When cloning efficiency and not just colony count matters, choose In‑Fusion Cloning

 As the first step in so many experiments, successful cloning is key to generating meaningful data. The cloning tools you use can be the difference between wasted effort and quick, accurate results. The products in the In‑Fusion Cloning portfolio enable insertion of any PCR fragment, or multiple fragments, into your linearized vector for fast, seamless cloning. The In‑Fusion Cloning reaction is specific and directional, ensuring an exceptionally high rate of cloning efficiency in all applications. Unlike transformation efficiency, which measures the number of transformed colonies on a plate, cloning efficiency is a measure of accuracy, providing information on the number of correct clones obtained from the cloning reaction. Our standards for accuracy involve more than simple transformation efficiency. Why waste time screening a large number of colonies when you can pick just a few colonies, generated with In‑Fusion technology, and be confident that you have the right clone?

The efficiency of your cloning experiment becomes even more vital when you need to create constructs from multiple fragments. Multiple-fragment cloning experiments pose additional challenges as each insert must be kept in frame in order to build complicated constructs, to stitch genes together from synthetic building blocks, or to engineer new functionalities through combinatorial protein domain swapping, etc. Given all of these concerns, we are gratified to see researchers finding success with In-Fusion technology where they had previously hit roadbloacks:

Years ago, I had tested a standard seamless Gibson Assembly cloning technology head-to-head against In-Fusion and had gotten zero colonies using the Gibson Assembly technique kit vs several hundred colonies using In-Fusion using the same 2 fragments plus a vector fragment. And 3/3 colonies tested that were obtained with In-Fusion were correct at the DNA sequence level. I have stuck with In-Fusion ever since.

—Dr. Raju Lathigra, Senior Scientist, Zalgen Labs LLC.

We have recently taken this technology to the next level—enhancing both the transformation and the cloning efficiency of the In‑Fusion Cloning reaction—for multiple-insert applications.

The In‑Fusion Cloning reaction generates accurate, directional cloning of desired fragments

The key to the In‑Fusion Cloning reaction is its proprietary enzyme that generates short regions of single-stranded overlaps between vector and insert(s), facilitating accurate, directional cloning of the desired fragments. This overlap is designed into the PCR primers used to amplify the desired insert sequences.

Figure 1. The In-Fusion Cloning workflow.

Optimized protocol improves cloning performance for multiple-insert experiments

Historically, the In‑Fusion Cloning reaction has required 15 bp of homologous overlap between adjacent fragments (e.g., vector and insert). While this 15-bp overlap provides excellent results for single-insert cloning reactions, our scientists have further optimized the protocol for multiple-insert cloning and found that increasing the overlap to 20 bp in this application improved both the colony count and the cloning accuracy. We tested this change from 15 bp to 20 bp using both the liquid and lyophilized (EcoDry) formats of the In‑Fusion HD Cloning Plus products in the construction of a vector plus five inserts. The results showed colony increases of 5.6X and 4.7X for the liquid and the lyophilized kits, respectively (Figure 2).

However, since colony count is only part of the performance equation, we also analyzed the accuracy obtained when using a 20-bp overlap protocol. Results indicate that our increase to a 20-bp homologous overlap improves upon the already highly accurate cloning results that we see with the 15-bp overlap, increasing to 90% and 100% accuracy for the liquid and lyophilized formats, respectively (Figure 2).

In other cloning systems, increasing the number of fragments can have a detrimental effect on both transformation efficiency and cloning accuracy. However, with this newly optimized protocol, In‑Fusion Cloning ensures the same high level of accuracy you see for single-insert cloning, even when you are performing more challenging multiple-fragment cloning projects.

New tools available to assist you in achieving a successful cloning project, every time

As the number of inserts required in your cloning experiment increases, so does the importance of using the right primers. To assist you with primer design, we have developed a new online tool to guide you through the process, step by step. The In‑Fusion Cloning Primer Design Tool allows for multiple-insert cloning, in addition to single-insert cloning and site-directed mutagenesis. Simply input the DNA sequences of your vector and multiple inserts along with your linearization method to automatically generate primers for your cloning experiment. This new tool provides both a final vector sequence and your primer sequences, enabling a seamless transition from design to bench work.

To coincide with the release of the optimized protocol and the new In‑Fusion Cloning Primer Design Tool, we have also updated our technical documentation to include new guidelines for multiple-insert cloning. While we continue to maintain our In-Fusion HD technology, we strongly recommend that you switch to the more recently developed In-Fusion Snap Assembly master mixes. These newest versions provide the same robustness and reliability you have come to expect from In-Fusion Cloning, but are optimized for enhanced cloning performance:

In-Fusion Snap Assembly (liquid)

• Multiple-Insert Cloning Protocol-At-A-Glance
• User Manual

In-Fusion Snap Assembly EcoDry (lyophilized)

• Multiple-Insert Cloning Protocol-At-A-Glance
• User Manual

With less time spent on experimental design and cloning, you can spend more time advancing your research. Check out our In‑Fusion Cloning selection guide to choose the right kit for you.