I’m helping a friend with a story they’re writing that features an amateur detective. She has found a clue that has a potential suspect’s DNA on it, and she wants to turn a little bit of DNA into a lot of DNA. How could she go about this?
By using the Polymerase chain reaction. I have no idea how easy it would be for an amateur to obtain the necessary tools and chemicals.
You can just buy PCR machines on the cheap these days. Or build one yourself from parts. They aren’t that complicated.
You don’t need a PCR machine to do PCR. All it actually does is raise and lower the temperature in cycles. You can do it manually with water baths, that’s how it was done originally.
But PCR will only amplify specific short segments of DNA, not entire genomes.
OP, a little more info is needed. What exactly does she plan to do with the large quantity of DNA?
I think you don’t do it that way. You test the small sample of degraded DNA using a very sensitive (amplifying) PCR test, but you don’t get “more DNA” as part of the process.
I could be wrong.
And I would think of testing the small degraded sample by sending it off to a test lab. The problem with “sending it off to a lab” is that unless it’s a dedicated forensics lab you don’t maintain a chain of evidence by doing that, but I hope that doing it myself would be open to the same objections.
IANAL but wouldn’t the fact that this amateur detective collected and handled the DNA mean it could no longer be used as evidence in any case
Wow, who’d’ve thunk amplifying DNA would be so complicated? 
The objective of the detective (hey, that rhymes) in the story* is to obtain a sample of the suspect’s DNA, amplify the appropriate segments, put the solution into a spray bottle and plant the DNA all over town for the police to find and analyze.
*I am really over simplifying the story, because the long plot explanation is, well, long. Also, if I give it away, then someone is likely to steal the plot, and this book by a middle-aged, first-time author who just got laid off from her accounting job is guaranteed to outsell the bible. (I’m talking cumulative sales.) A good analogy would be to something that happened to me in high school: Someone posted really racist flyers around campus, and nobody was allowed to leave the ensuing assembly until the guilty party came forward. After about 90 minutes of sitting in silence, the absolute sweetest girl in the school admitted she’d done it. It took about two minutes for the real culprit stepped forward, because he couldn’t let this girl take the blame for what he’d done.
This is not within the capabilities of an amateur. It doesn’t need advanced skills or experience specifically with forensics, but you’d need basic technical skills and access to some basic lab kit - I think your protagonist needs to be in cahoots with a grad student at a university lab or something.
CODIS DNA profiling analyzes 20 standard loci. So one approach would be to PCR amplify just these loci. You could dilute and plant these fragments, and a standard CODIS analysis would amplify off the fragments, making it appear for the purposes of the basic CODIS protocol that the suspect’s genomic DNA were present. With this method, if suspicion arose, it would be easy to do other tests (attempt PCR amplification of any other part of the genome) to prove that only the CODIS loci are present in the sample, and not genomic DNA - this could be a plot point to prove the plant. The 20 CODIS loci are published information, there are standard kits you can buy with the required primers, and information on protocols is publicly available. Here’s the main NIST page:
https://strbase.nist.gov/
The (possibly more straightforward) alternative would be Whole Genome Amplification, which again requires some basic skills and access to lab equipment, but commercial kits are available, so any competent grad student with access to a lab (but not an amateur) could figure out how to do it.
https://www.qiagen.com/us/service-and-support/learning-hub/technologies-and-research-topics/wga/overview-on-wga/
This method would be more robust to forensic detection if the plant were suspected.
To add - I don’t have specific experience with forensics, but forensic samples have tiny amounts of DNA. If you wanted a plot point that the “plant” is detected, one interesting way might be that the forensic test looks odd because after the amplification your protagonist made the mistake of not diluting enough, so that far too much DNA is present. But you’d need to talk to somebody in forensics if you wanted something really technically authentic here.
Correct – not within the capabilities of an amateur. But an amateur with the right connections, and it can easily happen.
As a software test engineer, one of my previous jobs about 15 years ago was working for Applied Biosystems on one of their PCR machines – the software that drove the amplification machine. A software tester, or software developer, or product manager working at such a company would have access to the chemicals and equipment and, talking to a friend at work who understands PCR, could do the amplification.
For PCR amplification, I’m definitely an amateur. I worked there about one year and never again got back into that field.
I never did it, but theoretically I’m certain it could happen this way.
In my scenario, the sample collecting and forensics skills is a key missing link.
ETA: and just now looking it up, I see that Kary Mullis passed away last August at 74 years old. He was the father of PCR, and he won the Nobel Prize for it. Not bad for a guy, while high and stoned, gets the inspiration for the idea that becomes PCR. Or is that a myth?
Thank you. Everything you wrote is extremely helpful.
I don’t know, but he apparently lacked the ability to reliably distinguish groundbreaking scientific inspiration from pseudoscientific fantasy. He notoriously went off the deep end later in life - with climate change denial, HIV-AIDS denial, conspiracy theories.
Why would they need to amplify it? Couldn’t they just collect the suspect’s DNA from some bodily fluids, dilute it, and spread it around?
What a nut case. But, hey, without PCR we wouldn’t have all the DNA evidence-based cases being solved. Or bodies being identified in other tragedies.
In a work of fiction, you would send it to a fictional company that let’s you take degraded DNA from a long-dead relative and analyze it for genealogical research.
We were doing PCR in high school, within a year after it was discovered. While it does take special skills and chemicals, those skills and chemicals are not at all hard to come by. It’d be an extremely weird hobby, but it requires considerably less specializations than a number of other real hobbies.
DNA “planting” has been used as a fictional plot device - i.e. getting hold of a used condom. You wouldn’t need to dilute the sample, as highly sensitive detection methods can pick up minute amounts of DNA* (not sure why the OP’s plot would require the DNA to be spread “all over town”). One (of many) problems with amateur PCR is avoiding contamination, difficult if one is not experienced with amplification protocols.
I suppose this could be worked into the plot, but it would probably look highly suspicious if “planted” DNA consisted of heavily amplified short segments of a genome, rather than the whole DNA techs are used to working with.
*see “touch” DNA.
The other problem is - so what?
You amplify segments of the DNA and plant them. The forensics team investigating likely does their routine work and does not notice the sample has been pre-sliced into analyzable segments.
(Plot twist - the forensics lab analyzes a few segments, IIRC about 16. Can yo fake a profile by selecting a segment from here, a segment from there, and mixing them together so it matches a third party? Can you sprinkle random segments to make the guilty party look like someone - or someones - else?)
Otherwise, you have your amplified DNA sample. Then what? The next step is electrophoresis(?) to get the profile and those classic series of lines, so this is another technical process our Nancy Drew needs to master. And some other profile to compare it to…