Open Source DNA Ladder Plasmids
Gene And Cell Technologies’ Open-Source DNA Ladder Plasmids can be used to manufacture your own DNA size standards easily and inexpensively.
Most people working with DNA use a size-standard containing DNA fragments of known sizes, the well known "Ladder". As shown in Figure 1, ladders are produced by restriction-digests of plasmids containing appropriately spaced restriction sites. These “source plasmids” can be grown inexpensively at large scale. But the linear fragments can no longer be replicated. These basic facts of nature allow anyone who goes through the trouble of actually creating a source plasmid to keep the plasmid itself locked away, while selling only the digested fragments that the user cannot make more of. To this day, every reagent vendor in the world capitalizes on this natural mechanism to keep their customers dependent on continued purchases, while securing a steady stream of profits.
These days have ended. Gene And Cell Technologies is proud to release the world’s first open-source DNA ladder plasmids. Our plasmids have been synthesized from scratch by our private company. They are not bound by any third party restrictions, MTAs or other intellecutal property. We release them to be used for any legal purpose including commercial. We hope that these plasmids will free scientists around the world from millions of unnecessary "rents" paid to the proprietary reagent vending industry.
Full Manual: GACT's DNA Ladder Plasmids
Why are we the only ones in the whole wide world releasing these plasmids?
It’s because at Gene And Cell Technologies, we don’t’ just say we’re different, but we really are different. We are not primarily a reagent company. We are primarily a science company, attempting to develop futuristic regenerative medicine therapies. There’s nothing wrong with earning some money along the way. But primarily, we do it because we want those medicines to exist. And you, the world’s scientists, and are discovering the knowledge needed for that. We will do business with you as equals at reasonable prices, but we will not attempt to trap you in the kinds of dependencies that traditional science vending companies do. Our open source ladder plasmids are just one small example of that.
The plasmids come in liquid form in TE buffer. In this form, they are stable against ambient temperature for a very longtime. Due to the EDTA in the TE, they are not suitable for direct enzymatic reactions. Instead, please transform them into a suitable E. coli strain for plasmid maintenance (e.g. 5alpha, 10beta). Freeze glycerol stocks, and do your own plasmid preps without EDTA to produce ladder.
It's possible to produce these ladders in the standard LB/amp shaker flask system, and many people have done that, for example for teaching purposes. A baffled flask with SB medium can give you more, for example to supply a small lab's internal needs. But to manufacture ladder economically or commercially, you'll probably want a highly oxygenated system like our SparkleCell desktop bioreactors.
We grow these plasmids in SparkleCell bioreactors / SB medium. We extract the plasmid by alkaline lysis, followed by isopropanol precipitation. Finally we purify it with a Sephacryl S500 size-exclusion step. Then, we cut, and remove the enzyme by ion-exchange chromatography.
Using this process, we typically see the following yields:
p100 bp (SparkleCell EasyGrow): 4.2 mg from a 2L culture.
p2kb (SparkleCell EasyGrow): 2.1 mg from a 2L culture.
p10kb (SparkleCell EasyGrow: 11.2 mg from a 2L culture.
It's already clear from these few example numbers that the yield of plasmid you can expect (expressed as mass) is proportional to its size. That's because the plasmids' origin of replication holds the copy number per cell constant, when other factors, such as nutrient supply, are not limiting. (In SparkleCell under standard conditions, it isn't).
The typical use case is 500 ng total DNA per gel, although with modern gel dyes (Sybr Green, Gel Green etc), one can get away with substantially less. In other words, a single 2L EasyGrow run will typically yield enough ladder for thousands to tens of thousands of gels.