In Search of the Ninja Molecule: DNA Assassin Quest

Boise State Researcher Greg Hampikian is on a research quest to find sequences of DNA whose peptide products are so deadly, that they have been bred out of all living things.

"There must be some DNA or protein sequences that are not compatible with life, perhaps because they bind some essential cellular component, for example, and have therefore been selected outof circulation. There may also be some that are lethal in some species, but not others. We'relooking for those sequences."

To do this, Hampikian and his colleage Tim Anderson, also at Boise, have developed softwarethat calculates all the possible sequences of nucleotides – the "letters" of DNA – up to a certainlength, and then scans sequence databases such as the US National Institutes of Health's Genbank to identify the smallest sequences that aren't present. Those that don't occur in one species but do in others are termed "nullomers", while those that aren't found in any species are termed primes.

Hampikian's team is deliberately searching for the shortest absent sequences in order to minimise the possibility that absent sequences are missing simply due to chance. So far they have found 86 sequences of 11 nucleotides long that have never been reported in humans.

They have also identified more than 60,000 primes of 15 nucleotides in length and 746 protein "peptoprime" strings of five amino acids that have never been reported in any species. "These represent the largest possible set of lethal sequences," says Hampikian, who expects the numbers to shrink as more sequence information is added to the database. He is presenting his results at the Pacific Symposium on Biocomputing in Maui, Hawaii, this week.

Whether these sequences have any biological significance in living organisms is not yet known – the next step is to test 20 of the peptoprimes in bacteria and human cells to see whether they have any effect such as causing de ath or provoking an immune reaction.

Source.

This is a fascinating line of research that is only possible because of the incredible progress in genetic sequencing across the species, and advances in bioinformatics hardware and software. Whether there is any validity to the concept of the ninja DNA sequence remains to be proven. Still, I salute Hampikian and his team for their far conceptual travels. And I very much hope there is nothing to the idea. There are more than sufficient ABC WMD's as it is.