title: A DNA computing readout operation based on structure-specific cleavage.
abstract: We describe a structure-specific cleavage-based READOUT strategy for surface-based DNA computing. The strategy was demonstrated in the solution of a 4-variable/3-satisfiability (SAT) problem. The READOUT step identifies the DNA molecules present at the end of the computational process. The specificity of the sequence detection used here derives from the sequence specificity of DNA hybridization coupled with the structure specificity of the enzymatic cleavage. The process is linear, yielding a higher uniformity of detection of the DNA computing products compared to that obtained with PCR amplification. The structure-specific cleavage-based readout is simple, accurate, and compatible with multiple-word DNA computing.
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
authors.forename: L
authors.initials: L
authors.lastname: Wang
authors.forename: J G
authors.initials: JG
authors.lastname: Hall
authors.forename: M
authors.initials: M
authors.lastname: Lu
authors.forename: Q
authors.initials: Q
authors.lastname: Liu
authors.forename: L M
authors.initials: LM
authors.lastname: Smith
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000032:analysis* / Q000378:metabolism; D006801:Humans; D008957:Models, Genetic; D009693:Nucleic Acid Hybridization / Q000379:methods*; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D015345:Oligonucleotide Probes; D016133:Polymerase Chain Reaction / Q000379:methods; D012680:Sensitivity and Specificity; D013379:Substrate Specificity
chemical_list: D009838:Oligodeoxyribonucleotides; D015345:Oligonucleotide Probes; D004247:DNA