Constructing Bio-molecular Databases on a DNA-based Computer

TL;DR

This paper demonstrates how DNA can be used to construct and operate bio-molecular relational databases, performing fundamental database operations through biological processes with high data density.

Contribution

It introduces DNA algorithms for executing eight relational algebra operations on bio-molecular databases, advancing molecular computing for data management.

Findings

DNA-based data storage achieves high density.

Biological operations can perform relational algebra.

Bio-molecular databases enable data retrieval.

Abstract

Codd [Codd 1970] wrote the first paper in which the model of a relational database was proposed. Adleman [Adleman 1994] wrote the first paper in which DNA strands in a test tube were used to solve an instance of the Hamiltonian path problem. From [Adleman 1994], it is obviously indicated that for storing information in molecules of DNA allows for an information density of approximately 1 bit per cubic nm (nanometer) and a dramatic improvement over existing storage media such as video tape which store information at a density of approximately 1 bit per 1012 cubic nanometers. This paper demonstrates that biological operations can be applied to construct bio-molecular databases where data records in relational tables are encoded as DNA strands. In order to achieve the goal, DNA algorithms are proposed to perform eight operations of relational algebra (calculus) on bio-molecular relational databases, which include Cartesian product, union, set difference, selection, projection, intersection, join and division. Furthermore, this work presents clear evidence of the ability of molecular computing to perform data retrieval operations on bio-molecular relational databases.