Biomedical Engineering Reference
In-Depth Information
3
APPLICATION OF BIOMOLECULAR COMPUTING
TO MEDICAL SCIENCE: A BIOMOLECULAR
DATABASE SYSTEM FOR STORAGE,
PROCESSING, AND RETRIEVAL OF
GENETIC INFORMATION AND MATERIAL
John H. Reif, Michael Hauser, Michael Pirrung,
and Thomas LaBean
Departments of Computer Science, Ophthalmology, and Chemistry,
Duke University, Durham, North Carolina
A key problem in medical science and genomics is that of the efficient storage, process-
ing, and retrieval of genetic information and material. This chapter presents an architec-
ture for a Biomolecular Database system that would provide a unique capability in
genomics. It completely bypasses the usual transformation from biological material (ge-
nomic DNA and transcribed RNA) to digital media, as done in conventional bioinformat-
ics. Instead, biotechnology techniques provide the needed capability of a Biomolecular
Database system without ever transferring the biological information into digital media.
The inputs to the system are DNA obtained from tissues: either genomic DNA, or re-
verse-transcript cDNA. The input DNA is then tagged with artificially synthesized DNA
strands. These "information tags" encode essential information (e.g., identification of the
DNA donor, as well as the date of the sample, gender, and date of birth) about the indi-
vidual or cell type that the DNA was obtained from. The resulting Biomolecular Database
is capable of containing a vast store of genomic DNA obtained from many individuals
(multiple army divisions, etc.). For example, the DNA of a million individuals requires
about 6 pedabits (6 + 10
15
bits), but due to the compactness of DNA a volume the size
of a conventional test tube with a few milliliters of solution could contain that entire
Biomolecular Database. Known procedures for amplification and reproduction of the
Address correspondence to: John H. Reif, Department of Computer Science, Room D223, LSRC
Building, Duke University, Durham, NC 27708 (reif@cs.duke.edu).
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