In previous articles (see Counterfeiting as an Art Form and Anti-Counterfeiting DNA Marking Gets a Boost), I wrote about DNA marking as an anti-counterfeiting measure. A few of the commenters suggested that the technology for sequencing authentication was too pricey to expect widespread deployments. My response was that costs will come down as a function of technology introductions that will put DNA sequencing equipment on the desktop at company receiving stations.
I mentioned that we might be looking out two to four years before this portable sequencer might become available. Also in the article, I wrote about a technology breakthrough that might make this a reality at $1,000. Well, I am delighted to say that there is a working handheld sequencer available using nanopore protein structures that can sequence up to 70,000 base pairs in a very short period of time.
Prior to this, turn-around sequencing times for even short sketches of DNA could take hours or days. To sequence just a few hundred base pairs, scientist had to mince up thousands of copies of the target DNA, sequence all the fragments, and use software to perform the reconstruction work by matching overlap within the fragments.
Lab in Your Hand
The MinION USB stick DNA sequencer costs under $1,000 and
sequences up to 150 million base pairs in its six-hour lifetime.
The nanopore technology virtually eliminates the need for overlap analysis, and saves an incredible amount of time and effort in the sequencing process using very long strands of DNA. The human genome consists of about a billion base pairs so 70,000 seems like a small number in comparison. But DNA marking that only uses segments for DNA taggants may now become more economically viable as an anticounterfeiting methodology.
So, open your hand and consider the breadth of your palm. The unit called "MiniON," pronounced "Min-ion" from Oxford Nanopore Technologies, fits nicely in your hand and includes a USB port that can plug into a laptop or a desktop PC. Here is how it works once you have swabbed the taggants and prepped the DNA:
- Drop the DNA sample into the integrated port on the MinION. Within the device is a silicon chip with thin polymer membranes with tiny pores.
- An enzyme carries or shuttles the DNA to the protein-based nanopore inserted through the polymer which is only a couple of nanometers in diameter. This is about 100,000 times thinner than a human hair. The enzyme unzips the base pairs and feeds one end into the nanopore. Imagine a railroad track that is divided such that only one rail goes through the tunnel at a time.
- Electrodes put a small current through the nanopore and as each base type, A,T,C, and G are passing through the pore, the current is interrupted and sensed in such as manner as to be able to identify what base has caused the interruption. Each base has a characteristic response.
A software application in the laptop analyzes the electrical signal and records the different bases as they pass through the portal in the linear progression. The software then stitches together the sequence of bases of the entire strand.
Lastly, the DNA reading is enhanced through the additional capability of reading the complementary strand. During the unzip process, the strand is prepared with a "hairpin"
connector that links the complementary strand that is subsequently pulled through the same pore for a "check" sequencing step. This is a kind of biological error detection much like a checksum on an EPROM program.
Blood DNA can also be sequenced in this application, so we are not too far from localized and mobilized DNA identification and authentication for security identification purposes. The nanopore technology could possibly open the door for low cost, DNA anti-counterfeiting measures. It seems like all of the technologies that are brought into being with human and business protections in mind, can also be subverted into loss of privacy concerns as information retrieval for various uses becomes more readily accessible.
I think this is a trade-off we may have to accept in order to ensure that we are not inadvertently endangering lives by using counterfeit electronics in mission critical and medical systems. We are in the business of industry and trade-offs.