Biomedical Engineering Reference
In-Depth Information
Suyama et al. (60) and Sakakibara and Suyama (59) have developed biomolecu-
lar computing methods for gene expression analysis. Garzon and colleagues (25)
recently analyzed the efficiency and reliability of associative search in DNA
databases, and Chen and colleagues (13) discussed DNA databases with natural
DNA based on the prior work of Reif et al. (55) and the present work.
3.
A BIOMOLECULAR DATABASE SYSTEM
3.1. Overview
The inputs to the system are natural DNA obtained from tissues: either ge-
nomic DNA or reverse-transcript cDNA obtained from mRNA expressed from
the DNA of a particular cell type. A short piece of synthetic DNA is added to
each natural DNA strand. This piece of synthetic DNA, called an information
tag, is used to code information about the original piece of DNA. This informa-
tion can include the age or gender of the person from whom the DNA came, or
the clinical symptoms of individuals suffering from a disease. In a typical appli-
cation, the Biomolecular Database consists of a mixture of DNA strands from
many different people (or other organisms). This Biomolecular Database system
is capable of storage, processing, and retrieval of genetic information and mate-
rial. Individual molecules of DNA in the Biomolecular Database can be selected
and removed from the mixture on the basis of the information encoded in their
information tag. This chapter describes several innovative biological applica-
tions for Biomolecular Databases; in particular, we discuss the application of our
Biomolecular Database system to a number of genomic information processing
applications.
3.2. Biological Inputs
The inputs to the system are DNA obtained from tissues. This input DNA is
typically either (i) genomic DNA, or (ii) reverse-transcript cDNA obtained from
mRNA expressed from the DNA of a particular cell type. (To ensure stability
and non-reactivity, we suggest that the database be composed of DNA rather
than RNA.)
3.3. Preprocessing the DNA
Biochemical operations can be used to partially digest the DNA by restric-
tion enzymes (ensuring the resulting DNA strands are of modest size), and then
label the resulting genomic DNA fragments with synthetic DNA information
tags.
