The Secret of the Persian Chessboard by Carl Sagan

Biology 205 PCR 2/9/04 Great PCR animations http://www.people.virginia.edu/~rjh9u/pcranim.html http://vector.cshl.org/resources/BiologyAnimationLibrary.htm Molecular Technology and its impact on Science and Society The Secret of the Persian Chessboard by Carl Sagan Parade Magazine Feb. 5, 1989 “The way I first heard this story, it happened in ancient Persia. But it might have be India or even China. Anyway, it happened a long time ago. The Grand Vizier, the principal advisor to the King, had invented a new game. it was played with moving pieces on a board of 64 squares. Why a king should delight in the creation of a game called “death to the king” is a mystery. But the story goes, he was so pleased that he asked the grand vizier to name is own reward for such a splendid invention. The Grand Vizier has his answer ready. He was a humble man, he told the king. He wished only for a humble reward. Gesturing to the 8 columns and 8 rows of squares on the board he had devised, he asked that he be given a single grain of wheat on the first square, twice that on the second square, twice that on the third square and so on, until each square had its complement of wheat. No, the king remonstrated. This is too modest a prize for so important an invention. He offered jewels, dancing girls, palaces. But the grand vizier, his eyes becomingly lowered refused them all. …. Eventually the king consented. When the Master of the Royal Granary begain to count out the grains, however, the King was in for rude surprise a: 1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024……263 263 = 9 X 1018 = 9 million trillion grains of wheat on the last square….. • A sequence of numbers like this - where each is a fixed multiple of the previous one -- is called a geometric progression and the process is called exponential increase. Exponentials show up in all sorts of places -- including the Polymerase Chain Reaction. • Explore DNA fingerprinting http://www.biology.washington.edu/fingerprint/dnaintro.html http://www.pbs.org/wgbh/nova/sheppard/analyze.html PCR and DNA fingerprinting You are a foresic scientist and you to determine if a particular tissue sample is from a particular individual… In order to study a specific gene or any specific site in the DNA you have to get around 2 problems: a) Can only obtain a small sample of tissue -- may be a somewhat limited amount of starting material and it may not be in great shape (especially if it is a forensic sample) b) DNA preparation that you generate from the tissue sample is a complex, heterogeneous mixture of sequences containing the entire human genome c) human genome: 3X109 = 3 X 106 kb ~40,000? genes So, what’s the problem with that? • Study sequence of DNA that is 3 kb = 3000 bases: 1 part in 1 million of the genome • Small quantity of your sequence and it’s contaminated with all of these other sequences WANT A TUBE LABELED PURIFIED GENE SEQUENCE Z How to purify the gene sequences that you want to study? Can take advantage of natural systems to amplify specific DNA sequences a) Use recombinant DNA techniques to generate a molecular clone of the DNA: use a cell such as E. coli to make lots of copies of your sequence -- put it in a DNA molecule that is easy to recover in a pure form from the cell b) amplify the gene or sequence using PCR -- an in vitro process PCR = polymerase chain reaction • Very sophisticated molecular technologies have developed based on our understanding of the enzymology of DNA replication • PCR is an in vitro DNA replication technology that has revolutionized basic research in molecular biology and genetics • PCR involves exponential amplification of a specific gene or region of DNA from a complex mixture of DNA See text discussion of PCR reaction What specific feature of DNA polymerase allows us to target the specific sequences that we want to be amplified? DNA polymerase can’t start a polymer, but it can add onto one that is already started. The experimenter controls what portion of the DNA molecule is copied by controlling the primers that are put into the reaction PCR has revolutionized basic research in molecular biology and genetics PCR has dramatically increased the variety and sensitivity of analytical techniques available to: d)clinical medicine e) forensic sciences f) many other disciplines such as ecology, taxonomy, evolutionary biology Science 287: 963 Feb. 11, 2000 British researchers say they are developing a DNA test that could help nab those who illegally trade in tigerproducts. And three recent raids in India that confiscated huge caches of tiger bones and hides suggest that the need for such policing tools is greater than ever. "Tigers are so highly endangered that they may soon be extinct in the wild," says Robert Hepworth of the United Kingdom's Department of the Environment. Last month, he led a three-member United Nations team that visited India and Japan to assess ways of stemming the illegal trade in tiger parts, which are highly valued by makers of traditional Asian medicines. Although officials can seize medicines that list tiger bone as an ingredient, they need proof of its presence to get criminal convictions. A tiger DNA test would be a "great boon" for law enforcement, says Hepworth. Jon Wetton and his co-workers at the Forensic Science Service believe that amplifying fragments of the cytochrome b gene of the tiger's mitochondrial DNA may fill the bill. The test can detect "as few as 10 tiger cytochrome b gene fragments, considerably fewer than are present in a single cell," says Wetton. Tiger blood, hair, and bone samples have all generated positive results, he says. The researchers are currently spiking Chinese medicines with progressively smaller doses of tiger bone to determine the limits of the test's sensitivity. Once they succeed, the next test may come in a courtroom.