DNA Hybridization as a Similarity Criterion for Querying Digital Signals Stored in DNA Databases

Abstract

We demonstrate via simulation that hybridization of DNA molecules can be used as a similarity criterion for retrieving digital signals encoded and stored in a synthesized DNA database. After introducing some necessary DNA terminology, we briefly explain how digital signals are transformed to DNA sequences. Since retrieval is achieved through hybridization of query and data carrying DNA molecules, we present a mathematical model to estimate hybridization efficiency (also known as selectivity annealing). We show that selectivity annealing is inversely proportional to the mean squared error (MSE) of the encoded signal values. In addition, we show that the concentration of the molecules plays the same role as the decision threshold employed in digital signal matching algorithms. Finally, similar to the digital domain, we define a DNA signal-to-noise ratio (SNR) measure to assess the performance of the DNA-based retrieval scheme. Simulations are presented to validate our arguments.