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Unformatted text preview: fore amplify them by PCR.
Inspect the result by gel electrophoresis to see if there are any strands
of the correct length.
If there are, then there is a HP; if not, then not.
¶13. Determining the path: The precise HP can be determined by a
graduated PCR procedure.
Run n 1 PCR reactions.
In the ith lane, vin is the left primer and vi is the right primer.
“[T]he unique HP . . . should produce bands of length 40, 60, 80, 100,
120, and 140 b.p. in lanes 1 through 6, respectively.” [Amos, p. 114]
That is, the primer that produced 40 is the second vertex in the HP;
the primer that produced 60 is the third, etc. B. FILTERING MODELS 235 ¶14. The ﬁnal process depends on there being only one HP and is error-prone
due to its dependence on PCR.
B.1.d Discussion ¶1. Linear: Adleman’s algorithm is linear in the number of nodes, since
the only iteration is Step 4, which is repeated for each vertex.
¶2. Adleman’s experiment took about a week, but with a more automated
approach it could be done in a few hours.
¶3. On the other hand, the PCR process cannot be signiﬁcantly shortened.
¶4. Molecular resources: The number of di↵erent oligos required is proportional to n.
¶5. Strands: The number of strands is much larger, since there must be
a number of representatives of each possible path.
If d is the average degree of the graph, then there are about dn possible
paths (exponential in n).
For example, if d = 10 and n = 80, then the 1080 DNA molecules is
more than the estimated number of atoms in the universe.
¶6. Hartmanis calculated that for n = 200 the weight of the DNA would
exceed the weight of the earth.
¶7. So this brute-force approach is st...
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This document was uploaded on 03/14/2014 for the course COSC 494/594 at University of Tennessee.
- Fall '13