How is dinosaur DNA purified?
Hi this is Steve Cherry from Lethbridge Alberta Canada. I listen to your great podcasts every weekend after our own domestic science show Quirks and Quarks. My question is: I read that a couple of researchers have said they have extracted dinosaur DNA, how do they separate it from other fragmentary remnants contaminating the sample from other micro-organisms?
Kat - Now it's time to look at your burning genetics questions, with the help of Naked Scientist Martha Henriques.
Martha - This month, listener Steve Cherry from Lethbridge, Alberta in Canada wanted to know how researchers extract dinosaur DNA from fossils and separate it from contaminant DNA from other organisms. Firstly, the bad news is, that no one has yet successfully isolated DNA from dinosaur fossils. Dr. Greger Larson from Durham University told me how DNA is isolated from fresh biological specimens and why doing the same for ancient specimens like dinosaur remnants is so difficult.
Greger - The way that we usually do it is to simply remove everything that isn't DNA and filter it off and that leaves us with the small tube that only has the DNA left in it. Of course, DNA exists in every single living organism, so we can't discriminate between all the different possible sources of DNA. All we can do is isolate DNA from everything that's non-DNA. And once we've got that in a tube then we can start to do all kinds of things including sequencing it or going after specific markers, or amplifying specific places, but the act of isolating it is a relatively straightforward process and we can do it from any number of things including skin cells or feathers or bone, or teeth, or anything that's biological and that is alive or was recently alive, we can isolate DNA from.
Martha - But when it comes to ancient specimens like dinosaur fossils, the chance of success with this method becomes vanishing small.
Greger - As soon as something dies, everything about that thing starts to degrade. So, the analogy would be, the bowl of fruit that you probably have in your kitchen and if you were just to leave that bowl of fruit there for a day or two, it'll be fine, but if you leave it there for a month, it will probably be no longer something that's even remotely appetizing. And if you leave it there for a year, it would be hard to differentiate the different kinds of fruit you had in that bowl a year before and if you leave it there for 20 years, there probably won't be anything even remotely resembling fruit in there and DNA is no different.
The longer that an organism is dead, the more of the DNA degrades and it degrades at a rate which is dependent upon lots of different factors including how long it's been, what temperature it's being stored at, or what sort of other organisms are eating it, or any number of other things. But even in the best case scenario where you have something frozen say, in the tundra where it's very cold, the half-life of DNA is somewhere in the order of maybe 100 or 200,000 years which means, half of the amount of DNA that you start with will be gone after about 100 and 200,000 years.
So, the reason it's difficult to get DNA out of dinosaur bones is simply because there is no DNA left. The same reason that if you were to leave the bowl of fruit on your kitchen table for 65 million years, the chances of you being able to come back and get any fruit out of that would be virtually nil. So, any reports that there's been of dinosaur DNA, they're either not reporting dinosaur DNA or they're reporting other bits of DNA that they've isolated that don't have anything whatsoever to do with that dinosaur bone.
Martha - This contaminant DNA is a problem for all work on ancient biological specimens. Dr. Mim Bower of Cambridge University worked from isolating DNA from prehistoric horse remains preserved in icy environments. These well-preserved specimens are much younger than dinosaur fossils and still have some of their original DNA present. Dr. Bower describes how she distinguishes any contaminant DNA from the horse DNA that she's interested in.
Mim - So, for every sample of bone that we try to extract DNA out of, we also examine a number of controls so that each time I do a DNA extraction, I work with a set number of 6 control reactions which have exactly the same components in except for the bone particle and that helps me control whether there is a DNA coming from me, or from the environment, or from the reagents that I'm using because if I see a positive DNA peak in my control samples which should have nothing in them then I know that I have made an error somewhere and I go back and I start again, and I'd clean everything down. So, we have a very strict contamination protocol nowadays and I have to say that most DNA researchers who are experienced can work very cleanly. And when we don't work cleanly, we can immediately see what has gone wrong and put it right.
Martha - That was Greger Larson from Durham University and Mim Bower from Cambridge University.