On the Design of Codes for DNA Computing

In this paper, we describe a broad class of problems arising in the context of designing codes for DNA computing. We primarily focus on design considerations pertaining to the phenomena of secondary structure formation in single-stranded DNA molecules and non-selective cross-hybridization. Secondary structure formation refers to the tendency of single-stranded DNA sequences to fold back upon themselves, thus becoming inactive in the computation process, while non-selective crosshybridization refers to unwanted pairing between DNA sequences involved in the computation process. We use the Nussinov-Jacobson algorithm for secondary structure prediction to identify some design criteria that reduce the possibility of secondary structure formation in a codeword. These design criteria can be formulated in terms of constraints on the number of complementary pair matches between a DNA codeword and some of its shifts. We provide a sampling of simple techniques for enumerating and constructing set...

• Type: Conference
• Year: 2005
• Where: WCC
• Authors: Olgica Milenkovic, Navin Kashyap
• Keywords: Cryptography, Dna Sequences, Secondary Structure Formation, Single-stranded Dna, WCC 2005