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A Simple Sequence

by Susan Lumpkin

Rob Fleischer
National Zoo geneticist Rob Fleischer
learns vast amounts of information from
tiny samples of hair, skin, or scat.(Jessie Cohen/NZP)

Genetic analysis can be done on a sample the size of a fleck of dandruff. But whatever a sample’s size and source, the recipe for analyzing its DNA is similar.

The first step is to grind it up and mix it with a buffer—a liquid with enzymes that break down cell walls so DNA and other cell components are released. Next, this soup is filtered to strain out all but the DNA. The amount of DNA in the broth is too little for most direct analyses, so a toaster-sized machine called the polymerase chain reaction (PCR) is put to work. This special piece of equipment works like a chemical photocopier.

The DNA and two primers—short, single-stranded sequences of code flanking genes that are informative when compared among individuals or species—go into a PCR machine, along with an enzyme that can synthesize a new strand of DNA. The machine runs this stuff through a series of heating and cooling cycles that ultimately make millions of copies of the DNA strands matching the sequence between the two primers. This goes through another set of reactions that builds a set of differentsized fragments individually labeled with a particular dye depending on whether they end with an adenine (A), thymine (T), guanine (G), or cytosine (C) nucleotide.

This mix goes into a sequencing machine that reads the DNA fragments in order of size, and spits the DNA sequence into an electronic file. The code is spelled out by the order, or sequence, of the A, T, G, and C nucleotides, each of whose dye reflects a different color to the machine’s laser reader. In software, the file produces a chromatogram—a graph showing color peaks that correspond to each of the nucleotides.

The resulting sequence, which can be hundreds or more letters long, is what helps scientists solve mysteries. For example, Zoo geneticist Jesus Maldonado can find out what kind of mouse genes he has on hand by first using the above procedure. Then he copies and pastes the mouse sequence from his computer screen to an entry box on the website of the National Center for Biotechnology Information, which maintains a large and rapidly growing database of gene sequences. Next, he clicks on a button labeled “Blast!”

Nine seconds later, up pops a list with the closest match—a Central American harvest mouse. There are a few differences between the sequences, say an A in the place of a T, suggesting his sample might be from a different population of the species but probably not enough to suggest it is a different but related species. As it turns out, his mouse was from Guatemala and the other from southern Mexico. When his study is complete, Maldonado will add his mouse’s sequence to the database for others to use.

 

More: "The Tales Genes Tell"

More: "Looks Can Be Deceiving"

 

 

 

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Smithsonian Zoogoer 38(5) 2009. Copyright 2009 Friends of the National Zoo. All rights reserved.