimization
  • No physical template required
  • 100% sequence verified
  • Convenient ordering
  • Design flexibility
  • Gene optimization
  • No synthesis and cloning  time needed
Labwork High Medium Low
Production time* NA

5 business days for Strings up to 1,000 bp

8 business days for Strings up to 3,000 bp

9 business days for genes up to 1,200 bp

15 business days for genes up to 3,000 bp

*Production time is the number of business days required to synthesize GeneArt® Strings™ DNA fragments in our manufacturing facility. Delivery time is in addition to production time and depends on the destination of the shipment.

For research use only. Not for use in diagnostic procedures.