What's in a miniprep? A "short" history of a taken for granted technique

If you’re a scientist chances are the miniprep was one of the first techniques you learned. I still remember opening my first blue box as an undergraduate and have done countless preps since. For non-scientists, a miniprep is a way to separate plasmid DNA from chromosomal DNA. Plasmids are DNA encoded on an enclosed circle that replicate inside bacteria independently from the much bigger, linear chromosomal DNA. Bacteria transfer these plasmids to each other, which give those bacteria special properties such as antibacterial resistance. Scientists have hijacked this system to put whatever DNA we want on this plasmid and put it inside bacteria which will quickly make more of that DNA, After purifying this foreign DNA away from bacterial junk, we can then do whatever it is we evil scientists do with foreign DNA…perhaps genetically modify some tomatoes just to make them less flavorful?  

The miniprep’s ease lies in its step-by-step instructions and pre-made buffers. The name doesn’t hurt either, sounding rather diminutive and much less threatening than a phenol/chloroform extraction. Many an older faculty has complained that science has become so automated young scientists don't even understand the basis for the miniprep technique. So for a description of how a miniprep kit works, see the end of the article, as "it's proprietary" probably won't work as a response on your GBO. 

But where did the miniprep technique come from? Probably not many people have wondered this and I hadn’t either until this week for some reason. Perhaps I’m starting to crack under the pressure of the new postdoc, but I decided to put some time into investigating, which, with the Internet, is not that difficult.

The basis of the miniprep kit, the alkaline lysis, was published by Birnboim and Doly in 1979 (Birboim and Doly 1979). In 1988, Dr. Birnboim recounted how he developed the technique in Citation Classics (Birnboim 1988), a feature in Current Contents that ran from 1977 to 1993 and sought to show the human side involved in putting out some of the most widely-cited papers. During a sabbatical in Paris, H. Chaim Birnboim decided he needed a fast and reproducible way to purify plasmid DNA. He was not sufficiently fluent in French and was therefore a little isolated in the lab, for which he attributes his ability to focus on solving this problem rather than working on another lab project. What Dr. Birnboim was actually interested in was identifying and studying a new class repetitive sequences in higher eukaryotes. The sequence (a polypyrimidine tract) was resistant to acid treatment so the idea was to examine clones from a mouse DNA library. He would screen for those regions with long pyrimidine tracts using acid treatment that would break other DNA sequences into short fragments. The DNA was labeled with ³²P, a radioactive isotope of phosphate, before acid treatment and the slow-moving piece of DNA containing the repetitive sequence would be identified with autoradiography. This screen required analysis of many clones, and hence, a quick way to purify the DNA. At the time of the article he had not received any awards, but said that it was “personally gratifying to have developed a procedure that has survived for nearly a decade.” 

Of course this is only the first part of the miniprep technique, the second being the spin column, which relies on the ability of nucleic acids to bind a silica membrane under certain conditions, such as high salt. Dr. Birnboim published the use of silica-glass powder to bind and purify nucleic acids in 1982 (Marko et al. 1982) and the technique was improved upon by other scientists using different chaotropic agents (Boom et al. 1990). By the mid 1980s, Qiagen began selling kits for purification of plasmids and in the early 1990s companies began patenting the technology with Promega filing a patent in 1995 for “Nucleic acid purification on silica gel and glass mixtures” (US Patent number: 5658548) and Qiagen filing a patent in 1994 for “A method for the purification and separation of a nucleic acid mixture by chromatography” (Patent number 6383393). And so the miniprep battle began. But that’s for the company reps to worry about.

I’ve always found minipreps to be pretty relaxing because of their foolproofness (aside from a mistaken miniprep attempt after Happy Hour). Despite their ease, there is enough room to make you feel as though you have somehow improved on the design. For example, “psst, if you heat the water before elution, it will increase your yield” or “hey, pass the elution over the column again, my friend.”

I am terrible with numbers. I can’t remember my anniversary and regularly invert the birth year and day for my husband. I also recently wrote 7/14/20 on an eppendorf tube. BUT if I get hit in the head and someone wants to assess my mental faculties you can ask me the protocol for a miniprep: 250 microliters P1, 250 microliters P2, 350 N2….and don’t forget to heat the water.

How a miniprep works: The first buffer (P1) is simply to resuspend the cells and digest RNA. The P2 lysis buffer contains a detergent to lyse the cell membrane and a high pH that denatures the DNA. This is because the hydroxide ions pull hydrogen ions off the DNA molecule, disrupting the hydrogen bond network that holds the DNA strands together. Addition of the neutralization buffer (N3) lowers the pH and allows the circular DNA to go back to being double-stranded while the large, bulky chromosomal DNA cannot and forms a precipitate. High-speed centrifugation pellets the chromosomal DNA away from the soluble plasmid DNA. The supernatant containing plasmid DNA is then added to a silica membrane under high salt conditions, which allow double-stranded, but not single-stranded RNA and DNA to bind. A chaotropic agent, such as guanidium HCl disrupts the hydration shell around DNA and allows positively charged ions to form a salt bridge between the phosphate backbone and negatively-charged silica membrane. The membrane is washed and then DNA is eluted with a low ionic strength buffer, such as water. And there you have it, more than you wanted to know about minipreps.

References:

Birnboim, H.C. and Doly, J. (1979). A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 7(6), 1513-23.

Birnboim, H.C. (Nov 7 1988). Citation Classic – A rapid alkaline extraction procedure for screening recombinant plasmid DNA. CC/Life Sci. 45, 12-1

Boom, R., Sol, C.J., Salimans, M.M., Jansen, C.L., Wertheim-van Dillen, P.M., van der Noordaa, J. (1990). Rapid and simple method for purification of nucleic acids. J Clin Microbiol. 3, 495-503.

Marko, M.A., Chipperfield, R., Birnboim, H.C. (1982). A procedure for the large-scale isolation of highly purified plasmid DNA using alkaline extraction and binding to glass powder. Anal Biochem. 2, 382-7.