(Almost) everything you need to know about gene fragments

The Takeaway: Gene fragments are double-stranded, linear DNA available in varying lengths that are critical in a wide variety of workflows and applications, from protein evolution to antibody engineering. Different types of gene fragments are best suited toward different types of experiments, and inherent qualities make some better than others for research types. This blog looks at gene fragments in more detail.

What are gene fragments?

Gene fragments are linear, double-stranded DNA made of synthetic DNA. Gene fragments vary in length depending on manufacturer and application, though generally they range in size from a few hundred base pairs to a few thousand.

What are gene fragments used for?

Gene fragments can be used in several application areas, including:

• As templates for transcription
• Cloning
• Antibody engineering
• Therapeutic protein engineering
• Donor constructs for gene editing research and knock-in experiments that require homology-directed repair (HDR)
• Assembly of multiple gene fragments to create full-length gene constructs for pathway development

What are clonal genes?

When researching gene fragments, you might come across the phrase “clonal genes.” Clonal genes are NGS sequence-verified DNA that are cloned into a particular vector. Clonal genes can cover a wide range of base pair sizes and are NGS-verified so the researcher knows that only the sequences that were requested were those that were manufactured and delivered.

What makes a good gene fragment?

Gene fragments are manufactured using high-quality oligonucleotides. Synthetic gene fragments are cost-effective, fast to produce, and an efficient way to obtain genes for research. By using high-quality gene fragments, researchers can spend less time at the bench and save money on their cloning and sequencing costs thanks to these characteristics:

• Easy assembly to create larger fragments
• High cloning accuracy
• Low cost
• High quality control procedures, including verification by next generation sequencing
• Fast turnaround time—synthetic genes can be available in just a few business days

As a leader in the manufacture of synthetic DNA, IDT has three options for gene fragments. Full genes can also be purchased to minimize work needed in-house.

eBlocks™ Gene Fragments

IDT’s eBlocks Gene Fragments boast a fast turnaround time, minimal screening effort, and budget-friendly availability. As IDT’s standard gene fragment option, these are available in three plate types and three buffer options. They are available in as little as one business day.

eBlocks are available in lengths from 300 to 1,500 base pairs with a median error rate of 1:5,000 base pairs. Because of optimized manufacturing and low error rates, data suggest you'll find the desired sequence by picking just a few colonies. Cloning efficiency is rated at 91 percent and predicted cloning success at the 900 base pair length benchmark is higher than 80 percent.

gBlocks™ and gBlocks HiFi Gene Fragments

IDT’s gBlocks Gene Fragments and gBlocks HiFi Gene Fragments are double-stranded DNA fragments up to 3,000 base pairs in length. Like eBlocks, they are designed for affordable and easy gene construction or modification and are suited for applications such as antibody research and CRISPR-mediated genome editing, qPCR and NGS controls, and more. gBlocks HiFi Fragments have superior quality since they are NGS verified, clonal fragments with a median error rate of 1:12000, perfect for sensitive applications. 

gBlocks and eBlocks are similar, but with a handful of key differences:

• eBlocks have the shortest turnaround time on the market at 1-3 business days
• eBlocks are available in plate only, while gBlocks are available in plates or tubes
• eBlocks are available in lengths from 300 to 1,500 base pairs, while gBlocks are available from 125 to 3,000 base pairs

Gene synthesis

Gene synthesis products from IDT are an easy-to-use solution for researchers who want to move right into functional studies using fully sequence-verified clonal DNA. These are shipped ready to use for a variety of applications, with guaranteed delivery dates, easy online ordering, and no minimum order size or additional charges for custom vectors. Gene lengths are available from 25 base pairs all the way up to 5,000 base pairs and custom projects can be requested for even larger genes. The desired sequence can be cloned into a variety of vector options or custom vector onboarding is also available.

Megamer™ Single-Stranded DNA Fragments

Megamer ssDNA Fragments are high-fidelity tools designed for homology-directed repair of CRISPR-mediated genome editing, transcription, and more. These single stranded fragments are available in both sense and antisense versions and at lengths of 201-2000 bases. 

Ready to learn more?

Order eBlocks Gene Fragments here. gBlocks can be ordered here in plates and tubes can be ordered here. Custom gene synthesis products can be ordered here. Click here to access the Megamer ssDNA Fragment Entry page.