Biomedical Engineering Reference
In-Depth Information
as the stringency of the methods increase. As mentioned above, the DNA of a
million individuals contains 6 pedabits, but due to the compactness of DNA a
volume the size of a conventional test tube can contain the entire Biomolecular
Database. A pedabit of information can be stored (with tenfold redundancy) in
less than a few milligrams of dehydrated DNA, or when hydrated may be stored
within a test tube containing a few milliliters of solution.
1.2.2. Construction of the Biomolecular Database System
The inputs to the system are DNA obtained from tissues: either ge-
nomic DNA, or reverse-transcript cDNA obtained from mRNA expressed from
the DNA of a particular cell type. The Biomolecular Database is constructed as
follows:
a. The input DNA strands are first fragmented, e.g., they may be par-
tially digested into moderate-length sequences by the use of re-
striction enzymes. We describe a variety of methods for frag-
mentation protocols, and compare them by their distribution of
strand lengths, and the predictability of the end sequences of the
fragmented DNA.
b. The DNA are then tagged with artificially synthesized DNA
strands. These "information tags" encode essential information
(e.g., identification of DNA donor, as well as the date of the sam-
ple, gender, date of birth) about the individual or cell type that the
DNA was obtained from. These "information tags" are represented
by a sequence of distinct DNA words, each encoding variables
over a small domain. We describe and test tagging protocols based
on primer extension and utilizing the predictability of the end se-
quences of the fragmented DNA.
1.2.3. Processing Queries in the Biomolecular Database System
The chapter then discusses how to execute queries on the resulting Bio-
molecular Database. The system makes use of biomolecular computing (also
known as DNA computing) methods to execute these queries, including the exe-
cution of parallel associative search queries on DNA databases, and the execu-
tion of logical operations using recombinant DNA operations. We also describe
the use of conventional biotechnology (recombinant DNA technology, DNA
hybridization arrays, DNA tagging methods, etc.), for example, output is via
DNA hybridization array technology.
