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Sequence for Yourself
Part IV: Detecting the Sequence
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Add DNA to Capillary
So now we have billions of copies of a unique DNA strand, of various lengths, and each marked with a color. To get the sequence of A's, G's, C's, and T's, all we need to do is sort the strands according to length, then read the color of the bases of the pieces that are the same length to determine the last base for that length.

We place our latest batch of DNA at one end of a capillary -- a thin plastic tube -- that is filled with a gel.

Initiate Electrophoresis
We apply an electric field to the gel -- positive at one end and negative at the other. This causes the negatively charged DNA pieces to migrate to the positive end.

Because of the gel's resistance, the smaller pieces of DNA travel faster through the gel than do the larger pieces. The movement of the pieces is very precise: For example, a piece that is 396 base pairs long will move ever so slightly faster than a piece that is 397 base pairs long.

Detection
As the DNA pieces move past the machine's detector, a laser causes the marker on the special nucleotide to fluoresce. There will be many copies of a DNA fragment of the exact same length passing the detector at the same time.

The combination of all of their tags will produce a reaction to the laser that is intense enough for the detector to read.

Data

Data Collection
The greens, yellows, blues, and reds scanned by the detector are sent to a computer, which converts the colors into A's, G's, C's, and T's. Because the sequence of the primer is known, the computer can determine the first base of the cloned DNA strand and then the subsequent 500 bases.

Shown here are only a few strands worth of data. Keep in mind that the lengths of many strands are much longer and that there are perhaps thousands of copies for each specific length.

Determine Sequence of 500 bp Reading
With information about both the lengths of the DNA strands and the strands' final bases, the computer can easily determine the sequence of the strand.

Next, we need to piece together 500 bp sections to reconstruct the 2,000 to 4,000 bp fragment.

Continue: Part V: Assembly and Finishing

Watch the Program Here | Our Genetic Future (A Survey)
Manipulating Genes: How Much is Too Much? | Understanding Heredity
Explore a Stretch of Code | Nature vs Nurture Revisited
Sequence for Yourself | Journey into DNA | Meet the Decoders
Resources | Update to Program | Teacher's Guide | Transcript
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