Extracting the DNA

"Bingo! Dino DNA!" - Mr. DNA, Jurassic Park


 * It is unknown which dinosaur the sample contains. It would be impossible to tell which species it is, because the DNA sequences would fit somewhere between that of birds and crocodiles. The book does address this, stating that they "just grow it and find out", to mathematician and chaos theorist Ian Malcolm's annoyance.


 * The dinosaur DNA has to be correct (it has to contain every chromosome) and should contain no sequence gaps. The book and movie did address this issue, however, and had the scientists use frog DNA (and also bird and lizard DNA in the novel) to compensate for the gaps in the dinosaur DNA.


 * The DNA is mixed with mosquito, bacterial, and viral DNA. Although Polymerase chain reaction is very specific, it is sensitive to contamination, and if the wrong primers are used, it will also amplify the other DNA.


 * Because DNA is broken down by nucleases in the mosquito gut, the mosquito would have to be preserved immediately after feeding; this would be problematic for the park's scientists, although it would explain the lack of mass contamination in the individual samples.


 * The processes of CpG methylation and cytosine deaminization must also be considered. A common regulatory device in eukaryotic DNA is the process of CpG methylation, where cytosine immediately preceding a guanine on the same strand is methylated. This acts as a molecular flag to control gene expression. Over time cytosine deamination can occur, in which a cytosine amine group is hydrolysed (replaced with a carbonyl oxygen). An unmethylated cytosine will read as uracil in any technique that relies on Watson-Crick base pairing. If the cytosine has been methylated then the product of deamination will be thymine, which again will be read as thymine. This issue can be addressed in a number of ways. If the DNA sample taken contains more than one copy of the DNA, a mixed signal of thymine and cytosine will suggest the occurrence of cytosine deamination. If the entire sample has suffered cytosine deamination at that point in the sequence, CpG tend to be found in "islands" rich in CpG, so TpG-rich islands or TpG/CpG rich islands would suggest cytosine deamination.

Furthermore, in the fossilization process, molecules are altered. Nevertheless, amber is the best preservative, because organic material is preserved. But DNA cannot survive completely without gaps for tens or hundreds of millions of years. The novel attempts to address this problem by mentioning that Hammond and INGEN have purchased virtually the world's entire stock of amber, in the quest for the maximum number of possible samples of blood from ancient mosquitoes. However (see below) the admixture of different strains of dinosaur genetic material makes the acquisition of viable genetic material haphazard at best, coupled with the CpG Methylation (see above). That said, the use of multiple Cray X-MP supercomputers whose sole task is pattern recognition is doubtless a shrewd guess as to the size of the task and the scale of resources needed to perform the feat.

Tens of thousands of DNA base pairs were recently sequenced from 40,000-year-old skeletal remains of cave bears without using PCR, establishing that, in principle, large-scale genomic sequencing of fossilized remains is possible. Of course, the remains used in this study are orders of magnitude younger than anything from the dinosaur era, and the technique might not extend to those creatures.

In the book the gaps in the DNA are filled by hybridizing the DNA with either bird, lizard, or frog DNA. In the movie, only frog DNA is used. This is extremely difficult, as one would need to know which dinosaur genes are homologous with frog genes. The use of frog genes was a plot device, to allow some females to change sex and breed (although natural sex change is also possible in other vertebrates, such as fish).