Biomedical Engineering Reference
In-Depth Information
c.
Differential expression analysis
is a technique for finding the difference
in gene expression, for example, between two distinct gene types. Lynx Thera-
peutics Inc. has developed a randomized tagging technique for differential ex-
pression analysis. The randomized tagging techniques of Lynx Therapeutics
may be adapted to determine the difference between two Biomolecular Database
subsets.
2.2. Relevant Biomolecular Computing Techniques: Biomolecular
Computing
In the field known as
Biomolecular Computing
(and also known as
DNA
Computing
), computations are executed on data encoded in DNA strands, and
computational operations are executed by use of recombinant DNA operations.
Surveys of the entire field of DNA-based computation are given in (50,52).
The first experimental demonstration of Biomolecular Computing was of-
fered by Adleman (1), who solved a small instance of a combinatorial search
problem known as the Hamiltonian path problem. Considerable effort in the
field of Biomolecular Computing methods has been made to solve Boolean sat-
isfiability problems (SAT) problems, that is, the problem of finding Boolean
variable assignments that satisfy a Boolean formula. Frutos and colleagues (24),
Faulhammer et al. (23), and Liu et al. (37) applied surface-chemistry methods
and Pirrung et al. (47) improved their fidelity. Adleman's group (11) recently
solved an SAT problem with 20 Boolean variables using gel-separation meth-
ods. While the 20 Boolean variables size problem is impressive, Reif (52,53) has
pointed out that the use of Biomolecular Computing to solve very large SAT
problems is limited to at most approximately 80 variables, so is not greatly scal-
able in terms of number of variables.
The use of Biomolecular Computing to store and access large databases, in
contrast, appears to be a much more scalable application. Baum (7) first dis-
cussed the use of DNA for information storage and associative search; Lipton
(36) and Bancroft and coworkers (6) also discussed this application. Reif and
LaBean (54) developed and Reif et al. (55) experimentally tested the synthesis
of very large DNA-encoded databases with the capability of storing vast
amounts of information in very compact volumes. Reif et al. (55) tested the use
of DNA hybridization to do fast associative searches within these DNA data-
bases. Reif (50) also developed theoretical DNA methods for executing more
sophisticated database operations on DNA data, such as database join operations
and various massively parallel operations on the DNA data. Gehani and Reif
(27) investigated methods for executing DNA-based computation using micro-
fluidics technologies. In addition, Gehani et al. (28) describe a number of meth-
ods for DNA-based cryptography and countermeasures for DNA-based
steganography systems as well as discuss various modified DNA steganography
systems that appear to have improved security. Kashiwamura and colleagues
(34) describe the use of nested PCR to do hierarchical memory operations.
