Experimental validation of DNA sequences for DNA computing: Use of a SYBR green I assay

Abstract

In developing hybridization-based DNA computing methods, DNA codes must be created that behave as predicted; otherwise computing errors can result. Here we describe the experimental validation of two DNA codes, each containing 16-nucleotide strands designed to hybridize only with their complements and not with themselves or with any other strands in the set. Code I was constructed simply to restrict potential for cross-hybridized (CH) secondary structure. Code II was constructed using the software SynDCode, incorporating nearest-neighbor thermodynamics and generalizations of the Levenshtein edit distance. Every combination of strands was tested for potential to mispair, both in individual pairings and in pools. Since the strands are designed to be linked together in a long bit string, we also tested end-to end junctions of Code II strands. Hybridization was examined by measuring fluorescence as a function of temperature in the presence of SYBR Green I, a dye whose fluorescence increases exponentially when bound to double-stranded DNA. This method shows promise as a means for rapid experimental validation of large numbers of sequences. © Springer-Verlag Berlin Heidelberg 2006.