Biomedical Engineering Reference
In-Depth Information
is photochemically cross-linked to the bottom strand of the library member, pre-
serving the color of the dye. The bottom strand can then be obtained in single-
strand form, which is hybridized to a cDNA microarray (see Figure 4). The
color(s) of the array element complementary to the biological DNA identify the
outcome of the queries of the tag sequences connected with it.
This concept could be applied in a similar fashion to a sequential (nested)
PCR process by omitting the terminators and psoralen and providing one primer
for the top strand and one for the bottom strand in each PCR. The eventual pro-
duction of a full-length amplicon is dependent on the complementarity of
each
of the primers (logical AND) with its cognate tag sequence. This approach lends
well to the use of DNA hybridization array technology for output of query re-
sults, providing distinct special locations for distinct outputs.
Another approach for executing Boolean queries on a Biomolecular Data-
base is to use the gel separation-based method for SAT from Braich et al. (11),
who succeeded in solving a 20-variable Boolean satisfiability problem. Al-
though the queries would be executed on the tag portions of the DNA strands of
the database, it is not clear how the efficiency of these separation methods
would be affected by the genomic portion of the DNA strands in the databases.
3.9.3. Executing Queries in the Biomolecular Database via PCR
Amplification Techniques
Another approach for Logical Query Processing is to use a variant of PCR
amplification. The goal of this query processing is to selectively amplify only
those DNA sequences (the
output strands
) whose information tags satisfy a
given logical query. After the amplification process is completed, the output
strands would vastly predominate all other strands of the Biomolecular Data-
base.
3.9.4. Initialization Before Logical Query Processing
First, operations are executed that generate, from each DNA strand in the
database, a new strand containing a concatenation of multiple copies of the Wat-
son-Crick complement of the original strand. This can be done by a known se-
quence of routine recombinant DNA operations known as rolling circle
replication (38). This begins by a circularization of each strand on the database,
and then a primer-extension reaction on the circularized strand that repeatedly
replicates the complement of the DNA strand to form a repeated sequence, fol-
lowed by denature and separation of the result. The length of the resulting DNA
strands is predictable (via the time duration and various parameters, including
temperature) only to a degree, but it is predictable enough to allow us to con-
