This preview shows page 1. Sign up to view the full content.
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 errorprone
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 bruteforce approach is st...
View
Full
Document
This document was uploaded on 03/14/2014 for the course COSC 494/594 at University of Tennessee.
 Fall '13
 BruceMacLennan

Click to edit the document details