Biomedical Engineering Reference
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strained to a surface). In both cases, one can apply DNA hybridization array
technology for output of query results.
3.9.2. Executing Queries into the Biomolecular Database via
Primer-Extension Techniques on Solid Support
A number of DNA computing researchers have developed microarray
methods for DNA-based computing, exploiting the high fidelity of the primer-
extension reaction to detect complementarity between primer libraries of all
solutions to SAT problems and logical queries as templates (see, e.g., the work
of Faulhammer et al. (23) and Liu et al. (37), and also that of Pirrung et al. (47),
which improved fidelity). Primer extension is a two-step process, involving first
annealing of a template molecule to the primer, the efficiency of which is di-
rectly related to sequence complementarity throughout the primer/template
complex (see Figure 3). Second, a polymerase enzyme binds to the primer/tem-
plate complex and adds a nucleotide or nucleotides complementary to the base
Figure 3 . A primer and template used in the primer-extension method for logical queries.
t h e b a s e
X, the first unpaired base at the 5'-end of the template, only when there is a per-
fect match in the last portion of base pairs of the primer/template complex. It is
important to emphasize that while primer extension was in this case performed
on a DNA microarray, the elementary step of a polymerase chain reaction (PCR)
is also a primer-extension process and thus is subject to the same stringent se-
quence requirements. The variables (primers) in the SAT computation of (47)
were composed of two portions, which can be considered the message (the last
few bases "m" at the 3'-end of the oligonucleotide) and the address (a sequence
of bases "a" at the 5'-end). With the base-4 encoding of DNA, a message se-
quence is capable of encoding 10 Boolean variables. For the experiment of (47)
all addresses were the same, as only one SAT problem was being addressed.
However, this need not be the case. Using similar designs, it is possible to de-
sign up to approximately 20 blocks of distinct address sequences, which con-
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